2013-12-02  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I05659554de4b5c7d74bfeba1dbc3e80f2db021ca

2013-11-25  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ia653309d4e4a71dd956d6855d389f59158dc1a1a

2013-11-18  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: If360428adfdb6da7a448f3782ba2f9c58d0bff1a

2013-11-11  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4be2a310c7cc070699ea94c9be87de25d98c542d

2013-11-04  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: If3080e7ae3cd28b1d3f5638b80393ddbd2b8415c

2013-10-29  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/gl2ps/gl2ps.c,
  libavogadro/src/extensions/gl2ps/gl2ps.h,
  libavogadro/src/extensions/gl2ps/gl2ps.pdf,
  libavogadro/src/extensions/gl2ps/gl2psTest.c,
  libavogadro/src/extensions/gl2ps/gl2psTestSimple.c: Import gl2ps 1.3.8 for
  upcoming Avogadro bugfix release.  Change-Id:
  I5fd18a6dc1599cf868336dd1733d0fc684e9dcb2

2013-10-28  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I3d2076c510d9cb1728ea9fc0617d875536f98c54

2013-10-21  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2b57d2dbef208d93aacae8586098fd7dff4b1797

2013-10-14  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I8c2f421dd7c47847f54da276cf360372b7614109

2013-10-07  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I20a5041d0427424e53e0eb13f33fa85f71d7d525

2013-09-30  Geoff Hutchison <geoff.hutchison@gmail.com>

  * CMakeLists.txt, INSTALL, cmake/modules/FindEigen2.cmake,
  cmake/modules/FindEigen3.cmake, libavogadro/src/config.h.in: Use Eigen3 in
  preference to Eigen2 if found, but in support mode.  Eigen3 allows a staged
  migration to the new API. This patch enables building with either Eigen2 or
  Eigen3 with complete compatibility. Future versions of Avogadro can use
  Eigen3 directly. In the meantime, both version 2.x and 3.x are now supported.
   Change-Id: Ibae3a7ca719124af73f52a19244beb9a2cbf180e

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Idba55093eec7517844553d8e39cd16d1cdadbde8

2013-09-23  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Iec7ff4cd3c3254af406730ff49ce60e7b9c36e03

2013-09-21  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h,
  libavogadro/src/extensions/qtaim/qtaimodeintegrator.h,
  libavogadro/src/glwidget.h: Removed unguarded GCC pragma calls  These were
  introduced as part of a larger cleanup, and should not be used unguarded.
  Reverting these, but leaving the rest of the changes in place.  Change-Id:
  Iea444b14e5f82663f7f3a54cebc9e643def7f322

2013-09-20  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/skeletontree.cpp: Fix crash when setting torsion angles
  PR#666.  Crash from incorrect memory access with SkeletonTree class. Make
  sure root node is initialized to NULL to avoid deleting. Also make sure to
  invalidate property table cache. Now setting a torsion rotates the angle and
  properly updates data.  Change-Id: I667cd3ac21d6cb59486483e6752210d5d393722d

2013-09-20  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/qtaim/qtaimmathutilities.cpp,
  .../src/extensions/qtaim/qtaimmathutilities.h: Make QTAIM compile and work on
  Windows  Rewrote the math utilities for QTAIM to be simple functions in a
  namespace, pass their arguments by reference and adjusted style to be a
  little more consistent.  Change-Id: I11737cb521359c1e038930f054630419d2309a30

2013-08-11  Andreas Schwab <schwab@linux-m68k.org>

  * libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt,
  libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt: Properly set
  PIC flag for libspglib and libtubegen   Change-Id:
  Ibe8f103fe3a6bfe0ad7c72c6cdfe37d0c2535899

2013-09-19  Geoff Hutchison <geoff.hutchison@gmail.com>

  * testfiles/methane.nwo, testfiles/methanol.nwo: Applied updated NWChem test
  files using v6.0  Contributed by Michael Banck to clarify distribution. Files
  remove strongly-worded statement from non-open NWChem.  Change-Id:
  I6ab01e496f05a8116e73e95e0a849c89b301db83

2013-08-14  Julien Nabet <serval2412@yahoo.fr>

  * avogadro/src/mainwindow.cpp, avogadro/src/pluginitemmodel.cpp,
  libavogadro/src/colors/smartscolor.cpp,
  .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h,
  .../src/extensions/qtaim/qtaimodeintegrator.h,
  .../src/extensions/quantuminput/gamessinputdata.cpp,
  .../extensions/quantuminput/molproinputdialog.cpp,
  .../src/extensions/surfaces/orbitalextension.cpp,
  libavogadro/src/tools/skeletontree.cpp: Fix warnings (final part)  Avogadro
  builds ok with -Werror with gcc 4.7.3  Change-Id:
  I524764748b4acd83a48cdb6a3a611e0d51ccb389

2013-08-13  Julien Nabet <serval2412@yahoo.fr>

  * libavogadro/src/extensions/cartesianextension.cpp,
  .../src/extensions/crystallography/crystallographyextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/selectrotatetool.cpp: Fix some warnings part2 
  Change-Id: Ic70ec3d18e999d05292a84e5df614aaec5d97cd6

2013-08-07  Julien Nabet <serval2412@yahoo.fr>

  * .../extensions/surfaces/openqube/gamessukout.cpp,
  .../src/extensions/surfaces/openqube/gamessus.cpp,
  .../src/extensions/surfaces/openqube/molden.cpp,
  .../src/extensions/surfaces/openqube/mopacaux.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/plotwidget.cpp: Fix some warnings  Change-Id:
  I37005da0d650744b0811c6d98d62e99d0dc738f6

2013-08-03  Julien Nabet <serval2412@yahoo.fr>

  * libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  .../extensions/quantuminput/gamessinputdialog.cpp: Cppcheck: fix duplicate
  branches for if and else  Change-Id:
  Idcadcca42053b05e5986c8bbc4f1d3fa671fb025

  * avogadro/src/pluginsettings.cpp, avogadro/src/projecttreeeditor.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/quantuminput/gamessinputdata.cpp,
  libavogadro/src/extensions/surfaces/openqube/slaterset.cpp,
  libavogadro/src/glwidget.cpp: Cppcheck: fix some reassignments  TODO:
  src/extensions/surfaces/openqube/gaussianset.cpp needs to be changed. Indeed,
  from line 356 there's a wrong use of switch Moreover indexMO is assigned but
  not used  Change-Id: Ie69082b43a72f8b138af2feba406a2b935e5bcc6

2013-08-02  Julien Nabet <serval2412@yahoo.fr>

  * .../src/extensions/quantuminput/gamessextension.cpp,
  .../src/extensions/quantuminput/gamessinputdata.cpp,
  libavogadro/src/primitivelist.h: Cppcheck: fix Prefer prefix ++/-- operators
  for non-primitive type  Change-Id: I9345e04ca9538028a340fba5bfcf2e58a9825bf9

2013-04-08  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I8bde8aadd032497f211acfcc07b2f64d37e7a59b

2013-04-01  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ic1198f50861ab4701335108ccc632cd4d4487ad0

2013-03-25  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ie932a8f5a74d4a183e41ac904ab5af25648fb54f

2013-03-18  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I6163f50df70c0c5b19a617d22f8442a529b3967b

2013-03-11  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4b9bedebe85c92c33fc52e5c31e198cc258424db

2013-03-04  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ib50256b8c3f8e9991b4c31c6fee678b476893476

2013-02-25  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2520f8078592426318785ff421adb6c10b1dfdc0

2013-02-18  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ifa1679c95c715e611260873f951a3a8d227bbe51

2013-02-11  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I7361983a5ffd57cce38bd9eaf535aa38f331aa0b

2013-02-04  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Iedd6b7f68b4f3e2c2958dfaee76ca4db8f918312

2013-01-28  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I147b3cac87ea3904bd76f9b0547f7f0654037e81

2013-01-21  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I393f81dd671a4e238b9905134a24642ecaee6440

2013-01-14  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I7878764b0386a68ccd42344e4884adef15392d78

2013-01-07  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4588704dfe775353db7440324da624085298b52d

2012-12-31  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I762a4cc98e82404c5815962090db40fcae8c2374

2012-12-24  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I84f7822e51324952a35bda86b0e291c9ada87818

2012-05-31  Geoff Hutchison <geoff.hutchison@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add a new "Copy As" SMILES or InChI command.  The
  SMILES, in particular, is useful for the new SMILES-based polymer builder. 
  Change-Id: I532923b78ca7e3c7334a7ea3bc7424d1cfd977dd

2012-12-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Icf387412235fd9ed7b29b5ecfa3db669034cfc9c

2012-12-12  Matthew Kennedy <matthew.kennedy.6@gmail.com>

  * .../src/extensions/quantuminput/CMakeLists.txt,
  .../extensions/quantuminput/inputfileextension.cpp,
  .../extensions/quantuminput/psi4inputdialog.cpp,
  .../src/extensions/quantuminput/psi4inputdialog.h,
  .../src/extensions/quantuminput/psi4inputdialog.ui: PSI4 Interface added. 
  Change-Id: I215c0d9f5f9b2e4c95790d2c278ff4f9ddb7aa75

2012-12-10  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I311675a1b101a3eeb779ed85f1f83531a2c7bc24

2012-12-03  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: If65fc6ab1c6b2251396d9110115d0c38a7224da5

2012-11-26  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4248d48233a9afb8e960848d49ca26a70680da9f

2012-11-19  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I823eb6c0c45253d127ac80ce0a7c2d65b0992ea6

2012-11-12  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: If2dbf0997c9adbb158ca937ee6c2a9a781d174c8

2012-11-05  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I7ab3bf618b12624b13c21be54a2e4365c83d0a6d

2012-10-29  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4f2bf5b08cceb085273610cafe6e80651f2ee4f9

2012-10-22  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I5611339f755c84cf8a78299b61bd652eedaae738

2012-10-15  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I1b69d3122b0f2c63c3fb94c2e19e249cc26e14ab

2012-10-08  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2476b9504742fc8311ce12909d1a7c2d0f5fa4ad

2012-10-01  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I9beee811d9723dfae5def9e6f1199306722d0418

2012-09-24  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I1d58396d32862747bd76b8d99eaefaff9145610d

2012-09-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/et.po,
  i18n/avogadro/eu.po, i18n/avogadro/fi.po, i18n/avogadro/fr.po,
  i18n/avogadro/gl.po, i18n/avogadro/he.po, i18n/avogadro/hi.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/ms.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sl.po, i18n/avogadro/sq.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/ta.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/et.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/gl.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/ms.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Idc8f8ad61c1f600e9502a28952f4c0098248eec4

2012-09-11  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/et.po, i18n/avogadro/hi.po, i18n/avogadro/ms.po,
  i18n/avogadro/sl.po, i18n/avogadro/sq.po, i18n/avogadro/ta.po,
  i18n/libavogadro/et.po, i18n/libavogadro/ms.po, i18n/libavogadro/sl.po,
  i18n/libavogadro/sq.po: New translation PO files from Launchpad.  Change-Id:
  I60e26bffa4f95968a2f47e4138bd5e8753495276

2012-09-10  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ie39643ae96e28879b4505e0e972f05da89ca5b7c

2012-09-03  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I67b31c4793b67436ccb8ea141158bf3dccd0c7c9

2012-08-27  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ic256d97c18526d54b295d0ec27889bac396c83f7

2012-08-20  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I1ba3162563569eaffb04c1d3ddbc8d49aa79fcb3

2012-08-13  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I0822a17e96ac792a5620b9355c603b7d4b68bdf5

2012-08-06  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2fe9a3c7bd7df4c5750086027f756132f5cb43ef

2012-07-30  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I770f655b710920abbb5fb871726ba2fb78937db4

2012-07-23  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I5803a9c71e672b93f49e8ce48ff5f4525bf9e214

2012-07-16  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I3241b90a48b5ed3d554d05bc1369180900dd1d19

2012-07-09  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ieaa0b07d0eb1f1d1772867a5a67388c9727890ee

2012-06-13  Geoff Hutchison <geoff.hutchison@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/molecule.cpp: Fix crash with
  dipole moment after optimization.  Fixes PR#3521044. Request new instance of
  force field object for calculating dipole moment. Otherwise, multi-threaded
  usage causes crashing.  Change-Id: Iaebf31c13677d29e7acec95b91a17f9e06a17aa4

2012-07-02  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: If7e7bded33c09da90fcf9ec974dbe51a747e95e7

2012-06-25  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I78e782a10e39b7d3488d5e5cc5a984682fbf3a1d

2012-06-15  Geoff Hutchison <geoff.hutchison@gmail.com>

  * testfiles/b2h6.wfn, testfiles/c4h4.wfn, testfiles/hco2.wfn: Add three
  example WFN files.  Gives test files for QTAIM analysis, including diborane
  (B2H6), C4H4, and HCO2. These files will be used for a tutorial.  Change-Id:
  I0489ea1b23ea4683596069bd219ef8cb3c9874d1

2011-12-22  Albert DeFusco <defusco@pitt.edu>

  * .../src/extensions/quantuminput/CMakeLists.txt,
  .../extensions/quantuminput/inputfileextension.cpp,
  .../extensions/quantuminput/lammpsinputdialog.cpp,
  .../extensions/quantuminput/lammpsinputdialog.h,
  .../extensions/quantuminput/lammpsinputdialog.ui: simple lammps input
  generator for water  This input generator along with the OpenBabel lmpdat
  format can be used to create input files for MD simulations.  The SPC and
  SPC/E water models are programmed.  J. Phys. Chem. A, 2001, 105 (43), pp
  9954–9960 DOI: 10.1021/jp003020w  Change-Id:
  Icf27536174cfa7a720ec3e625849310e71ff1bfd

2012-06-18  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ie559cf8bcd4b9cb57c342d52832a103780778de9

2012-06-15  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/atom.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculefile.cpp: Fix residue and atom code assignment.  Any
  time the selection was updated, residue codes would be killed. (No need to
  call Primitive::update()) Also, be conservative about changing elements when
  copying atoms for the same reason. Finally, avoid calling OBChainsParser
  unless *absolutely* necessary, because of bugs like PR#3102300. Fully fixes
  this bug.  Change-Id: If990ce1903d668f596fe67208e34094edb70cfc7

2012-06-12  Geoff Hutchison <geoff.hutchison@gmail.com>

  * .../src/extensions/insertfragmentextension.cpp,
  .../src/extensions/insertfragmentextension.h: Prevent a quick double-insert. 
  With the "grow by fragment" feature, accidentally double-clicking "insert"
  could give you much more than you intended. Adds a 2-second delay to ensure
  you actually want to grow the selected insert.  Change-Id:
  Ib9fb77b067a6470dd7d2672d8ba9e3b7e3738ca4

2012-06-11  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Idee86c73583a211ba091fa954ac4b0a1e5658bb4

2012-06-06  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h: Removing the overlay engine  It has
  issues leaking GL state, and is not in a finished state. This can be brought
  back if there is further motivation in the future.  Change-Id:
  Ie1a05b900ac0277ebefc72a43a9631d3713cb5a8

2012-06-04  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ic0a6b0727c85fc317a07e6ee57e628556f2824c0

2012-05-22  Geoff Hutchison <geoff.hutchison@gmail.com>

  * .../arsenides/Co.87Fe.11Ni.13As3-Skutterudite.cif,
  crystals/arsenides/CoAs3-Skutterudite.cif,
  crystals/clays/Al2Si2O9H4-Dickite.cif,
  crystals/clays/Al2Si2O9H4-Kaolinite.cif,
  crystals/clays/Al2Si2O9H4-Nacrite.cif,
  crystals/clays/Al2Si4O12Ca0.5-Montmorillonite.cif,
  crystals/clays/Al4KSi2O12-Illite.cif,
  crystals/clays/AlSi2O6H-Pyrophyllite.cif,
  crystals/clays/Fe2.25Cl0.5H2.75-Fougerite.cif,
  crystals/clays/FeSi2O6H-Nontronite.cif, crystals/clays/Lepidolite.cif,
  crystals/clays/Mg2Al2SiO9H4-Amesite.cif,
  crystals/clays/Mg3(O12Si4)H2-Vermiculite.cif,
  crystals/clays/Mg4Si6O22.82H13.64-Sepiolite.cif,
  ...n1.854Fe1.656Mg0.537Si0.953O9H4-Guidottiite.cif,
  crystals/clays/Zn2SiO5H2-Hemimorphite.cif, crystals/ice/H2O-Ice-II.cif,
  crystals/ice/H2O-Ice-III.cif, crystals/ice/H2O-Ice-IV.cif,
  crystals/ice/H2O-Ice-Ih.cif, crystals/ice/H2O-Ice-VI.cif,
  crystals/ice/H2O-Ice-VII.cif, crystals/ice/H2O-Ice.cif,
  crystals/nitrides/AlN.cif, crystals/nitrides/GaN.cif,
  crystals/nitrides/InN.cif, crystals/other/As3Co-Skutterudite.cif,
  crystals/other/H3N-Ammonia.cif, crystals/other/InSb.cif,
  crystals/other/LaAlO3.cif, crystals/other/LiH.cif,
  crystals/oxides/BaTiO3-BariumTitanate.cif,
  crystals/oxides/MgTiO3-MagnesiumTitanate.cif,
  crystals/selenides/Sb2Se3-Antimonselite.cif,
  crystals/sulfides/Bi2S3-Bismuthinite.cif,
  crystals/sulfides/Sb2S3-Stibnite.cif,
  crystals/titanates/SrTiO3-Tausonite.cif: Added a few more minor crystal
  structures.  Includes all remaining III-V semiconductors, common clays, and
  ice polymorphs.  Change-Id: If674b3af73c16e7754f0f0a1e922468f25c95859

2012-05-28  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I15ec3b28e39a19e9a06f713dfeae5a5b947dc2b2

2012-05-23  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/insertdnadialog.ui,
  libavogadro/src/extensions/insertdnaextension.cpp,
  libavogadro/src/extensions/insertdnaextension.h,
  .../src/extensions/insertpeptideextension.h: Add a DNA/RNA builder.  Uses
  Open Babel's FASTA format support. In OB 2.3.1, this enables single/double
  strand DNA and modifying the # of bp per turn.  Change-Id:
  I82e13b1ac9bd66eea18adadbd94dc7fc9c0793ff

2012-05-21  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I30dffaf9ac5e7f592e611ecead27d42e4f030af6

2012-05-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.h,
  libavogadro/src/molecule.cpp: Modify the setOBMol method to fill crystal
  cells.  The existing code will import only the asymmetric unit cell, which is
  surprising for most inorganic crystals. (It works fine for molecular
  crystals.) This patch adds a heuristic to fill the unit cell when presented
  with a crystal < 4 carbon atoms.  This also removes similar code from the
  insert crystal extension.  Change-Id:
  I07f613cebaa72bb6b51c7c6714f1e2d8533ab792

2011-08-23  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/manipulatesettingswidget.ui,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/moveatomcommand.cpp: Allow manual translation or
  rotation.  Adds a settings widget to the manipulate tool. This allows manual
  translation or rotation around the origin or the center of geometry. Also
  supports undo of manipulations.  Change-Id:
  I45a9e02dc6251dfc6f2f0f55d79ed6039ce88697

2012-05-14  Geoff Hutchison <geoff.hutchison@gmail.com>

  * .../crystallography/crystallographyextension.cpp,
  .../extensions/crystallography/ui/ceslabbuilder.cpp: Fix "rogue" slab atoms
  bug.  Adds a small amount of floating-point slop to comparisons when
  comparing atoms at unit cell boundaries. Fixes the "rogue atom" bug where
  edges of the slab weren't always uniform.  Change-Id:
  I195601f786ef9a9e8cb2546a50edc0971d72bbbf

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2f9420cbbbd42f37e17827196279a3582b4407c7

2012-05-07  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2308e7dbd38d410884af6d4568eac77185706d3d

2011-03-27  David C. Lonie <loniedavid@gmail.com>

  * .../src/extensions/crystallography/CMakeLists.txt,
  .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/ui/ceslabbuilder.cpp,
  .../extensions/crystallography/ui/ceslabbuilder.h,
  .../extensions/crystallography/ui/ceslabbuilder.ui,
  libavogadro/src/molecule.h: Add a slab builder extension.  Generates a
  slab/surface with arbitrary Miller plane, including producing a supercell
  beforehand. Generates lattice vectors for the surface.  Change-Id:
  If23e65a1e2cad7334bec37c1dab3b4eb54823954

2012-04-30  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I6be465a480863ba1d0820cd2396735f32a4a2655

2012-04-23  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ie48417f8f0593fdd7a3cf80c92cb8adbb3a4c343

2012-02-10  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/camera.cpp,
  .../crystallography/crystallographyextension.cpp, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/tools/navigatetool.cpp: Tweaks to
  camera initialization and navigation.  This patch improves camera
  initialization and navigation for both crystal structures and orthographic
  projections.  Change-Id: Ie838975a470740ea90647c22e1db55b3330af781

2012-04-17  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp: Fixed up a few minor
  style issues  Fixed some whitesapce issues, and use static_cast instead of C
  casts.  Change-Id: I2cd949f7f186e1da14545c04e4965cbe7254838f

2012-04-16  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I044a7ba16eb64771a14c6244b7e6612a8ec2b093

2012-04-12  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/FindSIP.cmake, cmake/modules/PythonDeps.cmake: Integrate
  FindSIP into the Python logic  Call find_package(SIP), modified FindSIP to
  look in the Python path first, as that was the only place we looked before
  and is likely to be the best candidate when available - it is installed
  alongside the Python headers we are compiling against.  Change-Id:
  I00aff319ba151e3d9b1995165d1a0b75d339f50c

2012-04-09  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I6a6371c9061cf3105d35e771055cb027608559a8

2012-04-02  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ie89a18143adda1da922ec5ad1099e994aa82ecf4

2012-02-21  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/unitcellparamdialog.ui: Remove old, deprecated
  unit cell extension.  New crystallography extension provides all the same
  features (and more) in a more user- friendly manner.  Change-Id:
  I05747b2aa8c2f2b648a9ee46ea81f8ff48c258ba

2012-04-01  David C. Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Starting removing unit cell rendering code from
  mainwindow.  The renderUnitCellAxes functionality is now available through
  the crystallography extension, and eventually should be isolated to an
  engine.  Change-Id: I99822d87a3212199d435e738a4f82e5cfb98b94e

  * .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/ui/ceviewoptionswidget.cpp,
  .../crystallography/ui/ceviewoptionswidget.h,
  .../crystallography/ui/ceviewoptionswidget.ui: Add option to change cell
  color to crystallography extension.  Also fix custom cell color persistence. 
  Eventually all of this functionality needs to be moved into an engine so that
  other painters (e.g. POV-ray) can correctly handle unit cells. For now, I've
  moved it into the crystallography extensions because it was the last missing
  bit needed to replace the old unitcellextension, which can now be removed. 
  Change-Id: If413d9aa19a48c827aa4f826f6e6ad96ed309a41

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add missing
  GLWidget API and use alpha value of cell color.  Change-Id:
  I338a5f4b2799e5609747689f2e8017c8c8deb1dd

  * libavogadro/src/color.cpp, libavogadro/src/color.h: Add QColor and copy
  constructors to Color.  Also fix QColor include.  Change-Id:
  If694f285db0a243c9d9f6b23480eb189a3a38564

2012-03-26  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2813aede48a9cf8850a334c47266d8638ec07208

2012-03-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  .../src/extensions/conformersearchdialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h: Add new conformer search
  options from openbabel (genetic algortihm)  Change-Id:
  I0fe483240257cc487524a49afe71389103ddd69b

2012-03-19  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I28248068381ecf60af46de8c68e27140ed9ddfd4

2012-03-12  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I8c9893e97f5ad8b5d4ac94b154e8b63eae55efa3

2012-03-05  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ie3b50aaf2a521006617ca9ae4300ec159f37e835

2012-02-27  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ibb013a35ecef88d025ce5302456e53dc50207c87

2012-02-22  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/ui/cetranslatewidget.cpp,
  .../crystallography/ui/cetranslatewidget.h,
  .../crystallography/ui/cetranslatewidget.ui: Added option to translate a
  crystal so that a specified atom is centered in the unit cell.  Change-Id:
  I2cc645b47b65b8ac39db38a2c00452b3eed874c6

2012-02-18  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/ui/ceviewoptionswidget.cpp,
  .../crystallography/ui/ceviewoptionswidget.h,
  .../crystallography/ui/ceviewoptionswidget.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Add option to only render one set of unit cell
  boundaries.  When an A, B, or C repeat is set, optionally only render the
  unit cell box for the unit cell at offset (0, 0, 0). This is a popular style
  for publication images.  Change-Id: I38f6206e550a010a3cd5bc9b8e9dd5dd89539aad

2011-08-18  Geoff Hutchison <geoff.hutchison@gmail.com>

  * .../src/extensions/crystallography/CMakeLists.txt,
  .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/ui/ceviewoptionswidget.cpp,
  .../crystallography/ui/ceviewoptionswidget.h,
  .../crystallography/ui/ceviewoptionswidget.ui: Add support for crystal view
  options.  Includes # of repeat cells and Miller plane. Supplants older
  UnitCellParam dialog.  Change-Id: I86b5f58659c6057aeeb6dc18d086f707004018f0

2012-02-20  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Id85c8e55fe03a51eae30b3054f82565ede79463a

2012-02-05  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/fragment.cpp, libavogadro/src/fragment.h,
  libavogadro/src/python/fragment.cpp: Compilation fixes for Python wrapping. 
  See Qt bug https://bugreports.qt-project.org/browse/QTBUG-22829 for issues
  introduced in Boost 1.48 that cause compilation errors in MOC. QString is
  implicitly shared in fragment, and the overload was causing compilation
  errors in the wrapping.  I also took a look at the fragment API, and made it
  more consistent with that of the molecule. The QList is implicitly shared,
  and so simply adding the missing const is enough. This then allows the Python
  wrapping to compile again.  Change-Id:
  I678d700e81226259bed55e51800baa5601ff64e1

2012-02-13  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I7f6c1d2527755b39d7622c95ee7879654c4aaa8e

2012-02-10  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/CMakeLists.txt,
  .../src/extensions/crystallography/avospglib.cpp,
  .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystalpastedialog.cpp,
  .../src/extensions/crystallography/obeigenconv.h,
  libavogadro/src/obeigenconv.h: Move obeigenconv.h to libavogadro public
  headers.  Change-Id: I2a3fe135a504e29b7dcc3719562e26ffd6df9a17

2011-12-02  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add the modelview
  matrix to the debug overlay  Change-Id:
  I3e2b26160c0dab3cc9aab9611f574141c3878d9c

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Make
  GLWidget::[abc]Cells() const  Change-Id:
  I990e917e8f01df2998503b12deef9fd8f3b2070f

2012-02-10  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/crystalpastedialog.cpp, testfiles/VASP-5.2-POSCAR.vasp:
  Allow import of VASP 5.x+ POSCARs from the clipboard.  VASP versions since
  5.2 allow an extra line to be inserted at line six that specifies the atomic
  symbols corresponding to the composition/coordinate data.  Testfile added. 
  Change-Id: I31058e29275a1ae9affa800ac8705e64b8742495

2012-02-06  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I5cc222e61862f31b6f508d0789a9a079dbdbc757

2012-01-05  David C. Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h, libavogadro/tests/moleculefiletest.cpp: Add
  an options argument to MoleculeFile::writeMolecule.  Change-Id:
  I31862372bda12ef3265dc1c1359c6441f4f138d6

2012-01-28  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/camera.cpp, libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/glpainter_p.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Fixed GL includes to work on Mac
  and other OSes.  On the Mac the OpenGL headers are typically installed in
  OpenGL rather than the more conventional GL directory on every other
  operating system. I also removed the povpainter GL include as it was not
  needed there.  Change-Id: Ie0bf5a9e97b792f9c4ca6890c4b1226df5d3ab60

2012-01-27  Albert DeFusco <defusco@pitt.edu>

  * .../src/extensions/quantuminput/CMakeLists.txt,
  .../extensions/quantuminput/inputfileextension.cpp,
  .../quantuminput/teracheminputdialog.cpp,
  .../extensions/quantuminput/teracheminputdialog.h,
  .../extensions/quantuminput/teracheminputdialog.ui: TeraChem input generator 
  This generator is a copy of the Q-Chem generator.  Just like Gaussian and
  Q-Chem, it is easier to support only single-point, gradient and optimization
  runs.  Important features include 1. If multiplicity > 1 : force unrestricted
  calculations  Since I do not know which basis sets have been included in
  version 1.45 I have provdided a few basis sets that contain up to d
  functions. From reading the mailing list I find that version 1.45 does not
  have gradients for d functions, but I have not implemented a warning. 
  http://petachem.com/doc/userguide.pdf  --- Patch 2: added dispersion combo
  --- Patch 3: fixed whitespace  Change-Id:
  I5d5577836d537c76f177821bc024f343eaf3664c

2011-05-22  Raimondas Galvelis <raimondas.galvelis@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/camera.cpp,
  libavogadro/src/camera.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/navigate.cpp: Orthographic
  projection  Ability to swith between perspective and orthographic projections
  of the molecule  Projection can be changed by "View > Projection"  Change-Id:
  I15c20715aed707c6d1efa13e5022698caadd92ca

2012-01-30  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I62a61dd268822b51e03f142180801582819fd84d

2012-01-23  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Iff81f32a10e2147205dd4550e841bc9989dfc1c3

2012-01-19  David C. Lonie <loniedavid@gmail.com>

  * .../src/extensions/swcntbuilder/tubegen/ANSR.cpp,
  libavogadro/src/extensions/swcntbuilder/tubegen/ANSR.h,
  .../src/extensions/swcntbuilder/tubegen/Bitmap.h,
  .../src/extensions/swcntbuilder/tubegen/Cell.cpp,
  .../extensions/swcntbuilder/tubegen/CrystalCell.cpp,
  .../src/extensions/swcntbuilder/tubegen/TubeGen.cpp,
  .../extensions/swcntbuilder/tubegen/TubuleBasis.cpp: Triage compilation of
  TubeGen on MSVC2008.  Change-Id: Ia22c91c6f4de3816bdefb45fda822df43cac3591

2012-01-16  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Id4cdd25aacf50d3896fca99f170f6976567ef746

2012-01-09  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I1a0ef42e42a5ebc27537b474e812d7efa35f2e83

2012-01-04  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt, cmake/modules/AvogadroConfig.cmake.in,
  cmake/modules/AvogadroUse.cmake: Removed deprecated build settings methods. 
  They have been deprecated by the CMake community, and were causing issues
  with linking to avogadro. In my tests, linking to avogadro works again after
  these changes. I will complete the update to use exported library targets
  soon to make this more reliable.

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  .../extensions/surfaces/openqube/CMakeLists.txt,
  .../src/extensions/surfaces/openqube/atom.cpp,
  .../src/extensions/surfaces/openqube/atom.h,
  .../src/extensions/surfaces/openqube/basisset.cpp,
  .../src/extensions/surfaces/openqube/basisset.h,
  .../surfaces/openqube/basissetloader.cpp,
  .../extensions/surfaces/openqube/basissetloader.h,
  .../src/extensions/surfaces/openqube/cube.cpp,
  .../src/extensions/surfaces/openqube/cube.h,
  .../extensions/surfaces/openqube/gamessukout.cpp,
  .../src/extensions/surfaces/openqube/gamessus.cpp,
  .../src/extensions/surfaces/openqube/gamessus.h,
  .../extensions/surfaces/openqube/gaussianfchk.cpp,
  .../extensions/surfaces/openqube/gaussianset.cpp,
  .../src/extensions/surfaces/openqube/gaussianset.h,
  .../src/extensions/surfaces/openqube/molecule.cpp,
  .../src/extensions/surfaces/openqube/molecule.h,
  .../src/extensions/surfaces/openqube/mopacaux.cpp,
  .../src/extensions/surfaces/openqube/mopacaux.h,
  .../src/extensions/surfaces/openqube/openqubeabi.h,
  .../src/extensions/surfaces/openqube/slaterset.cpp,
  .../src/extensions/surfaces/openqube/slaterset.h: Updated to latest version 
  of OpenQube.  This brings in several updates from David Lonie, Geoff
  Hutchison and myself. OpenQube is now on Gerrit, and will use the same review
  process as other libraries with automated testing coming very soon.

2012-01-02  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I817d56c558486e4ba50419345296d3344b16e7e9

2011-12-26  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4821723fca5c4c830e00450853f001af338bcc56

2011-12-19  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2dbb0c1f585138c338e1f7e6ed93fe1a54abf50d

2011-12-17  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/ui/cecoordinateeditor.ui,
  .../crystallography/ui/cematrixeditor.ui,
  .../crystallography/ui/ceparametereditor.ui: Make crystallographyextension
  DockWidgets look nicer.  Text was not fitting the edit boxes correctly on
  linux, clipping portions of the cell matrix etc off.  Change-Id:
  I8bb23d14546481662dd02519c2ef706ec9b59a42

2011-12-15  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/ui/ceabstractdockwidget.cpp,
  .../crystallography/ui/ceabstractdockwidget.h,
  .../crystallography/ui/ceabstracteditor.cpp,
  .../crystallography/ui/ceabstracteditor.h,
  .../crystallography/ui/cecoordinateeditor.cpp,
  .../crystallography/ui/cecoordinateeditor.h,
  .../crystallography/ui/cematrixeditor.cpp,
  .../extensions/crystallography/ui/cematrixeditor.h,
  .../crystallography/ui/ceparametereditor.cpp,
  .../crystallography/ui/ceparametereditor.h,
  .../crystallography/ui/cetranslatewidget.cpp,
  .../crystallography/ui/cetranslatewidget.h: Port the Crystallography
  extension to use the new DockWidget system.  I was able to remove a lot of
  the dependance on the hacky MainWindow grabbing code, although I left the
  hacky bit in (m_mainwindow is a good parent for dialog window placement). 
  Change-Id: If0720970e9656fa4dc3bfcc80d114bd303fab9af

2011-12-12  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I5aea5418e187ec25c6b7b57a22874ae59458eca9

2011-08-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * CMakeLists.txt, crystals/antimonides/AlSb.cif,
  crystals/antimonides/GaSb.cif, crystals/antimonides/InSb.cif,
  crystals/arsenides/AlAs.cif, crystals/arsenides/BAs.cif,
  crystals/arsenides/GaAs.cif, crystals/arsenides/InAs.cif,
  crystals/arsenides/NiAs-Nickeline.cif,
  crystals/carbides/SiC-2H-Moissanite.cif, crystals/carbides/SiC-3C-beta.cif,
  crystals/carbides/SiC-6H-alpha.cif, crystals/carbides/SiC-Moissanite.cif,
  crystals/carbides/SiC.cif, crystals/carbides/W2C.cif,
  crystals/carbides/WC.cif, crystals/carbonates/CaCO3-Calcite.cif,
  crystals/carbonates/CaMgC2O6-Dolomite.cif,
  crystals/carbonates/Li2CO3-Zabuyelite.cif,
  crystals/carbonates/MgCO3-Magnesite.cif,
  crystals/carbonates/Na2CO3-Natrite.cif, crystals/elements/Ac-Actinium.cif,
  crystals/elements/Ag-Silver.cif, crystals/elements/Al-Aluminum.cif,
  crystals/elements/Am-Americium.cif, crystals/elements/Ar-Argon.cif,
  crystals/elements/As-Arsenic.cif, crystals/elements/As-Arsenolamprite.cif,
  crystals/elements/Au-Gold.cif, crystals/elements/B-Boron.cif,
  crystals/elements/Ba-Barium.cif, crystals/elements/Be-Beryllium.cif,
  crystals/elements/Bi-Bismuth.cif, crystals/elements/Br-Bromine.cif,
  crystals/elements/C-Diamond.cif, crystals/elements/C-Graphite.cif,
  crystals/elements/C-Lonsdaleite.cif, crystals/elements/Ca-Calcium-alpha.cif,
  crystals/elements/Ca-Calcium-beta.cif,
  crystals/elements/Ca-Calcium-gamma.cif, crystals/elements/Cd-Cadmium.cif,
  crystals/elements/Ce-Cerium.cif, crystals/elements/Cl-Chlorine.cif,
  crystals/elements/Co-Cobalt.cif, crystals/elements/Cr-Chromium.cif,
  crystals/elements/Cs-Cesium.cif, crystals/elements/Cu-Copper.cif,
  crystals/elements/Dy-Dysprosium.cif, crystals/elements/Er-Erbium.cif,
  crystals/elements/Eu-Europium.cif, crystals/elements/Fe-Iron-alpha.cif,
  crystals/elements/Fe-Iron-beta.cif, crystals/elements/Fe-Iron-delta.cif,
  crystals/elements/Fe-Iron-gamma.cif, crystals/elements/Ga-Gallium.cif,
  crystals/elements/Gd-Gadolinium.cif, crystals/elements/Ge-Germanium.cif,
  crystals/elements/He-Helium.cif, crystals/elements/Hf-Hafnium.cif,
  crystals/elements/Ho-Holmium.cif, crystals/elements/I-Iodine.cif,
  crystals/elements/In-Indium.cif, crystals/elements/Ir-Iridium.cif,
  crystals/elements/K-Potassium.cif, crystals/elements/Kr-Krypton.cif,
  crystals/elements/La-Lanthanum.cif, crystals/elements/Li-Lithium.cif,
  crystals/elements/Lu-Lutetium.cif, crystals/elements/Mg-Magnesium.cif,
  crystals/elements/Mn-Manganese-alpha.cif,
  crystals/elements/Mn-Manganese-delta.cif,
  crystals/elements/Mn-Manganese-gamma.cif,
  crystals/elements/Mo-Molybdenum.cif, crystals/elements/N-Nitrogen.cif,
  crystals/elements/Na-Sodium.cif, crystals/elements/Nb-Niobium.cif,
  crystals/elements/Nd-Neodymium.cif, crystals/elements/Ne-Neon.cif,
  crystals/elements/Ni-Nickel.cif, crystals/elements/Np-Neptunium-alpha.cif,
  crystals/elements/Np-Neptunium-beta.cif,
  crystals/elements/Np-Neptunium-gamma.cif, crystals/elements/Os-Osmium.cif,
  crystals/elements/P-Phosphorus-black.cif, crystals/elements/P-Phosphorus.cif,
  crystals/elements/Pb-Lead.cif, crystals/elements/Pd-Palladium.cif,
  crystals/elements/Pr-Praseodymium.cif, crystals/elements/Pt-Platinum.cif,
  crystals/elements/Pu-Plutonium-alpha.cif,
  crystals/elements/Pu-Plutonium-epsilon.cif,
  crystals/elements/Pu-Plutonium-gamma.cif, crystals/elements/Rb-Rubidium.cif,
  crystals/elements/Re-Rhenium.cif, crystals/elements/Rh-Rhodium.cif,
  crystals/elements/Ru-Ruthenium.cif, crystals/elements/S6-Sulfur.cif,
  crystals/elements/S8-Sulfur-alpha.cif, crystals/elements/S8-Sulfur-beta.cif,
  crystals/elements/S8-Sulfur-gamma.cif, crystals/elements/Sb-Antimony.cif,
  crystals/elements/Sc-Scandium.cif, crystals/elements/Se-Selenium.cif,
  crystals/elements/Si-Silicon.cif, crystals/elements/Sm-Samarium.cif,
  crystals/elements/Sn-Tin-alpha.cif, crystals/elements/Sn-Tin-beta.cif,
  crystals/elements/Sr-Strontium.cif, crystals/elements/Ta-Tantalum.cif,
  crystals/elements/Tb-Terbium.cif, crystals/elements/Te-Tellurium.cif,
  crystals/elements/Th-Thorium.cif, crystals/elements/Ti-Titanium-alpha.cif,
  crystals/elements/Ti-Titanium-beta.cif, crystals/elements/Tl-Thallium.cif,
  crystals/elements/Tm-Thulium.cif, crystals/elements/U-Uranium-alpha.cif,
  crystals/elements/U-Uranium-gamma.cif, crystals/elements/V-Vanadium.cif,
  crystals/elements/W-Tungsten.cif, crystals/elements/Xe-Xenon.cif,
  crystals/elements/Y-Yttrium.cif, crystals/elements/Yb-Ytterbium.cif,
  crystals/elements/Zn-Zinc.cif, crystals/elements/Zr-Zirconium.cif,
  crystals/halides/AgBr-Bromargyrite.cif,
  crystals/halides/AgCl-Chlorargyrite.cif, crystals/halides/AlCl3.cif,
  crystals/halides/AlNa3F6-Cryolite.cif, crystals/halides/CaF2-Fluorite.cif,
  crystals/halides/CdCl2.cif, crystals/halides/CdI2.cif,
  crystals/halides/CrCl2.cif, crystals/halides/CrCl3.cif,
  crystals/halides/CsCl.cif, crystals/halides/FeCl3-Molysite.cif,
  crystals/halides/HgCl-Calomel.cif, crystals/halides/KBr.cif,
  crystals/halides/KCl-Sylvite.cif, crystals/halides/NaCl-Halite.cif,
  crystals/halides/PbFCl-Matlockite.cif, crystals/hydrides/KH.cif,
  crystals/hydrides/LiH.cif, crystals/hydrides/NaH.cif,
  crystals/hydrides/PdH.cif, crystals/hydroxides/Ca(OH)2-Portlandite.cif,
  crystals/hydroxides/KOH.cif, crystals/hydroxides/LiOH.cif,
  crystals/hydroxides/Mg(OH)2-Brucite.cif,
  crystals/hydroxides/Ni(OH)2-Theophrastite.cif,
  .../intermetallics/(Cu0.5Fe0.5)Pt-Tulameenite.cif,
  .../(Ni0.5Fe0.5)Pt-Ferronickelplatinum.cif,
  crystals/intermetallics/Au3Cu-Bogdanovite.cif,
  crystals/intermetallics/AuCu-Tetraauricupride.cif,
  crystals/intermetallics/BiPd-Sobolevskite.cif,
  crystals/intermetallics/CoFe-Wairauite.cif,
  crystals/intermetallics/Cu2MnAl-Heusler.cif,
  .../intermetallics/FePt-Tetraferroplatinum.cif,
  crystals/intermetallics/PtBi.cif, crystals/nitrides/BN.cif,
  crystals/nitrides/Si3N4-beta.cif,
  crystals/other/(NH4)MgPO4-6(H2O)-Struvite.cif,
  crystals/other/As3Co-Skutterudite.cif, crystals/other/C10H10Fe-Ferrocene.cif,
  .../other/Ca2C4O10H2.57-Oxalate-Whewellite.cif,
  crystals/other/CaC2O6.375H6-Oxalate-Weddellite.cif,
  crystals/other/FeMnO3-Bixbyite.cif, crystals/other/InSb.cif,
  crystals/other/LiH.cif, crystals/other/LiNbO3-LithiumNiobate.cif,
  crystals/other/Pb1Ti0.35Zr0.65O3-PZT-cub.cif,
  crystals/other/Pb1Ti0.35Zr0.65O3-PZT-rhomb.cif,
  crystals/other/YBa2Cu3O6.9-YBCO.cif, crystals/oxides/(MgAl2)O4-Spinel.cif,
  crystals/oxides/Ag2O.cif, crystals/oxides/AgO.cif,
  crystals/oxides/Al2O3-Corundum.cif, crystals/oxides/BaO.cif,
  crystals/oxides/BaTiO3-BariumTitanate.cif, crystals/oxides/CaO-Lime.cif,
  crystals/oxides/CdO-Monteponite.cif, crystals/oxides/CeO2-Cerianite.cif,
  crystals/oxides/CoFe2O4.cif, crystals/oxides/CoO.cif,
  crystals/oxides/Cr2O3-Eskolaite.cif, crystals/oxides/Cu2O-Cuprite.cif,
  crystals/oxides/CuO-Tenorite.cif, crystals/oxides/Fe2O3-Hematite.cif,
  crystals/oxides/Fe3O4-Magnetite.cif, crystals/oxides/FeO-Wustite.cif,
  crystals/oxides/GeO2-Argutite-tetrag.cif, crystals/oxides/GeO2-Argutite.cif,
  crystals/oxides/GeO2.cif, crystals/oxides/HfO2.cif,
  crystals/oxides/In2O3-IndiumOxide.cif, crystals/oxides/In2O3.cif,
  crystals/oxides/IrO2.cif, crystals/oxides/K2O.cif,
  crystals/oxides/La2O3-LanthanumOxide-A.cif, crystals/oxides/Li2O.cif,
  crystals/oxides/MgO-Periclase.cif,
  crystals/oxides/MgTiO3-MagnesiumTitanate.cif,
  crystals/oxides/MnO-Manganosite.cif, crystals/oxides/MnO2-Pyrolusite.cif,
  crystals/oxides/MoO2-Tugarinovite.cif, crystals/oxides/MoO3-Molybdite.cif,
  crystals/oxides/Na2O.cif, crystals/oxides/NbO.cif, crystals/oxides/NbO2.cif,
  crystals/oxides/NiFe2O4.cif, crystals/oxides/NiO-Bunsenite.cif,
  crystals/oxides/PbO.cif, crystals/oxides/PbO2-Scrutinyite.cif,
  crystals/oxides/PdO.cif, crystals/oxides/PtO2-beta.cif,
  crystals/oxides/Rb2O.cif, crystals/oxides/Rh2O3.cif,
  crystals/oxides/RuO2.cif, crystals/oxides/Sc2O3.cif,
  crystals/oxides/SiO2-Coesite.cif, crystals/oxides/SiO2-Cristobalite.cif,
  crystals/oxides/SiO2-Quartz-alpha.cif, crystals/oxides/SiO2-Quartz-beta.cif,
  crystals/oxides/SiO2-Stishovite.cif, crystals/oxides/SmO.cif,
  crystals/oxides/SnO.cif, crystals/oxides/SnO2-Cassiterite.cif,
  crystals/oxides/SrO.cif, crystals/oxides/TaO.cif,
  crystals/oxides/TiO2-Anatase.cif, crystals/oxides/TiO2-Brookite.cif,
  crystals/oxides/TiO2-Rutile.cif, crystals/oxides/UO.cif,
  crystals/oxides/UO2-Uraninite.cif, crystals/oxides/V2O3-Karelianite.cif,
  crystals/oxides/V2O5-Shcherbinaite.cif, crystals/oxides/VO.cif,
  crystals/oxides/VO2.cif, crystals/oxides/WO2.cif, crystals/oxides/Y2O3.cif,
  crystals/oxides/YbO.cif, crystals/oxides/ZnO-Zincite.cif,
  crystals/oxides/ZrO.cif, crystals/oxides/ZrO2-Cubic.cif,
  crystals/phosphides/AlP.cif, crystals/phosphides/BP.cif,
  crystals/phosphides/GaP.cif, crystals/phosphides/InP.cif,
  crystals/selenides/Bi2Se3.cif, crystals/selenides/BiSe.cif,
  crystals/selenides/CdSe-Cadmoselite.cif,
  crystals/selenides/HgSe-Tiemannite.cif,
  crystals/selenides/PbSe-Clausthalite.cif, crystals/selenides/ZnSe.cif,
  crystals/silicates/Be3Al2(SiO3)6-Beryl.cif,
  crystals/sulfates/BaSO4-Barite.cif,
  crystals/sulfates/CaSO4-2(H2O)-Gypsum.cif,
  crystals/sulfates/CaSO4-Anhydrite.cif, crystals/sulfates/CoSO4.cif,
  crystals/sulfates/CuSO4.cif, crystals/sulfates/MgSO4.cif,
  crystals/sulfates/PbSO4-Anglesite.cif, crystals/sulfates/SrSO4-Celestine.cif,
  crystals/sulfides/CdS-Greenockite.cif, crystals/sulfides/CdS-Hawleyite.cif,
  crystals/sulfides/FeS.cif, crystals/sulfides/FeS2-Pyrite.cif,
  crystals/sulfides/HgS-Metacinnabar.cif, crystals/sulfides/PbS-Galena.cif,
  crystals/sulfides/SnS-Herzenbergite.cif,
  crystals/sulfides/ZnS-Sphalerite.cif, crystals/sulfides/ZnS-Wurtzite-2H.cif,
  crystals/sulfides/ZnS-Zincblende.cif, crystals/telurides/Bi2Te3.cif,
  crystals/telurides/BiTe.cif, crystals/telurides/CdTe.cif,
  crystals/telurides/PbTe-Altaite.cif, crystals/telurides/ZnTe.cif,
  crystals/titanates/BaTiO3.cif, crystals/titanates/CaTiO3-Perovskite.cif,
  crystals/titanates/Mg2TiO4-Qandilite-cubic.cif,
  crystals/titanates/Mg2TiO4-Qandilite-tetrag.cif,
  crystals/titanates/MgTiO3.cif, crystals/zeolites/ABW.cif,
  crystals/zeolites/ACO.cif, crystals/zeolites/AEI.cif,
  crystals/zeolites/AEL.cif, crystals/zeolites/AEN.cif,
  crystals/zeolites/AET.cif, crystals/zeolites/AFG.cif,
  crystals/zeolites/AFI.cif, crystals/zeolites/AFN.cif,
  crystals/zeolites/AFO.cif, crystals/zeolites/AFR.cif,
  crystals/zeolites/AFS.cif, crystals/zeolites/AFT.cif,
  crystals/zeolites/AFX.cif, crystals/zeolites/AFY.cif,
  crystals/zeolites/AHT.cif, crystals/zeolites/ANA.cif,
  crystals/zeolites/APC.cif, crystals/zeolites/APD.cif,
  crystals/zeolites/AST.cif, crystals/zeolites/ASV.cif,
  crystals/zeolites/ATN.cif, crystals/zeolites/ATO.cif,
  crystals/zeolites/ATS.cif, crystals/zeolites/ATT.cif,
  crystals/zeolites/ATV.cif, crystals/zeolites/AWO.cif,
  crystals/zeolites/AWW.cif, crystals/zeolites/BCT.cif,
  crystals/zeolites/BEA.cif, crystals/zeolites/BEC.cif,
  crystals/zeolites/BIK.cif, crystals/zeolites/BOF.cif,
  crystals/zeolites/BOG.cif, crystals/zeolites/BPH.cif,
  crystals/zeolites/BRE.cif, crystals/zeolites/BSV.cif,
  crystals/zeolites/CAN.cif, crystals/zeolites/CAS.cif,
  crystals/zeolites/CDO.cif, crystals/zeolites/CFI.cif,
  crystals/zeolites/CGF.cif, crystals/zeolites/CGS.cif,
  crystals/zeolites/CHA.cif, crystals/zeolites/CHI.cif,
  crystals/zeolites/CLO.cif, crystals/zeolites/CON.cif,
  crystals/zeolites/CZP.cif, crystals/zeolites/DAC.cif,
  crystals/zeolites/DDR.cif, crystals/zeolites/DFO.cif,
  crystals/zeolites/DFT.cif, crystals/zeolites/DOH.cif,
  crystals/zeolites/DON.cif, crystals/zeolites/EAB.cif,
  crystals/zeolites/EDI.cif, crystals/zeolites/EMT.cif,
  crystals/zeolites/EON.cif, crystals/zeolites/EPI.cif,
  crystals/zeolites/ERI.cif, crystals/zeolites/ESV.cif,
  crystals/zeolites/ETR.cif, crystals/zeolites/EUO.cif,
  crystals/zeolites/EZT.cif, crystals/zeolites/FAR.cif,
  crystals/zeolites/FAU.cif, crystals/zeolites/FER.cif,
  crystals/zeolites/FRA.cif, crystals/zeolites/GIS.cif,
  crystals/zeolites/GIU.cif, crystals/zeolites/GME.cif,
  crystals/zeolites/GON.cif, crystals/zeolites/GOO.cif,
  crystals/zeolites/HEU.cif, crystals/zeolites/IFR.cif,
  crystals/zeolites/IHW.cif, crystals/zeolites/IMF.cif,
  crystals/zeolites/IRR.cif, crystals/zeolites/ISV.cif,
  crystals/zeolites/ITE.cif, crystals/zeolites/ITH.cif,
  crystals/zeolites/ITR.cif, crystals/zeolites/ITV.cif,
  crystals/zeolites/ITW.cif, crystals/zeolites/IWR.cif,
  crystals/zeolites/IWS.cif, crystals/zeolites/IWV.cif,
  crystals/zeolites/IWW.cif, crystals/zeolites/JBW.cif,
  crystals/zeolites/JRY.cif, crystals/zeolites/KFI.cif,
  crystals/zeolites/LAU.cif, crystals/zeolites/LEV.cif,
  crystals/zeolites/LIO.cif, crystals/zeolites/LIT.cif,
  crystals/zeolites/LOS.cif, crystals/zeolites/LOV.cif,
  crystals/zeolites/LTA.cif, crystals/zeolites/LTF.cif,
  crystals/zeolites/LTL.cif, crystals/zeolites/LTN.cif,
  crystals/zeolites/MAR.cif, crystals/zeolites/MAZ.cif,
  crystals/zeolites/MEI.cif, crystals/zeolites/MEL.cif,
  crystals/zeolites/MEP.cif, crystals/zeolites/MER.cif,
  crystals/zeolites/MFI.cif, crystals/zeolites/MFS.cif,
  crystals/zeolites/MON.cif, crystals/zeolites/MOR.cif,
  crystals/zeolites/MOZ.cif, crystals/zeolites/MRE.cif,
  crystals/zeolites/MSE.cif, crystals/zeolites/MSO.cif,
  crystals/zeolites/MTF.cif, crystals/zeolites/MTN.cif,
  crystals/zeolites/MTT.cif, crystals/zeolites/MTW.cif,
  crystals/zeolites/MVY.cif, crystals/zeolites/MWW.cif,
  crystals/zeolites/NAB.cif, crystals/zeolites/NAT.cif,
  crystals/zeolites/NES.cif, crystals/zeolites/NON.cif,
  crystals/zeolites/NPO.cif, crystals/zeolites/NSI.cif,
  crystals/zeolites/OBW.cif, crystals/zeolites/OFF.cif,
  crystals/zeolites/OSI.cif, crystals/zeolites/OSO.cif,
  crystals/zeolites/OWE.cif, crystals/zeolites/PAR.cif,
  crystals/zeolites/PAU.cif, crystals/zeolites/PHI.cif,
  crystals/zeolites/PON.cif, crystals/zeolites/PUN.cif,
  crystals/zeolites/RHO.cif, crystals/zeolites/RON.cif,
  crystals/zeolites/RRO.cif, crystals/zeolites/RSN.cif,
  crystals/zeolites/RTE.cif, crystals/zeolites/RTH.cif,
  crystals/zeolites/RUT.cif, crystals/zeolites/RWR.cif,
  crystals/zeolites/RWY.cif, crystals/zeolites/SAF.cif,
  crystals/zeolites/SAO.cif, crystals/zeolites/SAS.cif,
  crystals/zeolites/SAT.cif, crystals/zeolites/SAV.cif,
  crystals/zeolites/SBE.cif, crystals/zeolites/SBN.cif,
  crystals/zeolites/SBS.cif, crystals/zeolites/SBT.cif,
  crystals/zeolites/SFE.cif, crystals/zeolites/SFF.cif,
  crystals/zeolites/SFG.cif, crystals/zeolites/SFH.cif,
  crystals/zeolites/SFN.cif, crystals/zeolites/SFO.cif,
  crystals/zeolites/SFS.cif, crystals/zeolites/SGT.cif,
  crystals/zeolites/SIV.cif, crystals/zeolites/SOD.cif,
  crystals/zeolites/SOF.cif, crystals/zeolites/SOS.cif,
  crystals/zeolites/SSF.cif, crystals/zeolites/SSY.cif,
  crystals/zeolites/STF.cif, crystals/zeolites/STI.cif,
  crystals/zeolites/STO.cif, crystals/zeolites/STT.cif,
  crystals/zeolites/STW.cif, crystals/zeolites/SVR.cif,
  crystals/zeolites/SZR.cif, crystals/zeolites/TER.cif,
  crystals/zeolites/THO.cif, crystals/zeolites/TOL.cif,
  crystals/zeolites/TON.cif, crystals/zeolites/TSC.cif,
  crystals/zeolites/TUN.cif, crystals/zeolites/UEI.cif,
  crystals/zeolites/UFI.cif, crystals/zeolites/UOS.cif,
  crystals/zeolites/UOZ.cif, crystals/zeolites/USI.cif,
  crystals/zeolites/UTL.cif, crystals/zeolites/UWY.cif,
  crystals/zeolites/VET.cif, crystals/zeolites/VFI.cif,
  crystals/zeolites/VNI.cif, crystals/zeolites/VSV.cif,
  crystals/zeolites/WEI.cif, crystals/zeolites/WEN.cif,
  crystals/zeolites/YUG.cif, crystals/zeolites/ZON.cif,
  crystals/zeolites/ZSM-5.cif, libavogadro/src/extensions/insertcommand.cpp,
  .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.h,
  libavogadro/src/extensions/insertfragmentdialog.ui,
  .../src/extensions/insertfragmentextension.cpp,
  .../src/extensions/insertfragmentextension.h, libavogadro/src/molecule.cpp:
  Add new action to insert crystals.  Generalized insert fragment dialog and
  extension to handle multiple directory roots. Additional cleanup of insert
  code.  (Rebased on current master)  Change-Id:
  Ifa898fbd937bbc0a6cca58701a5f19f89fc47f92

2011-12-05  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I5b950de54f5a8b77e8816d3fd49b223530d15df5

2011-11-28  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I542916eaa947f5e0dffee5890d98c29aa542957b

2011-11-25  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/moleculebench.cpp: Fix
  and expand moleculebench.cpp.  Fix issues with repeated benchmarking and
  added benchmarks for new Molecule API.  The benchmark times are small and
  unstable, but it appears that the atomicNum and position addAtom overload is
  comparable to not using the convenience function, and the copy overload takes
  approximately twice as long due to the call to the assignment operator.  The
  copyAtomsAndBonds functions return variable benchmark times, but are of the
  same order of magnitude as just adding the atoms and bonds alone. The mapping
  implementation doesn't add excessive overhead, even for 25,000 atom + 25,000
  bond copies.  Change-Id: I59f0dd58cf4d59fdc77820b5d8a4399509333580

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Add convenience
  methods for adding Atoms and Bonds to Molecule.  Atom * addAtom(int
  atomicNum, const Vector3d &pos) Atom * addAtom(const Atom &otherAtom) Bond *
  addBond(unsigned long beginAtomId, unsigned long endAtomId, short order = 1)
  Bond * addBond(Atom *beginAtom, Atom* endAtom, short order = 1) 
  PrimitiveList copyAtomsAndBonds(const QList<Atom*>&,const QList<Bond*>&)
  PrimitiveList copyAtomsAndBonds(const PrimitiveList &)  Change-Id:
  Ib8d19156dac782e735356db43537e69a978994de

2011-09-06  Geoff Hutchison <geoff.hutchison@gmail.com>

  * fragments/alcohols/2-aminoethanol.cml,
  fragments/alcohols/but-2-yne-1_4-diol.cml,
  fragments/alcohols/cyclohexanol.cml, fragments/alcohols/cyclopentanol.cml,
  fragments/alcohols/ethane-1_2-diol.cml,
  fragments/alcohols/propane-1_2_3-triol.cml, fragments/alkanes/butane.cml,
  fragments/alkanes/decane.cml, fragments/alkanes/dodecane.cml,
  fragments/alkanes/eicosane.cml, fragments/alkanes/heptane.cml,
  fragments/alkanes/hexadecane.cml, fragments/alkanes/hexane.cml,
  fragments/alkanes/nonane.cml, fragments/alkanes/octane.cml,
  fragments/alkanes/pentadecane.cml, fragments/alkanes/pentane.cml,
  fragments/alkanes/tetracosane.cml, fragments/alkanes/tetradecane.cml,
  fragments/alkanes/tridecane.cml, fragments/alkanes/undecane.cml,
  fragments/alkenes/2-methylbut-2-ene.cml,
  fragments/alkenes/2-methylbuta-1_3-diene.cml,
  fragments/alkenes/3E-penta-1_3-diene.cml,
  fragments/alkenes/3Z-penta-1_3-diene.cml,
  fragments/alkenes/3Z_3-ethylhepta-1_3-diene.cml,
  fragments/alkenes/E-but-2-ene.cml, fragments/alkenes/E-hept-2-ene.cml,
  fragments/alkenes/E-hept-3-ene.cml, fragments/alkenes/E-hex-2-ene.cml,
  fragments/alkenes/E-hex-3-ene.cml, fragments/alkenes/E-oct-2-ene.cml,
  fragments/alkenes/E-oct-3-ene.cml, fragments/alkenes/E-oct-4-ene.cml,
  fragments/alkenes/E-pent-2-ene.cml, fragments/alkenes/Z-but-2-ene.cml,
  fragments/alkenes/Z-hept-2-ene.cml, fragments/alkenes/Z-hept-3-ene.cml,
  fragments/alkenes/Z-hex-2-ene.cml, fragments/alkenes/Z-hex-3-ene.cml,
  fragments/alkenes/Z-oct-2-ene.cml, fragments/alkenes/Z-oct-3-ene.cml,
  fragments/alkenes/Z-oct-4-ene.cml, fragments/alkenes/Z-pent-2-ene.cml,
  fragments/alkenes/hept-1-ene.cml, fragments/alkenes/hex-1-ene.cml,
  fragments/alkenes/oct-1-ene.cml, fragments/alkenes/pent-1-ene.cml,
  fragments/alkenes/propene.cml, fragments/amines/1H-azepine.cml,
  fragments/amines/2-aminopropane.cml, fragments/amines/S-sec-butylamine.cml,
  fragments/amines/diethylamine.cml, fragments/amines/dimethylamine.cml,
  fragments/amines/piperazine.cml, fragments/amines/piperidine.cml,
  fragments/amines/pyrrolidine.cml, fragments/amines/tert-butylamine.cml,
  fragments/amines/triethylamine.cml, fragments/amines/triethylenediamine.cml,
  fragments/amines/trimethylamine.cml, fragments/aromatics/1H-indole.cml,
  fragments/aromatics/1_10-phenanthroline.cml,
  fragments/aromatics/1_8-naphthyridine.cml,
  fragments/aromatics/2H-chromene.cml, fragments/aromatics/4H-chromene.cml,
  fragments/aromatics/7H-purine.cml, fragments/aromatics/9H-carbazole.cml,
  fragments/aromatics/9H-fluorene.cml, fragments/aromatics/9H-xanthene.cml,
  fragments/aromatics/acenaphthene.cml,
  fragments/aromatics/acenaphthenequinone.cml,
  fragments/aromatics/acenaphthylene.cml, fragments/aromatics/acridine.cml,
  fragments/aromatics/benzofuran.cml, fragments/aromatics/benzothiophene.cml,
  fragments/aromatics/chromone.cml, fragments/aromatics/cinnoline.cml,
  fragments/aromatics/coumarin.cml, fragments/aromatics/isoquinoline.cml,
  fragments/aromatics/phenanthrene.cml, fragments/aromatics/phthalimide.cml,
  fragments/aromatics/quinazoline.cml, fragments/aromatics/quinoline.cml,
  fragments/aromatics/tetralin.cml, fragments/aromatics/uric_acid.cml,
  fragments/buckminsterfullerene.cml,
  fragments/carboxylic_acids/E-butanoic_acid.cml,
  fragments/carboxylic_acids/E-butenedioic_acid.cml, fragments/cyclic
  alkanes/adamantane.cml, fragments/cyclic alkanes/cubane.cml, fragments/cyclic
  alkanes/cyclobutane.cml, fragments/cyclic alkanes/cycloheptane.cml,
  fragments/cyclic alkanes/cyclohexane-chair.cml, .../cyclic
  alkanes/cyclohexane-twist-boat.cml, fragments/cyclic alkanes/cyclohexane.cml,
  fragments/cyclic alkanes/cyclopentane.cml, fragments/cyclic
  alkanes/cyclopropane.cml, fragments/cyclic alkanes/norbornane.cml,
  fragments/cyclic sugars/alpha-D-allopyranose.cml, .../cyclic
  sugars/alpha-D-arabinopyranose.cml, fragments/cyclic
  sugars/alpha-D-fucopyranose.cml, .../cyclic
  sugars/alpha-D-galactopyranose.cml, .../cyclic
  sugars/alpha-D-galacturonopyranose.cml, fragments/cyclic
  sugars/alpha-D-glucopyranose.cml, .../cyclic
  sugars/alpha-D-glucuronopyranose.cml, fragments/cyclic
  sugars/alpha-D-gulopyranose.cml, fragments/cyclic
  sugars/alpha-D-idopyranose.cml, fragments/cyclic
  sugars/alpha-D-lyxopyranose.cml, fragments/cyclic
  sugars/alpha-D-mannopyranose.cml, fragments/cyclic
  sugars/alpha-D-psicopyranose.cml, fragments/cyclic
  sugars/alpha-D-rhamnopyranose.cml, fragments/cyclic
  sugars/alpha-D-ribopyranose.cml, fragments/cyclic
  sugars/alpha-D-tagatopyranose.cml, fragments/cyclic
  sugars/alpha-D-talopyranose.cml, fragments/cyclic
  sugars/alpha-D-xylopyranose.cml, .../cyclic
  sugars/alpha-L-arabinopyranose.cml, fragments/cyclic
  sugars/alpha-L-fucopyranose.cml, .../cyclic
  sugars/alpha-L-galactopyranose.cml, fragments/cyclic
  sugars/alpha-L-lyxopyranose.cml, fragments/cyclic
  sugars/alpha-L-rhamnopyranose.cml, fragments/cyclic
  sugars/alpha-L-ribopyranose.cml, fragments/cyclic
  sugars/alpha-L-sorbopyranose.cml, fragments/cyclic
  sugars/alpha-L-xylopyranose.cml, fragments/cyclic
  sugars/beta-D-allopyranose.cml, fragments/cyclic
  sugars/beta-D-arabinopyranose.cml, fragments/cyclic
  sugars/beta-D-fructopyranose.cml, fragments/cyclic
  sugars/beta-D-fucopyranose.cml, fragments/cyclic
  sugars/beta-D-galactopyranose.cml, fragments/cyclic
  sugars/beta-D-glucopyranose.cml, fragments/cyclic
  sugars/beta-D-gulopyranose.cml, fragments/cyclic
  sugars/beta-D-idopyranose.cml, fragments/cyclic
  sugars/beta-D-lyxopyranose.cml, fragments/cyclic
  sugars/beta-D-mannopyranose.cml, fragments/cyclic
  sugars/beta-D-rhamnopyranose.cml, fragments/cyclic
  sugars/beta-D-ribopyranose.cml, fragments/cyclic
  sugars/beta-D-tagatopyranose.cml, fragments/cyclic
  sugars/beta-D-talopyranose.cml, fragments/cyclic
  sugars/beta-D-xylopyranose.cml, fragments/cyclic
  sugars/beta-L-arabinopyranose.cml, fragments/cyclic
  sugars/beta-L-lyxopyranose.cml, fragments/cyclic
  sugars/beta-L-ribopyranose.cml, fragments/cyclic
  sugars/beta-L-xylopyranose.cml, fragments/cyclic_alkanes/1R-camphene.cml,
  fragments/cyclic_alkanes/1R-camphor.cml,
  fragments/cyclic_alkanes/abietic_acid.cml,
  fragments/cyclic_alkanes/adamantane.cml,
  .../cyclic_alkanes/cis-decahydronaphthalene.cml,
  fragments/cyclic_alkanes/cubane.cml,
  fragments/cyclic_alkanes/cyclobutane.cml,
  fragments/cyclic_alkanes/cyclodecane.cml,
  fragments/cyclic_alkanes/cycloheptane.cml,
  fragments/cyclic_alkanes/cyclohexane-chair.cml,
  .../cyclic_alkanes/cyclohexane-twist-boat.cml,
  fragments/cyclic_alkanes/cyclohexane.cml,
  fragments/cyclic_alkanes/cyclononane.cml,
  fragments/cyclic_alkanes/cyclooctane.cml,
  fragments/cyclic_alkanes/cyclopentane.cml,
  fragments/cyclic_alkanes/cyclopropane.cml,
  fragments/cyclic_alkanes/norbornane.cml,
  .../cyclic_alkanes/trans-decahydronaphthalene.cml,
  fragments/cyclic_alkenes/Z-cycloheptene.cml,
  fragments/cyclic_alkenes/Z-cyclooctene.cml,
  fragments/cyclic_alkenes/cyclohepta-1_3-diene.cml,
  .../cyclic_alkenes/cyclohepta-1_3_5-triene.cml,
  fragments/cyclic_alkenes/cyclohepta-1_4-diene.cml,
  fragments/cyclic_alkenes/cyclohexa-1_3-diene.cml,
  fragments/cyclic_alkenes/cyclohexa-1_4-diene.cml,
  fragments/cyclic_alkenes/cyclohexene.cml,
  fragments/cyclic_alkenes/cycloocta-1_3-diene.cml,
  .../cyclic_alkenes/cycloocta-1_3_5-triene.cml,
  .../cyclic_alkenes/cycloocta-1_3_5_7-tetraene.cml,
  fragments/cyclic_alkenes/cyclopenta-1_3-diene.cml,
  fragments/cyclic_alkenes/cyclopentene.cml,
  fragments/cyclic_sugars/alpha-D-allopyranose.cml,
  .../cyclic_sugars/alpha-D-arabinopyranose.cml,
  fragments/cyclic_sugars/alpha-D-fucopyranose.cml,
  .../cyclic_sugars/alpha-D-galactopyranose.cml,
  .../cyclic_sugars/alpha-D-galacturonopyranose.cml,
  fragments/cyclic_sugars/alpha-D-glucopyranose.cml,
  .../cyclic_sugars/alpha-D-glucuronopyranose.cml,
  fragments/cyclic_sugars/alpha-D-gulopyranose.cml,
  fragments/cyclic_sugars/alpha-D-idopyranose.cml,
  fragments/cyclic_sugars/alpha-D-lyxopyranose.cml,
  fragments/cyclic_sugars/alpha-D-mannopyranose.cml,
  fragments/cyclic_sugars/alpha-D-psicopyranose.cml,
  fragments/cyclic_sugars/alpha-D-rhamnopyranose.cml,
  fragments/cyclic_sugars/alpha-D-ribopyranose.cml,
  fragments/cyclic_sugars/alpha-D-tagatopyranose.cml,
  fragments/cyclic_sugars/alpha-D-talopyranose.cml,
  fragments/cyclic_sugars/alpha-D-xylopyranose.cml,
  .../cyclic_sugars/alpha-L-arabinopyranose.cml,
  fragments/cyclic_sugars/alpha-L-fucopyranose.cml,
  .../cyclic_sugars/alpha-L-galactopyranose.cml,
  fragments/cyclic_sugars/alpha-L-lyxopyranose.cml,
  fragments/cyclic_sugars/alpha-L-rhamnopyranose.cml,
  fragments/cyclic_sugars/alpha-L-ribopyranose.cml,
  fragments/cyclic_sugars/alpha-L-sorbopyranose.cml,
  fragments/cyclic_sugars/alpha-L-xylopyranose.cml,
  fragments/cyclic_sugars/beta-D-allopyranose.cml,
  fragments/cyclic_sugars/beta-D-arabinopyranose.cml,
  fragments/cyclic_sugars/beta-D-fructopyranose.cml,
  fragments/cyclic_sugars/beta-D-fucopyranose.cml,
  fragments/cyclic_sugars/beta-D-galactopyranose.cml,
  fragments/cyclic_sugars/beta-D-glucopyranose.cml,
  fragments/cyclic_sugars/beta-D-gulopyranose.cml,
  fragments/cyclic_sugars/beta-D-idopyranose.cml,
  fragments/cyclic_sugars/beta-D-lyxopyranose.cml,
  fragments/cyclic_sugars/beta-D-mannopyranose.cml,
  fragments/cyclic_sugars/beta-D-rhamnopyranose.cml,
  fragments/cyclic_sugars/beta-D-ribopyranose.cml,
  fragments/cyclic_sugars/beta-D-tagatopyranose.cml,
  fragments/cyclic_sugars/beta-D-talopyranose.cml,
  fragments/cyclic_sugars/beta-D-xylopyranose.cml,
  fragments/cyclic_sugars/beta-L-arabinopyranose.cml,
  fragments/cyclic_sugars/beta-L-lyxopyranose.cml,
  fragments/cyclic_sugars/beta-L-ribopyranose.cml,
  fragments/cyclic_sugars/beta-L-xylopyranose.cml,
  fragments/ethers/1_4-dioxane.cml, fragments/ethers/tetrahydropyran.cml,
  fragments/fatty acids/decanoic_acid.cml, fragments/fatty
  acids/hexanoic_acid.cml, fragments/fatty acids/lauric_acid.cml,
  fragments/fatty acids/linoleic_acid.cml, fragments/fatty
  acids/octanoic_acid.cml, fragments/fatty acids/oleic_acid.cml,
  fragments/fatty acids/palmitic_acid.cml, fragments/fatty
  acids/stearic_acid.cml, fragments/fatty_acids/arachidonic_acid.cml,
  fragments/fatty_acids/cervonic_acid.cml,
  fragments/fatty_acids/decanoic_acid.cml,
  fragments/fatty_acids/hexanoic_acid.cml,
  fragments/fatty_acids/lauric_acid.cml,
  fragments/fatty_acids/linoleic_acid.cml,
  fragments/fatty_acids/linolenic_acid.cml,
  fragments/fatty_acids/myristic_acid.cml,
  fragments/fatty_acids/octanoic_acid.cml,
  fragments/fatty_acids/oleic_acid.cml,
  fragments/fatty_acids/palmitic_acid.cml,
  fragments/fatty_acids/pentanoic_acid.cml,
  fragments/fatty_acids/stearic_acid.cml, fragments/fullerenes/C180.cml,
  fragments/fullerenes/C20.cml, fragments/fullerenes/C24.cml,
  fragments/fullerenes/C240.cml, fragments/fullerenes/C26.cml,
  fragments/fullerenes/C28.cml, fragments/fullerenes/C30.cml,
  fragments/fullerenes/C32.cml, fragments/fullerenes/C36.cml,
  fragments/fullerenes/C50.cml,
  fragments/fullerenes/C60-buckminsterfullerene.cml,
  fragments/fullerenes/C70.cml, fragments/fullerenes/C76.cml,
  fragments/fullerenes/C78.cml, fragments/fullerenes/C80.cml,
  fragments/fullerenes/PC70BM.cml, fragments/fullerenes/PCBM.cml,
  fragments/heteroaromatics/isonicotinamide.cml,
  fragments/heteroaromatics/isonicotinic_acid.cml,
  fragments/heteroaromatics/nicotinamide.cml,
  fragments/heteroaromatics/nicotinic_acid.cml,
  fragments/heteroaromatics/picolinamide.cml,
  fragments/heteroaromatics/picolinic_acid.cml,
  fragments/ketones/cyclohexanone.cml,
  fragments/ketones/methyl_vinyl_ketone.cml,
  fragments/ketones/p-benzoquinone.cml,
  fragments/ligands/Cp-cyclopentadienyl.cml,
  fragments/macrocycles/phthalocyanine.cml,
  fragments/nitriles/1_1_1-trichloroacetonitrile.cml,
  fragments/nitriles/acetonitrile.cml, fragments/nitriles/butyronitrile.cml,
  fragments/nitriles/isobutyronitrile.cml,
  fragments/nitriles/propionitrile.cml,
  fragments/thiols/2-methylproprane-2-thiol.cml,
  fragments/thiols/R_butane-2-thiol.cml, fragments/thiols/butane-1-thiol.cml,
  fragments/thiols/ethane-1_2-dithiol.cml,
  fragments/thiols/heptane-1-thiol.cml, fragments/thiols/hexane-1-thiol.cml,
  fragments/thiols/octane-1-thiol.cml, fragments/thiols/proprane-1-thiol.cml,
  fragments/thiols/proprane-2-thiol.cml: Update molecular fragments from
  chemical-structures project.  Added several new fragments, plus extensive
  list of fullerenes.  Change-Id: Id1e87013853f43701d9a33fe348b00f99cb1e841

2011-11-21  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: If9e37f39b96e320be2bd3d699196c7454527b525

2011-11-14  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I957c8e16ab9d9222eb548629532e6fd0c512a2ad

2011-10-17  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/swcntbuilder/CMakeLists.txt,
  .../src/extensions/swcntbuilder/avotubegen.cpp,
  .../src/extensions/swcntbuilder/avotubegen.h,
  .../swcntbuilder/swcntbuilderextension.cpp,
  .../swcntbuilder/swcntbuilderextension.h,
  .../extensions/swcntbuilder/swcntbuilderwidget.cpp,
  .../extensions/swcntbuilder/swcntbuilderwidget.h,
  .../extensions/swcntbuilder/swcntbuilderwidget.ui,
  .../src/extensions/swcntbuilder/tubegen/ANSR.cpp,
  .../src/extensions/swcntbuilder/tubegen/ANSR.h,
  .../src/extensions/swcntbuilder/tubegen/AUTHORS,
  .../src/extensions/swcntbuilder/tubegen/Bitmap.c,
  .../src/extensions/swcntbuilder/tubegen/Bitmap.h,
  .../extensions/swcntbuilder/tubegen/CMakeLists.txt,
  .../src/extensions/swcntbuilder/tubegen/Cell.cpp,
  .../src/extensions/swcntbuilder/tubegen/Cell.h,
  .../extensions/swcntbuilder/tubegen/Constants.h,
  .../extensions/swcntbuilder/tubegen/Core3DMath.c,
  .../extensions/swcntbuilder/tubegen/Core3DMath.h,
  .../extensions/swcntbuilder/tubegen/CoreConst.h,
  .../swcntbuilder/tubegen/CrystalCell.cpp,
  .../extensions/swcntbuilder/tubegen/CrystalCell.h,
  .../extensions/swcntbuilder/tubegen/LICENSE.html,
  .../extensions/swcntbuilder/tubegen/TubeGen.cpp,
  .../swcntbuilder/tubegen/TubuleBasis.cpp,
  .../extensions/swcntbuilder/tubegen/TubuleBasis.h,
  .../extensions/swcntbuilder/tubegen/diamond.cpp,
  .../src/extensions/swcntbuilder/tubegen/eprintf.c,
  .../src/extensions/swcntbuilder/tubegen/eprintf.h,
  .../src/extensions/swcntbuilder/tubegen/fcc.cpp,
  .../extensions/swcntbuilder/tubegen/graphite.cpp: Add a nanotube builder that
  uses the TubeGen code[1] (BSD license).  [1]
  http://turin.nss.udel.edu/research/tubegenonline.html  Change-Id:
  I2b2c97498b4a973cc20c3ea69fe8926137d3cbcf

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/dockwidget.cpp, libavogadro/src/dockwidget.h,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h: Add the
  DockWidget class to wrap QDockWidget.  This will eventually simplify the
  extension hierarchy by removing the DockExtension class (Extension already
  had a dockWidget() method) and adding the "preferredDockWidgetArea" property
  to the widget itself.  This allows extensions to have as many dockwidgets as
  needed and individually specify their locations.  Change-Id:
  I8148e9def8416cd5c1c611b4f1aec61d049d4cc1

2011-11-07  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I2545b68c5e2aab8cb91de2d1ddc4c447391ea5be

2011-08-22  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/plugin.h, libavogadro/src/pythontool_p.cpp,
  libavogadro/src/pythontool_p.h, libavogadro/src/tool.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/moveatomcommand.cpp,
  libavogadro/src/tools/moveatomcommand.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/zmatrixtool.h: Add a double-click event to tools. 
  Navigate tool will re-center the view. Select tool will select the entire
  fragment. Other tools currently defer.  Fixes feature request #2899910. 
  Bumps plugin version ABI.  Change-Id:
  I87158e3fb74da07db0a81db9d0cee017822dbe9f

2011-11-01  Geoff Hutchison <geoff.hutchison@gmail.com>

  * .../extensions/surfaces/openqube/gaussianfchk.cpp,
  .../extensions/surfaces/openqube/gaussianset.cpp,
  .../src/extensions/surfaces/openqube/gaussianset.h,
  testfiles/CO-cc-6Z.fchk.gz: Fix crash with Gaussian FCHK and f-orbitals. 
  Also adds support for skipping higher-order shells, including g, h, and i.
  Now supports reading calcs with up to cc-pV6Z, although high shells (f and
  above) are still ignored.  Change-Id:
  I41067e6cbdddd1b66470dc446c506fdec9ef48b7

2011-05-27  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.h,
  libavogadro/src/extensions/insertfragmentdialog.ui,
  .../src/extensions/insertfragmentextension.cpp,
  .../src/extensions/sortfiltertreeproxymodel.cpp,
  .../src/extensions/sortfiltertreeproxymodel.h: Add a search filter for file
  and dir names.  Includes a new filter proxy which fetches and checks
  subdirectories recursively. Filter works in a case-insensitive and UNIX
  wildcard manner, allowing clean, intuitive filtering.  Change-Id:
  I0f252ed315284f2ae45803c7f81a8439a0259136

2011-10-31  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I0d4ccdbfc56049b8ac8bdc1565691da322844026

2011-10-24  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I54f0a60c8f61fa8aba434d1760b8bd55b83d8a0b

2011-10-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I90c96ac40173c0c118503ae1d26d6de997832ba9

2011-10-13  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/glpainter_p.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Add #include <GL/glu.h> for
  compatibility with Qt 4.8 (at least on Mac)  Change-Id:
  Icd3c586fbfa9cc3c74564ee799fa96a6612ed420

2011-10-10  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/fragment.cpp, libavogadro/src/fragment.h: Add const-correct
  overloads to Fragment.  Change-Id: I5cf787f7484881d8488536dfb2424c7115f1e1c7

2011-10-10  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I030ac1f298933805aed2c7c8001f885798cdbb37

2011-10-03  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ic8e72a9a7bc9206bfe8fee913856a0179836c166

2011-09-26  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I179942e3bb71b2e8e029f8997bd2f163ed964b33

2011-09-19  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I13fa3c6375a9ef9836a34106e77eaf9c528679be

2011-09-12  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I9baff97c97dcd1c1060bdc54fe8adfe540a216a5

2011-09-09  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/periodictablescene_p.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/tools/drawtool.cpp: Add keyboard access to the periodic
  table.  Type an atomic number or element symbol to change the active,
  selected element.  The draw tool now provides keyboard focus when the
  periodic table is open.  Change-Id: Id23391b53ac5dff64e7ad09e741e6b460d1a3476

2011-09-03  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h: Replace the unit cell
  orientation code with a safer implementation.  Change-Id:
  I0438c407bce57696b7dff117193a5c854940d524

2011-07-07  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/CMakeLists.txt, .../crystallography/ui/cematrixeditor.cpp,
  .../extensions/crystallography/ui/cematrixeditor.h,
  .../crystallography/ui/cematrixeditor.ui,
  libavogadro/src/textmatrixeditor.cpp, libavogadro/src/textmatrixeditor.h: Add
  TextMatrixEditor, a widget to edit 3x3 matrices as plain text.  This is the
  matrix editor widget from the Crystallography extension's CEMatrixEditor unit
  cell matrix editor, split out into a reusable class.  Change-Id:
  I54343a18e29af96544615dd865be3df1ad132a75

2011-09-03  David C. Lonie <loniedavid@gmail.com>

  * .../src/extensions/surfaces/orbitalextension.cpp,
  .../extensions/surfaces/orbitalsettingsdialog.cpp,
  .../extensions/surfaces/orbitalsettingsdialog.h,
  .../extensions/surfaces/orbitalsettingsdialog.ui,
  .../src/extensions/surfaces/orbitalwidget.cpp,
  .../src/extensions/surfaces/orbitalwidget.h: Limit orbital precalculations to
  a specified number of orbitals.  Change-Id:
  I46e1c53bc7e32b54ba382e296054f9c72ed100e7

2011-08-29  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ieecdcf0117fda8b8c70938fb6c4d434ae0736f1f

2011-08-22  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: I4dc9f49dd6a613389a458b9b0fdf4a8c0456dcb7

2011-08-16  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sr.po, i18n/avogadro/sv.po,
  i18n/avogadro/th.po, i18n/avogadro/tr.po, i18n/avogadro/ug.po,
  i18n/avogadro/uk.po, i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Automated update of translation templates (POT) using latest strings. 
  Change-Id: Ia5835bdb84a216b01080d477230838a904bee718

2011-01-26  Jens Thomas <linucks42@gmail.com>

  * libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h: Extend the properties widget to
  handle conformers.  As we are dealing with multiple conformers, we no longer
  cache an OBMol in the PropertiesModel. Instead we cache the data we need as
  class variables and these are accessed by the call to data. This means that
  nothing is actually calculated in the data call.  The variable
  m_displayConformers now controls whether we display the data for just the
  current or all conformers.  Change-Id:
  Ie00de041b53a2bb2a56a1b42dc41a0a03b0b0918

2011-05-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/cartesianextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/ui/cecoordinateeditor.cpp,
  .../extensions/crystallography/ui/cecoordinateeditor.ui,
  .../extensions/crystallography/ui/cematrixeditor.cpp,
  .../src/extensions/crystallography/ui/cematrixeditor.ui: Adjust the font and
  font size on Mac and Windows.  Previous font wasn't monospaced and very
  unreadable. Now uses Courier on Mac/Win and Monospace (which is an alias) on
  Linux.  Change-Id: I198e5afc5ed22a0d74b1d8a5cdc41d74e9fcd304

2011-05-26  David C. Lonie <loniedavid@gmail.com>

  * .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h: Fix failing dashboards for
  crystallography extension.  Two issues addressed in this patch:  1) Control
  reached end of non-void currentLatticeType() 2) Incorrect signature of
  read/writeSettings(QSetting&)  Several other functions were made const to fix
  (2) as well (they should have been const anyway).  Change-Id:
  I85cb3d1b77e5f88c59cc24d450da6ad152fc3ae6

  * libavogadro/src/extensions/crystallography/ui/cecoordinateeditor.cpp,
  libavogadro/src/extensions/crystallography/ui/cecoordinateeditor.ui,
  libavogadro/src/extensions/crystallography/ui/cematrixeditor.cpp,
  libavogadro/src/extensions/crystallography/ui/cematrixeditor.ui,
  libavogadro/src/extensions/crystallography/ui/ceparametereditor.ui: Remove
  shortcut keys from dockwidget titles.  They aren't interpreted correctly on
  Windows and don't seem to work on other platforms, either.  Change-Id:
  I53ad9b676d3983108e2e78576fc8e758c7a651b9

2011-05-03  David C. Lonie <loniedavid@gmail.com>

  * .../src/extensions/crystallography/CMakeLists.txt,
  .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/ui/cetranslatewidget.cpp,
  .../crystallography/ui/cetranslatewidget.h,
  .../crystallography/ui/cetranslatewidget.ui: Added an atomic translation tool
  to the crystallography extension.  Change-Id:
  If20ace6b16b0010431490033b95f8a5f58986b23

2011-04-12  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/glpainter_p.cpp, libavogadro/src/glpainter_p.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h: Added drawLineLoop,
  and drawBoxEdges to Painter and GLPainter.  Change-Id:
  Id43612457015e45d32b23435d1239645f843a7f8

  * libavogadro/src/painter.cpp, libavogadro/src/painter.h: Added a default
  implementation of Painter::drawQuadrilateral, cleaned some whitespace. 
  Change-Id: I0b0d9a6fd7989aaa8b9318e829b818dec1bf4cf3

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h: Added
  Camera::nearClippingPlane.  This function can be used to obtain a normal
  vector and point defining the near-plane of the viewing volume.  Change-Id:
  I7bee08d6cbbcdf03796a6129ffbadf9f62bca698

2011-04-18  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt, libavogadro/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animation.qrc,
  libavogadro/src/extensions/animationextension.qrc,
  libavogadro/src/extensions/cartesianextension.qrc,
  libavogadro/src/extensions/edit.qrc, libavogadro/src/pluginmanager.cpp:
  Changes necessary to initialize resources.  Some extra work is required to
  initialize the resource files from a static plugin. Accumulate the plugins
  that have resource files, and then construct a function in the static plugin
  header that is called once from the PluginManager code. A few resource files
  needed to be renamed to match the name of their plugin.  This now allows for
  an Avogadro that has all of its plugins built in statically. These are
  defined at compile time using the CMake cache variable.  Change-Id:
  I7176c06fd8adcb60c2ad234bfb48a0fba230f738

2011-04-15  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/pluginmanager.cpp: Added a simple way to create static
  plugins.  There is a default list, which can be manipulated at configure
  time. In addition, the variable can be set to ALL in order to build and link
  all plugins statically.  Change-Id: I0532b3d5cfb56414b01c4f16c205c6d35694e852

2011-05-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  .../src/extensions/surfaces/htmldelegate.cpp,
  libavogadro/src/extensions/surfaces/htmldelegate.h,
  .../src/extensions/surfaces/orbitalextension.cpp,
  .../src/extensions/surfaces/orbitaltablemodel.cpp,
  .../src/extensions/surfaces/orbitaltablemodel.h,
  .../src/extensions/surfaces/orbitalwidget.cpp, libavogadro/src/molecule.cpp,
  testfiles/benzene.fchk, testfiles/benzene.g03: Use OBOrbitalData when
  available (e.g., Gaussian) to display orbital energies.  Uses QObject dynamic
  properties, storing alpha energies and symmetries. Converts energies from
  Hartree to eV. Needs better support in OB for data. Also adds HTML display of
  symmetry symbols, where available.  Change-Id:
  I9388c43ca2ee60d010cb7d44939f5172d93a55e0

2011-05-06  Geoff Hutchison <geoff.hutchison@gmail.com>

  * doc/mainpage.dox, .../thirdPartyExtensions/02-DynamicDisplay.dox,
  libavogadro/examples/thirdPartyExtensions/toc.dox: Update main doxygen page
  with improved links, including to the third-party extension tutorial
  documentation.  Change-Id: I0aaa6456631d90273bd882756f9213c44106a52f

2011-05-03  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * Doxyfile, avogadro/Doxyfile, doc/CMakeLists.txt, doc/Doxyfile.in: Create a
  custom doxygen target, use Qt tag file.  Find and use doxygen, make doxygen
  will build the documentation. Use the installed qt.tags file, and removed an
  old Doxyfile that was not used. If the Doxygen docs are built, download the
  Open Babel tag file and use that to link to their docs too.  Change-Id:
  I818d2b5de9886c8b040625b48102b59258594436

2011-04-15  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/FindOpenBabel2.cmake,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/spectra/cd.cpp,
  libavogadro/src/extensions/spectra/dos.cpp,
  libavogadro/src/extensions/spectra/raman.cpp,
  .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  libavogadro/src/extensions/spectra/uv.cpp,
  .../src/extensions/spectra/vibrationwidget.cpp,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/molecule.cpp: Bump our dependency to Open Babel 2.3.0.  This
  simplifies our code base, and allows us to easily test whether Avogadro
  compiles as compilation against earlier versions of Open Babel is no longer
  well tested.

2011-04-07  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/glwidget.cpp, libavogadro/src/pythonextension_p.h,
  libavogadro/src/pythonthread_p.h: Fixed deadlock when threaded GL and Python
  are enabled simultaneously  Direct call of PythonExtension::paint from
  rendering thread lead to deadlock when GIL was acquired by GLWidget. This
  patch replaces it with queued metacall  Change-Id:
  I164a34b5b7f41d40c55b1a6cefab27ccd3921c79

2011-05-02  David Lonie <loniedavid@gmail.com>

  * .../thirdPartyExtensions/02-DynamicDisplay/dynamicdisplayextension.cpp,
  .../examples/thirdPartyExtensions/03-ViewPlane/viewplaneextension.h: Clean up
  some trivial issues in the 3rd party tutorials.  DynamicDisplay had an
  uninitialized pointer, and ViewPlane had an unused member.  Change-Id:
  Ia6f1557bb4de23b0966604175df287a272dda4d2

2011-04-29  David C. Lonie <loniedavid@gmail.com>

  * .../src/extensions/crystallography/CMakeLists.txt,
  .../crystallography/ui/ceabstractdockwidget.cpp,
  .../crystallography/ui/ceabstractdockwidget.h,
  .../crystallography/ui/ceabstracteditor.cpp,
  .../crystallography/ui/ceabstracteditor.h: Split an abstract dockwidget class
  out of CEAbstractEditor.  Change-Id:
  I0592dde7f8ef501dd0abd96920d5b6f27c572cad

2011-04-08  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h: Bug #3043641, fix auto-bonding
  in saved animation.  Have makeVideo also use the Animation class, and respect
  the autobonding option exposed in the animation dialog.  Change-Id:
  I483de30b7c79d8aed7e8e33a1bce3a9816426bfc

2011-02-07  Geoff Hutchison <geoff@geoffhutchison.net>

  * .../src/extensions/quantuminput/CMakeLists.txt,
  .../extensions/quantuminput/abinitinputdialog.cpp,
  .../extensions/quantuminput/abinitinputdialog.h,
  .../extensions/quantuminput/abinitinputdialog.ui,
  .../extensions/quantuminput/inputfileextension.cpp: ENH: Added abinit input
  generator.  Contributed by Matthieu Verstraete.  Change-Id:
  I35220825f5e1758c9f35ef1623514f087196eddf

2011-04-13  Geoff Hutchison <geoff.hutchison@gmail.com>

  * scripts/extract-application-messages.sh,
  scripts/extract-library-messages.sh: Update to exclude example tools and use
  new xgettext plural forms.

2011-03-17  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/extensions/animationextension.cpp,
  .../src/extensions/insertfragmentdialog.cpp,
  .../src/extensions/insertpeptideextension.cpp,
  .../extensions/quantuminput/inputfileextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/moleculefile.cpp: Finally fixed OB file operations with
  non-Latin characters in file paths  QFile::encodeName() and
  QString::toLocal8Bit() do not allow correct opening of fstream objects on
  localized Windows if Avogadro is compiled with MSVC. This patch should fix
  all related issues.  Change-Id: Ifeab228e8d97c7c5eb64e3c4b74a78518da98f2a

2011-02-14  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/pythonengine_p.cpp: Fixed readSettings and writeSettings in
  PythonEngine  To illustrate bugfix, saving of width was added to Python
  wireframe engine  Change-Id: I07d374154a228ad0eb96bf288c7e64c7c879c705

2011-04-11  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/bg.po,
  i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po,
  i18n/avogadro/es.po, i18n/avogadro/eu.po, i18n/avogadro/fi.po,
  i18n/avogadro/fr.po, i18n/avogadro/gl.po, i18n/avogadro/he.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/nb.po, i18n/avogadro/nl.po,
  i18n/avogadro/oc.po, i18n/avogadro/pl.po, i18n/avogadro/pt.po,
  i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po, i18n/avogadro/sk.po,
  i18n/avogadro/sr.po, i18n/avogadro/sv.po, i18n/avogadro/th.po,
  i18n/avogadro/tr.po, i18n/avogadro/ug.po, i18n/avogadro/uk.po,
  i18n/avogadro/vi.po, i18n/avogadro/zh_CN.po, i18n/avogadro/zh_TW.po,
  i18n/libavogadro/ar.po, i18n/libavogadro/bg.po, i18n/libavogadro/bs.po,
  i18n/libavogadro/ca.po, i18n/libavogadro/ca@valencia.po,
  i18n/libavogadro/cs.po, i18n/libavogadro/da.po, i18n/libavogadro/de.po,
  i18n/libavogadro/el.po, i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sr.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/ug.po, i18n/libavogadro/uk.po,
  i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Updated translations from Launchpad.

2010-11-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/color.h, libavogadro/src/engine.h,
  libavogadro/src/extension.h, libavogadro/src/tool.h: Fix 3104853: allow
  plugin macros to be used outside of the Avogadro namespace.  Change-Id:
  Ib832a3f9ef4fe56a45b06e2e2d8f7d5a026cb902

2011-04-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro/avogadro.pot, i18n/libavogadro/libavogadro.pot: Updated
  translation templates. (Merge with Launchpad for trunk shortly.)

2011-04-08  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Create dummy atoms at center of
  geom and center of mass.

2011-02-06  David C. Lonie <loniedavid@gmail.com>

  * avogadro/src/editcommands.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/crystallography/CMakeLists.txt,
  libavogadro/src/extensions/crystallography/COPYING,
  .../src/extensions/crystallography/avospglib.cpp,
  .../src/extensions/crystallography/avospglib.h,
  .../src/extensions/crystallography/ceundo.cpp,
  .../src/extensions/crystallography/ceundo.h,
  .../crystallography/crystallographyextension.cpp,
  .../crystallography/crystallographyextension.h,
  .../crystallography/crystalpastedialog.cpp,
  .../crystallography/crystalpastedialog.h,
  .../crystallography/crystalpastedialog.ui,
  .../src/extensions/crystallography/obeigenconv.h,
  .../crystallography/spglib/CMakeLists.txt,
  .../src/extensions/crystallography/spglib/COPYING,
  .../src/extensions/crystallography/spglib/cell.c,
  .../src/extensions/crystallography/spglib/cell.h,
  .../src/extensions/crystallography/spglib/debug.c,
  .../src/extensions/crystallography/spglib/debug.h,
  .../crystallography/spglib/hall_symbol.c,
  .../crystallography/spglib/hall_symbol.h,
  .../extensions/crystallography/spglib/lattice.c,
  .../extensions/crystallography/spglib/lattice.h,
  .../extensions/crystallography/spglib/mathfunc.c,
  .../extensions/crystallography/spglib/mathfunc.h,
  .../extensions/crystallography/spglib/pointgroup.c,
  .../extensions/crystallography/spglib/pointgroup.h,
  .../extensions/crystallography/spglib/primitive.c,
  .../extensions/crystallography/spglib/primitive.h,
  .../extensions/crystallography/spglib/refinement.c,
  .../extensions/crystallography/spglib/refinement.h,
  .../extensions/crystallography/spglib/spacegroup.c,
  .../extensions/crystallography/spglib/spacegroup.h,
  .../crystallography/spglib/spg_database.c,
  .../crystallography/spglib/spg_database.h,
  .../src/extensions/crystallography/spglib/spglib.c,
  .../src/extensions/crystallography/spglib/spglib.h,
  .../extensions/crystallography/spglib/symmetry.c,
  .../extensions/crystallography/spglib/symmetry.h,
  .../crystallography/spglib/symmetry_kpoint.c,
  .../crystallography/spglib/symmetry_kpoint.h,
  .../extensions/crystallography/stablecomparison.h,
  .../crystallography/ui/ceabstracteditor.cpp,
  .../crystallography/ui/ceabstracteditor.h,
  .../crystallography/ui/cecoordinateeditor.cpp,
  .../crystallography/ui/cecoordinateeditor.h,
  .../crystallography/ui/cecoordinateeditor.ui,
  .../crystallography/ui/cematrixeditor.cpp,
  .../extensions/crystallography/ui/cematrixeditor.h,
  .../crystallography/ui/cematrixeditor.ui,
  .../crystallography/ui/ceparametereditor.cpp,
  .../crystallography/ui/ceparametereditor.h,
  .../crystallography/ui/ceparametereditor.ui: Added Crystallography extension 
  Change-Id: Ib1ccd4d732f0f5832929010000v200000badc0de

2011-03-17  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add access to
  GLWidget's text overlay.  Extend the GLWidget text overlay from debug info to
  any specified collection of strings.  This deprecates renderDebugOverlay, as
  renderTextOverlay will now render the debug info in the appropriate location.
   Change-Id: Ib33cefa8ee3bf49c078a5fe28c4eece56c911da1

2011-03-17  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Load engines with
  missing settings.  Currently if Avogadro has non-empty settings, it loads
  only those engines that are present in settings. This issue requires complete
  erasing of user settings as the only workaround in the next cases:  a)
  Loading 3rd party engine(s) b) Editing python engine (because ID changes) c)
  Developing new C++ engine or switching branch from 1.0 to master  Also some
  code duplication was removed.  Change-Id:
  I69062fbb2292d122058030ea1c577864a24c2d23

2011-03-04  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/atom.cpp, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/molecule.cpp: Lazy evaluation of group indices  Recalculates
  group indices if Atoms of Molecule were changed on first call of
  Atom::groupIndex  Change-Id: I4d3e9dbb2ce93af9359cf9402b5d0703ad5c1cc4

2011-02-18  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/atom.h, libavogadro/src/colors/atomindexcolor.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/smartscolor.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/extensions/invertchiralextension.cpp,
  libavogadro/src/neighborlist.cpp, libavogadro/src/tools/selectrotatetool.cpp:
  Removed some unnecessary qobject_casts  Change-Id:
  I9c56d510f70f44699868da08d94ec1d05a612b08

2011-02-03  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/ca@valencia.po,
  i18n/avogadro/cs.po, i18n/avogadro/da.po, i18n/avogadro/de.po,
  i18n/avogadro/el.po, i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/eu.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/gl.po,
  i18n/avogadro/he.po, i18n/avogadro/hr.po, i18n/avogadro/hu.po,
  i18n/avogadro/id.po, i18n/avogadro/it.po, i18n/avogadro/ja.po,
  i18n/avogadro/kn.po, i18n/avogadro/ko.po, i18n/avogadro/nb.po,
  i18n/avogadro/nl.po, i18n/avogadro/oc.po, i18n/avogadro/pl.po,
  i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po,
  i18n/avogadro/sk.po, i18n/avogadro/sv.po, i18n/avogadro/th.po,
  i18n/avogadro/tr.po, i18n/avogadro/uk.po, i18n/avogadro/vi.po,
  i18n/avogadro/zh_CN.po, i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po,
  i18n/libavogadro/bg.po, i18n/libavogadro/bs.po, i18n/libavogadro/ca.po,
  i18n/libavogadro/ca@valencia.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/gl.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sv.po, i18n/libavogadro/tr.po,
  i18n/libavogadro/uk.po, i18n/libavogadro/vi.po, i18n/libavogadro/zh_CN.po,
  i18n/libavogadro/zh_TW.po: ENH: Updated trunk with latest Launchpad
  translations and templates.

2011-01-30  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: Address bug #3019539 - add wireframe
  pick method.  The pick method actually renders balls and sticks so that the
  bonds do not clobber the atoms. This could probably be streamlined, but
  provides one possible solution to this issue.  Change-Id:
  I187d71bbe6092683645aa7c3d97c2ef9e50d07e3

2011-01-25  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/config.h.in, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h: Moved plugin path initialization from
  libavogadro to avogadro-app.  For compatibility PluginManager uses Avogadro
  plugin path settings or AVOGADRO_PLUGINS variable if client application does
  not specify plugin path.  Change-Id:
  I58722e393ea02471812c92ea55a9a15fc0f72f67

  * .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h,
  .../src/extensions/qtaim/qtaimodeintegrator.h,
  .../src/extensions/qtaim/qtaimwavefunction.h,
  .../qtaim/qtaimwavefunctionevaluator.cpp,
  .../extensions/qtaim/qtaimwavefunctionevaluator.h: Fixed some compilation
  warnings in QTAIM extension  const qualifiers on primitive return types are
  ignored by GCC and produce too many warnings on each file  Also some unused
  variables were removed  Change-Id: I4410b3ab34ea0f8911845c601fc167f807fb28cf

2011-01-21  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/PythonDeps.cmake, libavogadro/src/python/sip.cpp: Clean up
  the SIP support, import suggested fixes.  This will also apply cleanly to the
  1.0 branch. I have tested with both master and 1.0 using SIP 4.12. Get rid of
  the symbol definitions - use the ones provided by SIP instead. This means we
  no longer need to run the sip binary to get the SIP version. Thanks to all
  the distro guys for putting patches up pointing me in the right direction. 
  Change-Id: I96f8277dd63a3ad726869b1123e2238aad114c97

2011-01-15  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Moved variables to d
  pointer, initialized them.  Some of the variables were not being initialized,
  such as m_groupIndex, added them to the initializer list. Moved to the d
  pointer so that they could actually move to be molecule properties in vectors
  in the future (initialized lazily upon first use).  The d pointer was not
  being deleted, took care of that too.  Change-Id:
  I86b973208489be197abe73d0519d924b4ae29ed8

2010-12-28  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/basisset.cpp,
  libavogadro/src/extensions/surfaces/basisset.h,
  .../src/extensions/surfaces/gamessukout.cpp,
  libavogadro/src/extensions/surfaces/gamessukout.h,
  libavogadro/src/extensions/surfaces/gamessus.cpp,
  libavogadro/src/extensions/surfaces/gamessus.h,
  .../src/extensions/surfaces/gaussianfchk.cpp,
  libavogadro/src/extensions/surfaces/gaussianfchk.h,
  .../src/extensions/surfaces/gaussianset.cpp,
  libavogadro/src/extensions/surfaces/gaussianset.h,
  libavogadro/src/extensions/surfaces/molden.cpp,
  libavogadro/src/extensions/surfaces/molden.h,
  libavogadro/src/extensions/surfaces/mopacaux.cpp,
  libavogadro/src/extensions/surfaces/mopacaux.h,
  .../extensions/surfaces/openqube/CMakeLists.txt,
  .../src/extensions/surfaces/openqube/basisset.h,
  .../surfaces/openqube/basissetloader.cpp,
  .../extensions/surfaces/openqube/basissetloader.h,
  .../src/extensions/surfaces/openqube/cube.cpp,
  .../src/extensions/surfaces/openqube/cube.h,
  .../extensions/surfaces/openqube/gamessukout.cpp,
  .../src/extensions/surfaces/openqube/gamessukout.h,
  .../src/extensions/surfaces/openqube/gamessus.cpp,
  .../src/extensions/surfaces/openqube/gamessus.h,
  .../extensions/surfaces/openqube/gaussianfchk.cpp,
  .../extensions/surfaces/openqube/gaussianfchk.h,
  .../extensions/surfaces/openqube/gaussianset.cpp,
  .../src/extensions/surfaces/openqube/gaussianset.h,
  .../src/extensions/surfaces/openqube/molden.cpp,
  .../src/extensions/surfaces/openqube/molden.h,
  .../src/extensions/surfaces/openqube/mopacaux.cpp,
  .../src/extensions/surfaces/openqube/mopacaux.h,
  .../src/extensions/surfaces/openqube/openqubeabi.h,
  .../src/extensions/surfaces/openqube/slaterset.cpp,
  .../src/extensions/surfaces/openqube/slaterset.h,
  .../src/extensions/surfaces/orbitalextension.cpp,
  .../src/extensions/surfaces/orbitalextension.h,
  libavogadro/src/extensions/surfaces/slaterset.cpp,
  libavogadro/src/extensions/surfaces/slaterset.h,
  .../src/extensions/surfaces/surfaceextension.cpp,
  .../src/extensions/surfaces/surfaceextension.h: Import OpenQube snapshot -
  port to use it.  Imported the first snapshot of OpenQube, and ported the two
  extensions to use the new split out library. Build the library as a shared
  object and link to it from the two plugins. Removed quite a bit of code
  duplication between the two extensions and within each extension.  Change-Id:
  I3d98f1eaf93fb5d8cede7ea56e5fc3182ff2c03e

2011-01-04  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h: Handle some command line arguments - config reset.
   Allow a --erase-config option to ignore any configuration options saved for
  the current user. Useful for testing, and for users wishing to reset their
  settings.  Change-Id: I34c4e2586301f18e6020d89e3d7141b2f7e63752

  * libavogadro/src/engines/labelengine.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h: Stop recalculating group indices all of the time.
   The group index is only used by the label engine, avoid calculating it every
  time an atom is added/removed or the geometry is changed for something many
  people never use. I am not convinced that feature has any use outside of the
  label engine, and would rather see it moved there.  Change-Id:
  I8ce9d03798765d550bf7b74ff4fd19542fb8461b

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h: Optionally build against Qt Testing.  This allows
  Avogadro to optionally build against Qt Testing from the ParaView project. It
  adds two new entries to the settings menu to record and play back an XML
  test. The Qt Testing code can be obtained by,  git clone
  git://paraview.org/QtTesting.git  It should be built in its own out of source
  tree, and you can point to the build tree from Avogadro's build tree to use
  the library.  Change-Id: I7395960b912a6c1467e24fbb68db6de58dc87962

  * .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/spectra/dos.cpp,
  .../src/extensions/spectra/spectradialog.ui,
  .../src/extensions/spectra/vibrationextension.cpp,
  .../src/extensions/spectra/vibrationwidget.cpp: Fixes for compiler warnings,
  indentation in spectra.

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  AutoOptTool compiler warnings and indentation.

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Fixed compiler warnings,
  fixed up indentation, style.

2010-12-31  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/pythonengine_p.cpp, libavogadro/src/pythonerror.cpp,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythontool_p.cpp:
  Caught a few Python only moc includes.

2010-12-30  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/animation.cpp,
  libavogadro/src/atom.cpp, libavogadro/src/bond.cpp,
  libavogadro/src/color.cpp, libavogadro/src/colorbutton.cpp,
  libavogadro/src/colors/elementcolor.cpp, libavogadro/src/cube.cpp,
  libavogadro/src/dockextension.cpp, libavogadro/src/elementdetail_p.cpp,
  libavogadro/src/elementtranslator.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/extension.cpp,
  libavogadro/src/fragment.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/mesh.cpp, libavogadro/src/meshgenerator.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/moleculefile.cpp,
  libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plugin.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/protein.cpp,
  libavogadro/src/readfilethread_p.cpp, libavogadro/src/residue.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/toolgroup.cpp,
  libavogadro/src/zmatrix.cpp: Use qt4_wrap_cpp to run Qt's moc.

  * libavogadro/src/CMakeLists.txt, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h, libavogadro/src/readfilethread_p.cpp,
  libavogadro/src/readfilethread_p.h: Split ReadFileThread out into a private
  class.  This was causing lots of warnings due to being a QObject derived
  class with Q_OBJECT macro. Splitting it out into a private class allows us to
  add back in the Q_OBJECT macro that should be there and fix the warnings. The
  functionality remains the same.

2010-12-04  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/molecule.cpp, libavogadro/src/tools/drawcommand.cpp: Update
  molecule when hydrogens are added.  Multiple returns were causing the
  molecule to not be marked as updated in some circumstances, such as when
  hydrogens are added to two new atoms. This is easily observed with quick
  render on and the "appearing disappearing hydrogens" can be seen (or not)
  when you rotate the scene.  Change-Id:
  I173a675ec12efd5e9f490cc36357c669b0c3451b

  * scripts/cc, scripts/cxx: Removed cc and cxx files.  These do not belong in
  Avogadro's source tree.

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Fixed a
  few minor line length issues.

2010-11-22  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/AvogadroUse.cmake, libavogadro/src/CMakeLists.txt: Removed
  GLEW_LIBRARY_DIR link directory calls.

  * libavogadro/src/molecule.cpp, libavogadro/src/moleculefile.cpp: Fixes for
  compiler warnings.

2010-11-18  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Added
  possibility to load fixed lists of plugins  Currelntly libavogadro supports
  only loading of plugin directories. This patch allows client applications to
  load fixed subset of plugins  Change-Id:
  I408fada3fb1350681006221a4253427b0dcf0109

2010-11-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po,
  i18n/avogadro/es.po, i18n/avogadro/eu.po, i18n/avogadro/fi.po,
  i18n/avogadro/fr.po, i18n/avogadro/he.po, i18n/avogadro/hr.po,
  i18n/avogadro/hu.po, i18n/avogadro/id.po, i18n/avogadro/it.po,
  i18n/avogadro/ja.po, i18n/avogadro/kn.po, i18n/avogadro/ko.po,
  i18n/avogadro/nb.po, i18n/avogadro/nl.po, i18n/avogadro/oc.po,
  i18n/avogadro/pl.po, i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po,
  i18n/avogadro/ru.po, i18n/avogadro/sk.po, i18n/avogadro/sv.po,
  i18n/avogadro/tr.po, i18n/avogadro/uk.po, i18n/avogadro/vi.po,
  i18n/avogadro/zh_CN.po, i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po,
  i18n/libavogadro/bg.po, i18n/libavogadro/ca.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_AU.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/eu.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/he.po,
  i18n/libavogadro/hi.po, i18n/libavogadro/hu.po, i18n/libavogadro/id.po,
  i18n/libavogadro/it.po, i18n/libavogadro/ja.po, i18n/libavogadro/kn.po,
  i18n/libavogadro/ko.po, i18n/libavogadro/libavogadro.pot,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/uk.po, i18n/libavogadro/vi.po,
  i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po: Updated translations
  and merged from Launchpad.

2010-11-17  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Added const values for atom and bond
  scaling.  Added two new, constant values for atom and bond scaling, fixing a
  bug introduced during all of the changes to atom and bond radii. Also fixed
  declaration order/initialization.

2010-11-15  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/engines/qtaimengine.cpp,
  libavogadro/src/engines/qtaimengine.h,
  libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  libavogadro/src/extensions/qtaim/qtaimcubature.h,
  .../src/extensions/qtaim/qtaimextension.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/primitive.h,
  libavogadro/src/qtaimbondcriticalpoint.cpp,
  libavogadro/src/qtaimbondcriticalpoint.h,
  libavogadro/src/qtaimnuclearcriticalpoint.cpp,
  libavogadro/src/qtaimnuclearcriticalpoint.h: QTAIM: Remove additions to
  molecule class. All data now through Properties.

  * .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimwavefunction.cpp,
  .../src/extensions/qtaim/qtaimwavefunction.h,
  libavogadro/src/extensions/surfaces/basisset.h,
  .../src/extensions/surfaces/gaussianset.cpp,
  libavogadro/src/extensions/surfaces/gaussianset.h,
  .../src/extensions/surfaces/orbitalextension.cpp,
  libavogadro/src/extensions/surfaces/slaterset.h, libavogadro/src/molecule.h:
  QTAIM: Utilize orbitals from Surface/Orbital Extension. Make sure to use 6D
  10F (Cartesian Orbitals) in Electronic Structure program.

2010-10-27  Jens Thomas <linucks42@gmail.com>

  * libavogadro/src/extensions/quantuminput/gamessukinputdialog.cpp,
  libavogadro/src/extensions/quantuminput/gamessukinputdialog.h: Small fix to
  initialisation.  Changed the order of declaration of m_coodType and m_output
  to stop compiler complaining.  Also initialised m_title in the constructor as
  it can't be initialised in the initialisation list as it resides in the base
  class.  Change-Id: I2cd006fb7cc7e4f85acc16041d7891b28dac1ffc

2010-11-14  David Lonie <loniedavid@gmail.com>

  * .../05-ConformerPlot/CMakeLists.txt,
  .../05-ConformerPlot/conformerplotdialog.cpp,
  .../05-ConformerPlot/conformerplotdialog.h,
  .../05-ConformerPlot/conformerplotdialog.ui,
  .../05-ConformerPlot/conformerplotextension.cpp,
  .../05-ConformerPlot/conformerplotextension.h,
  .../thirdPartyExtensions/images/05-promote.png: Added initial version of the
  ConformerPlot third party extension example.  Change-Id:
  I7cfa1bb9f9439609339fb8b77f0e65a2d3f54f40

  * .../04-RotateSelection/CMakeLists.txt,
  .../04-RotateSelection/rotateselectiondialog.cpp,
  .../04-RotateSelection/rotateselectiondialog.h,
  .../04-RotateSelection/rotateselectiondialog.ui,
  .../rotateselectionextension.cpp,
  .../04-RotateSelection/rotateselectionextension.h: Added initial version of
  the RotateSelection third party extension example.  Change-Id:
  Iac5104eb322a2068d2ce27f015b2130fcea9e266

  * .../03-ViewPlane/CMakeLists.txt, .../03-ViewPlane/viewplaneextension.cpp,
  .../03-ViewPlane/viewplaneextension.h: Added initial version of the ViewPlane
  third party extension example.  Change-Id:
  I1565100c22e6afad102ae894ee32d0d550fe5ba0

2010-11-08  David C. Lonie <loniedavid@gmail.com>

  * .../thirdPartyExtensions/02-DynamicDisplay.dox,
  .../02-DynamicDisplay/CMakeLists.txt,
  .../02-DynamicDisplay/dynamicdisplaydialog.cpp,
  .../02-DynamicDisplay/dynamicdisplaydialog.h,
  .../02-DynamicDisplay/dynamicdisplaydialog.ui,
  .../02-DynamicDisplay/dynamicdisplayextension.cpp,
  .../02-DynamicDisplay/dynamicdisplayextension.h,
  libavogadro/examples/thirdPartyExtensions/toc.dox: Added initial version of
  the DynamicDisplay third party extension example.

  * .../thirdPartyExtensions/01-HelloWorld.dox,
  .../01-HelloWorld/CMakeLists.txt, .../01-HelloWorld/helloworlddialog.cpp,
  .../01-HelloWorld/helloworlddialog.h, .../01-HelloWorld/helloworlddialog.ui,
  .../01-HelloWorld/helloworldextension.cpp,
  .../01-HelloWorld/helloworldextension.h,
  libavogadro/examples/thirdPartyExtensions/toc.dox: Added initial version of
  the HelloWorld third party extension example.

2010-11-09  David C. Lonie <loniedavid@gmail.com>

  * Doxyfile, libavogadro/examples/thirdPartyExtensions/toc.dox: First draft of
  the tutorial TOC.

2010-11-05  Eric Brown <brown@brown.chem.luc.edu>

  * .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  .../extensions/qtaim/qtaimcriticalpointlocator.h,
  libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  libavogadro/src/extensions/qtaim/qtaimcubature.h,
  .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h,
  .../src/extensions/qtaim/qtaimmathutilities.cpp,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp,
  .../src/extensions/qtaim/qtaimodeintegrator.h,
  .../src/extensions/qtaim/qtaimwavefunction.h,
  .../qtaim/qtaimwavefunctionevaluator.cpp,
  .../extensions/qtaim/qtaimwavefunctionevaluator.h: QTAIM: Lone Pairs from
  Topology of Laplacian

2010-11-04  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  libavogadro/src/extensions/qtaim/qtaimextension.cpp: MINOR: add 1 to the
  basin index print out to qDebug to avoid confusion

2010-11-03  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h: QTAIM: Adaptive Integration
  with explicit determination of basin.\n\nThis integration strategy allows the
  integrals to be calculated to higher accuracy.

2010-10-19  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  libavogadro/gl2ps/COPYING.GL2PS, libavogadro/gl2ps/COPYING.LGPL,
  libavogadro/gl2ps/README.txt, libavogadro/gl2ps/TODO.txt,
  libavogadro/gl2ps/gl2ps.c, libavogadro/gl2ps/gl2ps.h,
  libavogadro/gl2ps/gl2ps.pdf, libavogadro/gl2ps/gl2psTest.c,
  libavogadro/gl2ps/gl2psTestSimple.c, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gl2ps/COPYING.GL2PS,
  libavogadro/src/extensions/gl2ps/COPYING.LGPL,
  libavogadro/src/extensions/gl2ps/README.txt,
  libavogadro/src/extensions/gl2ps/TODO.txt,
  libavogadro/src/extensions/gl2ps/gl2ps.c,
  libavogadro/src/extensions/gl2ps/gl2ps.h,
  libavogadro/src/extensions/gl2ps/gl2ps.pdf,
  libavogadro/src/extensions/gl2ps/gl2psTest.c,
  libavogadro/src/extensions/gl2ps/gl2psTestSimple.c,
  libavogadro/src/extensions/gl2psextension.cpp,
  libavogadro/src/extensions/gl2psextension.h: Moved gl2ps export into
  extension  gl2ps code was directly linked with avogadro-app, but Avogadro
  client should not make assumptions about renderer nature to allow more
  flexibility in renderer architecture in future. Also it should fix linking
  error on Windows  Change-Id: I8d2de2c7a8d6c645f0695e92a90e9489ea05f53f

2010-11-01  Eric Brown <brown@brown.chem.luc.edu>

  * .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimmathutilities.h,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp,
  .../qtaim/qtaimwavefunctionevaluator.cpp,
  .../extensions/qtaim/qtaimwavefunctionevaluator.h: Fix errors found by Dave's
  MSVC compilation

2010-10-31  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  libavogadro/src/extensions/qtaim/qtaimcubature.h,
  .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp: QTAIM: Adaptive
  Integration over Atomic Basins (parallel version)

2010-10-26  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Added Del as
  alternative shortcut for actionClear  Change-Id:
  I378b532aa18bca21892790da0740b3203d244328

2010-10-26  Eric Brown <brown@brown.chem.luc.edu>

  * CMakeLists.txt, libavogadro/src/extensions/qtaim/CMakeLists.txt,
  .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  libavogadro/src/extensions/qtaim/qtaimcubature.cpp,
  libavogadro/src/extensions/qtaim/qtaimcubature.h,
  .../src/extensions/qtaim/qtaimextension.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp,
  libavogadro/src/extensions/qtaim/test/c4h4.wfn,
  libavogadro/src/extensions/qtaim/test/hco2.wfn: Adaptive Integration over
  Atomic Basins (serial version). Output via qDebug(). Memory Leak in LSODA
  quashed.

2010-10-25  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h:
  drawtool: Converted m_addHydrogens and adjustHydrogens from int to bool

2010-10-20  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.cpp,
  libavogadro/src/extensions/qtaim/qtaimextension.cpp,
  libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h,
  libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp,
  libavogadro/src/extensions/qtaim/qtaimmathutilities.h,
  libavogadro/src/extensions/qtaim/qtaimodeintegrator.h,
  libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.h: Fixed
  compilation with older Eigen versions  There was a problem in Eigen2 make
  install that prevented some headers (including Eigen/Eigen) from being
  installed, that's why these headers are usually missing in Linux packages

2010-10-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * fragments/cyclic alkanes/cyclohexane-chair.cml, .../cyclic
  alkanes/cyclohexane-twist-boat.cml, fragments/cyclic alkanes/cyclohexane.cml:
  Fixed cyclohexane template, thanks to Visvaldas K. for the pointer. 
  Change-Id: Ia86c4894b068c565d17d34d842bdbbb2f69fbb81

2010-10-07  David C. Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add option to align the view to the coordinate
  axes.  Change-Id: Iaecd4f1ac8fe52144cdb57888213470633faaacf

2010-10-14  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  libavogadro/src/extensions/qtaim/qtaimlsodaintegrator.h,
  libavogadro/src/extensions/qtaim/qtaimodeintegrator.cpp,
  libavogadro/src/extensions/qtaim/qtaimodeintegrator.h,
  libavogadro/src/extensions/qtaim/qtaimwavefunction.cpp,
  libavogadro/src/extensions/qtaim/qtaimwavefunction.h: removed QObject
  inheritance

  * libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.cpp,
  libavogadro/src/extensions/qtaim/qtaimcriticalpointlocator.h: Added m_
  prefixes to private members, removed QObject inheritance

  * .../qtaim/qtaimwavefunctionevaluator.cpp,
  .../extensions/qtaim/qtaimwavefunctionevaluator.h: Added m_ prefixes to
  private members, removed QObject inheritance

2010-10-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/qtaim/CMakeLists.txt,
  libavogadro/src/molecule.cpp, libavogadro/src/qtaimnuclearcriticalpoint.cpp:
  Removed some whitespace from a few files.  Also removed the duplicate
  removeAtom I introduced during previous rebase of this topic branch. It had
  moved, not been removed.

2010-09-28  Eric Brown <brown@brown.chem.luc.edu>

  * .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h,
  .../src/extensions/qtaim/qtaimmathutilities.cpp,
  .../src/extensions/qtaim/qtaimmathutilities.h,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp,
  .../src/extensions/qtaim/qtaimodeintegrator.h,
  .../src/extensions/qtaim/qtaimwavefunction.cpp,
  .../src/extensions/qtaim/qtaimwavefunction.h,
  .../qtaim/qtaimwavefunctionevaluator.cpp,
  libavogadro/src/qtaimbondcriticalpoint.h,
  libavogadro/src/qtaimnuclearcriticalpoint.cpp,
  libavogadro/src/qtaimnuclearcriticalpoint.h: Capitalization problem in
  include statements  Convert malloc to qMalloc, and whitespace.  Change-Id:
  I46b0da2468f97548a7cf86b5049bafcf33e575cf

2010-09-21  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/extensions/qtaim/CMakeLists.txt,
  .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.cpp,
  .../src/extensions/qtaim/qtaimlsodaintegrator.h,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp: QTAIM LSODA Integrator.
  Improves speed by almost an order of magnitude.  Change-Id:
  I81229883f8f89c2ff35d3bc92a66eb90e55ab3d7

2010-09-17  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/qtaimengine.cpp,
  libavogadro/src/engines/qtaimengine.h,
  libavogadro/src/engines/qtaimsettingswidget.ui,
  libavogadro/src/extensions/qtaim/CMakeLists.txt,
  .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  .../src/extensions/qtaim/qtaimextension.cpp,
  libavogadro/src/extensions/qtaim/qtaimextension.h,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/primitive.h, libavogadro/src/qtaimbondcriticalpoint.cpp,
  libavogadro/src/qtaimbondcriticalpoint.h,
  libavogadro/src/qtaimnuclearcriticalpoint.cpp,
  libavogadro/src/qtaimnuclearcriticalpoint.h: QTAIM Extension, Engine, Minor
  Change to ODE.  Please make sure to add Display Type QTAIM, and reduce
  opacity on BSDY etc.  Change-Id: I8a4812352e09733f7f62b7dcf7803bee893aca74

  * libavogadro/src/extensions/qtaim/CMakeLists.txt,
  .../extensions/qtaim/qtaimcriticalpointlocator.cpp,
  .../extensions/qtaim/qtaimcriticalpointlocator.h: QTAIM Nuclear and Bond
  Critical Point Locator, Bond Path Tracer

  * libavogadro/src/extensions/qtaim/CMakeLists.txt,
  .../src/extensions/qtaim/qtaimodeintegrator.cpp,
  .../src/extensions/qtaim/qtaimodeintegrator.h: QTAIM ODE Integrator

  * .../src/extensions/qtaim/qtaimmathutilities.cpp,
  .../src/extensions/qtaim/qtaimmathutilities.h,
  .../qtaim/qtaimwavefunctionevaluator.cpp,
  .../extensions/qtaim/qtaimwavefunctionevaluator.h: QTAIM Wavefunction and
  Evaluator (All Derivatives)

  * .../src/extensions/qtaim/qtaimwavefunction.cpp,
  .../src/extensions/qtaim/qtaimwavefunction.h,
  .../qtaim/qtaimwavefunctionevaluator.cpp,
  .../extensions/qtaim/qtaimwavefunctionevaluator.h: Wavefunction and Evaluator

2010-09-15  Eric Brown <brown@brown.chem.luc.edu>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/qtaim/CMakeLists.txt,
  .../src/extensions/qtaim/qtaimmathutilities.cpp,
  .../src/extensions/qtaim/qtaimmathutilities.h: QTAIM Math Utilities

2010-09-17  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/invertchiralextension.cpp,
  libavogadro/src/extensions/invertchiralextension.h: Generate enantiomer or
  flip stereo on selected atoms.  Change-Id:
  Iee678ddeab3a5ff2ae8f4c7c60f160c03c573fba

2010-09-28  Jens Thomas <linucks42@gmail.com>

  * .../src/extensions/quantuminput/CMakeLists.txt,
  .../quantuminput/gamessukinputdialog.cpp,
  .../extensions/quantuminput/gamessukinputdialog.h,
  .../extensions/quantuminput/gamessukinputdialog.ui,
  .../extensions/quantuminput/inputfileextension.cpp: A basic input dialogue
  for GAMESS-UK  Currently supports single-point energies, optimisations and
  frequency calculations for closed-shell Hartree-Fock, DFT and MP2 theories in
  conventional and direct mode.  Change-Id:
  I85d999265585b3c92cc98f726f70096cba0aa672

2010-09-26  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/surfaces/gamessus.cpp,
  .../src/extensions/surfaces/gaussianset.cpp: Fix bug with atom coordinate
  parsing. Now reads simple GAMESS files.  Change-Id:
  Ib030ac885af12dca499cc3633597b319ad06853f

2010-09-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/surfaces/gaussianfchk.cpp,
  libavogadro/src/extensions/surfaces/gaussianset.cpp: Fixed the MO matrix
  resize calls.  Also added some debugging to help with GAMESS-US support. 
  Change-Id: Iea7fb063303d03e936773a55361fd2bd516cbd4c

2010-09-16  Jens Thomas <linucks42@gmail.com>

  * libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h: Changed runPovRay to return a
  bool that can be checked to see if it has worked.  Also moved the call to the
  dialogue to inform the user that it hasn't worked into the calling routine. 
  This was because, if povray isn't present, the dialogue is popped up and
  needs to be clicked on for every single frame, which can be a little
  overwhelming if you have several hundred frames...  Change-Id:
  Id2c746973083a1de6a7a408c0b076a611f032267

2010-09-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/insertcommand.cpp,
  libavogadro/src/extensions/insertfragmentextension.cpp: Support for inserting
  a fragment that connects to the selected atom.  Change-Id:
  I525eb056e91f74f21d1d0e36da4407ff7bc7354f

  * libavogadro/src/extensions/insertcommand.cpp,
  libavogadro/src/extensions/insertcommand.h,
  .../src/extensions/insertfragmentextension.cpp: Initial support for "growing
  fragments." Select an atom, insert smiles.  Change-Id:
  I729310c21f57c43a516549a93da1daef31ad0dc5

2010-09-16  Jens Thomas <linucks42@gmail.com>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h: Added support for DL-POLY
  HISTORY files.  I've changed the readTrajFromXYZ to readTrajFromFile, which
  just selects the correct format based on the filename, as the code is
  identical in both cases otherwise.  Prevent crash with empty molecule,
  translate file filters correctly.  Change-Id:
  I06e65634ff845dd4ada431b6ef912ecbcc7db95b

2010-09-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/moleculefile.cpp: Fix reading
  of conformer files. MainWindow will check for conformers and add them
  correctly. MoleculeFile will properly reserve vectors of conformers. 
  Change-Id: Ia38f231e1bc9dc19becb2a6155ecb6a3d85b81fe

2010-09-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: Name improvements. Generate
  InChI and cache to throttle requests.  Change-Id:
  I57271aa4a7d9eea50bcbf37c287a2f3ec3c237c2

2010-09-05  David Lonie <loniedavid@gmail.com>

  * .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: Limit network calls for IUPAC
  name to every three seconds.  Change-Id:
  Idaab1bac048f5c8cb19c809ab370c4fa119d8352

2010-09-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po,
  i18n/avogadro/es.po, i18n/avogadro/eu.po, i18n/avogadro/fi.po,
  i18n/avogadro/fr.po, i18n/avogadro/he.po, i18n/avogadro/hr.po,
  i18n/avogadro/hu.po, i18n/avogadro/id.po, i18n/avogadro/it.po,
  i18n/avogadro/ja.po, i18n/avogadro/kn.po, i18n/avogadro/ko.po,
  i18n/avogadro/nb.po, i18n/avogadro/nl.po, i18n/avogadro/oc.po,
  i18n/avogadro/pl.po, i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po,
  i18n/avogadro/ru.po, i18n/avogadro/sk.po, i18n/avogadro/sv.po,
  i18n/avogadro/tr.po, i18n/avogadro/uk.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/ca.po, i18n/libavogadro/cs.po, i18n/libavogadro/da.po,
  i18n/libavogadro/de.po, i18n/libavogadro/el.po, i18n/libavogadro/en_AU.po,
  i18n/libavogadro/en_CA.po, i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sv.po, i18n/libavogadro/tr.po,
  i18n/libavogadro/uk.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Updated translation templates.  Change-Id:
  I85ab19cf6f24e4e07351263cee443b375761a2af

2010-09-02  Geoff Hutchison <geoff.hutchison@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/molecularpropdialog.ui,
  .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: First pass at naming molecules
  through the NIH resolver.

2010-08-29  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Load icons from
  active desktop theme  If compiled with Qt >= 4.6.0, try to load icons from
  current desktop theme unstead of bundled ones from Oxygen. If some icon is
  missing, or environment is not compatible to Freedesktop standards, bundled
  icons will be loaded

  * .../extensions/quantuminput/nwcheminputdialog.cpp,
  .../extensions/quantuminput/nwcheminputdialog.ui: Fixed format of generated
  NWChem z-matrix and made it look better  Change-Id:
  I100f17dae2c539f4adb46c10ec8404256c021049

2010-08-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * .../src/extensions/surfaces/surfacedialog.cpp,
  .../src/extensions/surfaces/surfacedialog.h,
  .../src/extensions/surfaces/surfacedialog.ui: SurfaceDialog: Add Very low
  resolution (0.5A) and custom resolution (0.01-2.0A) with QDoubleSpinBox.

2010-08-18  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_AU.po, i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po,
  i18n/avogadro/es.po, i18n/avogadro/eu.po, i18n/avogadro/fi.po,
  i18n/avogadro/fr.po, i18n/avogadro/he.po, i18n/avogadro/hr.po,
  i18n/avogadro/hu.po, i18n/avogadro/id.po, i18n/avogadro/it.po,
  i18n/avogadro/ja.po, i18n/avogadro/kn.po, i18n/avogadro/ko.po,
  i18n/avogadro/nb.po, i18n/avogadro/nl.po, i18n/avogadro/oc.po,
  i18n/avogadro/pl.po, i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po,
  i18n/avogadro/ru.po, i18n/avogadro/sk.po, i18n/avogadro/sv.po,
  i18n/avogadro/tr.po, i18n/avogadro/uk.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/ca.po, i18n/libavogadro/cs.po, i18n/libavogadro/da.po,
  i18n/libavogadro/de.po, i18n/libavogadro/el.po, i18n/libavogadro/en_AU.po,
  i18n/libavogadro/en_CA.po, i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po,
  i18n/libavogadro/eu.po, i18n/libavogadro/fi.po, i18n/libavogadro/fr.po,
  i18n/libavogadro/he.po, i18n/libavogadro/hi.po, i18n/libavogadro/hu.po,
  i18n/libavogadro/id.po, i18n/libavogadro/it.po, i18n/libavogadro/ja.po,
  i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro.pot, i18n/libavogadro/nb.po,
  i18n/libavogadro/nl.po, i18n/libavogadro/oc.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sv.po, i18n/libavogadro/tr.po,
  i18n/libavogadro/uk.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po:
  Launchpad sync (for real)  Change-Id:
  Ide95e3a6a213763000ce86d9a3095ccddb0223d3

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po, i18n/avogadro/es.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/he.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/nb.po, i18n/avogadro/nl.po,
  i18n/avogadro/oc.po, i18n/avogadro/pl.po, i18n/avogadro/pt.po,
  i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po, i18n/avogadro/sk.po,
  i18n/avogadro/sv.po, i18n/avogadro/tr.po, i18n/avogadro/uk.po,
  i18n/avogadro/zh_CN.po, i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po,
  i18n/libavogadro/bg.po, i18n/libavogadro/ca.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_CA.po, i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/he.po,
  i18n/libavogadro/hi.po, i18n/libavogadro/hu.po, i18n/libavogadro/id.po,
  i18n/libavogadro/it.po, i18n/libavogadro/ja.po, i18n/libavogadro/kn.po,
  i18n/libavogadro/ko.po, i18n/libavogadro/libavogadro.pot,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/uk.po, i18n/libavogadro/zh_CN.po,
  i18n/libavogadro/zh_TW.po: Translation updates, including Launchpad sync. 
  Change-Id: I35a1f690275a24ed5de27495eb1c7089536238a8

2010-08-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: *
  libavogadro/src/glwidget.cpp: Use Tool::identifier() to find Navigate tool
  (was Tool::name()).  * avogadro/src/mainwindow.cpp: Call
  GLWidget::setToolGroup() when (re)loading tools to ensure the glwidget always
  has a pointer to the Navigate tool.

2010-08-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfaces/gaussianset.cpp,
  libavogadro/src/extensions/surfaces/molden.cpp,
  libavogadro/src/extensions/surfaces/molden.h: Minor changes - removed debug
  output, removed includes.

2010-08-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/elementitem_p.cpp, libavogadro/src/glwidget.cpp: Warning
  fixes.

2010-08-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/gamessus.cpp,
  libavogadro/src/extensions/surfaces/gamessus.h,
  .../src/extensions/surfaces/gaussianset.cpp,
  .../src/extensions/surfaces/orbitalextension.cpp: Initial modifications for
  GAMESS-US support. Reads MOs from standard DFT / 6-31G* basis.  Change-Id:
  I40cc65d19dfb9acd6d393b2e422cc29dafb7738f

2010-08-11  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  .../src/extensions/surfaces/gaussianset.cpp,
  libavogadro/src/extensions/surfaces/molden.cpp,
  libavogadro/src/extensions/surfaces/molden.h,
  .../src/extensions/surfaces/orbitalextension.cpp,
  .../src/extensions/surfaces/surfaceextension.cpp, testfiles/benzene.mold:
  Initial support for reading MOs and GTOs from Molden files (.mold, .molf,
  .molden).  Change-Id: I081912c118592cdb8670a7eb1f655832dd64560d

2010-08-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/atom.cpp, libavogadro/src/molecule.cpp: Store and retain
  atomic partial charges.  Change-Id: I181adbe6b41be6fc3cd2256030c0c12977fea3fe

  * libavogadro/src/elementitem_p.cpp, libavogadro/src/glwidget.cpp: Warning
  fixes.

2010-07-16  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/bond.cpp, libavogadro/src/molecule.cpp: Added possibility
  to read and save bond labels to CML files  Before this patch custom label
  were not saved and read

2010-07-15  Jens Thomas <linucks42@gmail.com>

  * libavogadro/src/extensions/surfaces/gamessukout.cpp,
  libavogadro/src/extensions/surfaces/gamessukout.h,
  .../src/extensions/surfaces/surfaceextension.cpp: Small changes necessitated
  by changes on the master branch while I was working.

2010-07-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/surfaces/approxmath.h,
  .../src/extensions/surfaces/gaussianset.cpp,
  .../src/extensions/surfaces/orbitalextension.cpp,
  .../src/extensions/surfaces/orbitalextension.h: Added timer (for performance)
  in orbital extension. Use approx exp() for speed boost.  Added better
  comments in header, including origins of methods.  Change-Id:  
  Ia5168f9a6ed46cf7526e91f17f3aecdd64a1e280

2010-07-14  Jens Thomas <linucks42@gmail.com>

  * .../src/extensions/surfaces/gamessukout.cpp,
  libavogadro/src/extensions/surfaces/gamessukout.h: First cut of the code to
  parse the coordinates, basis set and MO vectors from a GAMESS-UK output 
  file.  This has been written with the idea that it might end up in OpenBabel,
  so no use has been made of Qt.  This is currently pretty rudimentary, only
  tested with s and p functions, and only works with rhf.

2010-07-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro/avogadro.pot, i18n/libavogadro/libavogadro.pot: Updated PO
  templates with latest code. Start of monthly sync with Launchpad.

2010-07-07  David Lonie <loniedavid@gmail.com>

  * .../src/extensions/surfaces/orbitaltablemodel.cpp,
  .../src/extensions/surfaces/orbitaltablemodel.h,
  .../src/extensions/surfaces/orbitalwidget.cpp: Use progress bars to show the
  status of the orbital calculations.  Change-Id:
  I96b2bc63a1ba67f6bdb83694fb3cc83da78f78b1

2010-07-07  David C. Lonie <loniedavid@gmail.com>

  * .../src/extensions/surfaces/orbitalextension.cpp,
  .../src/extensions/surfaces/orbitalextension.h,
  .../src/extensions/surfaces/orbitaltablemodel.cpp,
  .../src/extensions/surfaces/orbitaltablemodel.h,
  .../src/extensions/surfaces/orbitalwidget.cpp,
  .../src/extensions/surfaces/orbitalwidget.h: Show progress of orbital
  calculations.

  * libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Add
  options to update the progress of the mesh calculation.

2010-07-07  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Better range for bond radii 
  Old settings of slider don't allow fine tuning of bond radii  Change-Id:
  I434feca70ab82d82f30afb999368d9ecfa7c7965

2010-06-13  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  .../src/extensions/surfaces/orbitalextension.cpp,
  .../src/extensions/surfaces/orbitalextension.h,
  .../extensions/surfaces/orbitalsettingsdialog.cpp,
  .../extensions/surfaces/orbitalsettingsdialog.h,
  .../extensions/surfaces/orbitalsettingsdialog.ui,
  .../src/extensions/surfaces/orbitaltablemodel.cpp,
  .../src/extensions/surfaces/orbitaltablemodel.h,
  .../src/extensions/surfaces/orbitalwidget.cpp,
  .../src/extensions/surfaces/orbitalwidget.h,
  .../src/extensions/surfaces/orbitalwidget.ui,
  .../src/extensions/surfaces/surfaceextension.cpp: Added orbital extension 
  Change-Id: I0cbfb3ebeee716954b5e22ae345fcfb5430d7cd9

2010-07-03  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Removed excessive branching from
  BSDYEngine::radius()  Now radius() function doesn't check if VdW or Covalent
  is used, but calls appropriate function by pointer stored in BSDYEngine,
  which is changed when user switches radius type in UI  Change-Id:
  I967431710154bd3ef717510ac09580d4ecf70a57

2010-07-01  annulen <annulen@yandex.ru>

  * libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/spectra/cd.cpp,
  libavogadro/src/extensions/spectra/dos.cpp,
  libavogadro/src/extensions/spectra/raman.cpp,
  .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  libavogadro/src/extensions/spectra/uv.cpp,
  .../src/extensions/spectra/vibrationwidget.cpp,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/molecule.cpp: Use new OB_VERSION_CHECK macro instead of
  OPENBABEL_IS_NEWER_THAN_2_2_99  New macro OB_VERSION_CHECK allows comparison
  of current OpenBabel version to any given version, not only 2.2.99 (hope the
  next versions will also add functionality)

2010-06-13  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/basisset.cpp,
  libavogadro/src/extensions/surfaces/basisset.h,
  .../src/extensions/surfaces/gaussianfchk.cpp,
  libavogadro/src/extensions/surfaces/gaussianfchk.h,
  .../src/extensions/surfaces/gaussianset.cpp,
  libavogadro/src/extensions/surfaces/gaussianset.h,
  libavogadro/src/extensions/surfaces/molpro.cpp,
  libavogadro/src/extensions/surfaces/molpro.h,
  libavogadro/src/extensions/surfaces/slaterset.cpp,
  libavogadro/src/extensions/surfaces/slaterset.h,
  .../src/extensions/surfaces/surfaceextension.cpp,
  .../src/extensions/surfaces/surfaceextension.h: Created an abstract basis set
  class, and changed old basisset.* to gaussianset.*  Change-Id:
  I77ef8e5ed62cc298ee4f1ae4534b1479d1c7cf79

2010-06-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro.pot,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po, i18n/avogadro/es.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/he.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/nb.po, i18n/avogadro/nl.po,
  i18n/avogadro/oc.po, i18n/avogadro/pl.po, i18n/avogadro/pt.po,
  i18n/avogadro/pt_BR.po, i18n/avogadro/ru.po, i18n/avogadro/sk.po,
  i18n/avogadro/sv.po, i18n/avogadro/tr.po, i18n/avogadro/uk.po,
  i18n/avogadro/zh_CN.po, i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po,
  i18n/libavogadro/bg.po, i18n/libavogadro/ca.po, i18n/libavogadro/cs.po,
  i18n/libavogadro/da.po, i18n/libavogadro/de.po, i18n/libavogadro/el.po,
  i18n/libavogadro/en_CA.po, i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po,
  i18n/libavogadro/fi.po, i18n/libavogadro/fr.po, i18n/libavogadro/he.po,
  i18n/libavogadro/hi.po, i18n/libavogadro/hu.po, i18n/libavogadro/id.po,
  i18n/libavogadro/it.po, i18n/libavogadro/ja.po, i18n/libavogadro/kn.po,
  i18n/libavogadro/ko.po, i18n/libavogadro/libavogadro.pot,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/uk.po, i18n/libavogadro/zh_CN.po,
  i18n/libavogadro/zh_TW.po, i18n/libqperiodictable/ar.po,
  i18n/libqperiodictable/bg.po, i18n/libqperiodictable/ca.po,
  i18n/libqperiodictable/cs.po, i18n/libqperiodictable/da.po,
  i18n/libqperiodictable/de.po, i18n/libqperiodictable/el.po,
  i18n/libqperiodictable/en_CA.po, i18n/libqperiodictable/en_GB.po,
  i18n/libqperiodictable/es.po, i18n/libqperiodictable/fi.po,
  i18n/libqperiodictable/fr.po, i18n/libqperiodictable/he.po,
  i18n/libqperiodictable/hi.po, i18n/libqperiodictable/hu.po,
  i18n/libqperiodictable/id.po, i18n/libqperiodictable/it.po,
  i18n/libqperiodictable/ja.po, i18n/libqperiodictable/kn.po,
  i18n/libqperiodictable/ko.po, i18n/libqperiodictable/libqperiodictable.pot,
  i18n/libqperiodictable/nb.po, i18n/libqperiodictable/nl.po,
  i18n/libqperiodictable/pl.po, i18n/libqperiodictable/pt.po,
  i18n/libqperiodictable/pt_BR.po, i18n/libqperiodictable/ru.po,
  i18n/libqperiodictable/sk.po, i18n/libqperiodictable/sv.po,
  i18n/libqperiodictable/tr.po, i18n/libqperiodictable/uk.po,
  i18n/libqperiodictable/zh_CN.po, i18n/libqperiodictable/zh_TW.po,
  scripts/extract-periodictable-messages.sh: Update with Launchpad
  translations. Merge periodic table messages back into libavogadro
  translations template.

2010-06-07  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/quantuminput/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/CMakeLists.txt: Re-merged from Cryos
  repo, now compiles.

2010-06-01  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Changeable bond labels  Added
  possibility to set custom bond labels in right-click menu of
  selectrotatetool. Some unneeded comments and whitespaces were also removed
  Change-Id:Ib61613ac

2010-05-31  annulen <annulen@yandex.ru>

  * libavogadro/src/elementitem_p.cpp, libavogadro/src/elementitem_p.h: Made
  periodic table proof to missing elements in OB (cell is skipped)  Skip
  element cell if (for some reason) it's symbol is missing in OB table.
  Change-Id:I56a85bbf

  * avogadro.pc.in, avogadro.prf.in: Synchronized pkg-config and qmake
  integration files with recent changes

2010-05-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Fixed the location of the inline hint. 
  Please see http://www.parashift.com/c++-faq-lite/inline-functions.html for
  more details on the correct use of the inline keyword.

2010-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * AvogadroCore.pc.in, AvogadroWidget.pc.in, CMakeLists.txt,
  QPeriodicTable.pc.in, QPlotWidget.pc.in, avogadro/CMakeLists.txt,
  avogadro/src/CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/examples/c++/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/quantuminput/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/tests/CMakeLists.txt: Removed unused files, updated CMake
  syntax/style.  Removed a few files that are not needed anymore. Took a pass
  at the CMake files to update their style, remove superfluous calls, fixed
  indentation and a few other things. Builds successfully on Linux, but it is
  possible that some of the platform dependent code needs more testing.  I am
  not sure what some of the new compiler logic aims to do, and it looks like
  most of that logic should be refactored into a support file. Please let me
  know if you hit any problems.

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/elementdetail_p.cpp, libavogadro/src/elementdetail_p.h,
  libavogadro/src/elementitem_p.cpp, libavogadro/src/elementitem_p.h,
  libavogadro/src/elementtranslator.cpp, libavogadro/src/elementtranslator.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/quantuminput/CMakeLists.txt,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/extensions/spectra/spectradialog.h,
  .../src/extensions/spectra/spectradialog.ui,
  libavogadro/src/extensions/spectra/spectratype.h,
  libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/periodictablescene_p.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/plotaxis.cpp, libavogadro/src/plotaxis.h,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.cpp, libavogadro/src/plotpoint.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h,
  libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/elementtranslator.cpp,
  libavogadro/src/python/periodictableview.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  periodictable/CMakeLists.txt, periodictable/examples/qperiodictable.cpp,
  periodictable/examples/qperiodictable.h,
  periodictable/examples/qperiodictable.pro, periodictable/src/CMakeLists.txt,
  periodictable/src/config.h.in, periodictable/src/elementdetail_p.cpp,
  periodictable/src/elementdetail_p.h, periodictable/src/elementitem_p.cpp,
  periodictable/src/elementitem_p.h, periodictable/src/elementtranslator.cpp,
  periodictable/src/elementtranslator.h, periodictable/src/global.cpp,
  periodictable/src/global.h, periodictable/src/periodictablescene_p.cpp,
  periodictable/src/periodictablescene_p.h,
  periodictable/src/periodictableview.cpp,
  periodictable/src/periodictableview.h, periodictable/src/qperiodictable.cpp,
  periodictable/src/qperiodictable.h, plotwidget/CMakeLists.txt,
  plotwidget/src/CMakeLists.txt, plotwidget/src/global.h,
  plotwidget/src/plotaxis.cpp, plotwidget/src/plotaxis.h,
  plotwidget/src/plotobject.cpp, plotwidget/src/plotobject.h,
  plotwidget/src/plotpoint.cpp, plotwidget/src/plotpoint.h,
  plotwidget/src/plotwidget.cpp, plotwidget/src/plotwidget.h: Restored the old
  source/library structure.  Restored the old source/library structure in
  Avogadro. Note that any headers in libavogadro_HDRS are installed and part of
  our public API. They cannot be removed, nor can any API incompatible changes
  be made. Ideally no ABI incompatible changes can be made either, but for the
  1.1/1.2 cycle this restriction is being waved.  Please be especially wary
  about modifying any of the headers in that list. Look to the list in the 1.0
  release for the released headers that are part of our public API.  I also
  took the opportunity to clean up our CMakeLists.txt files a little, and will
  continue to do so in order to make things a little clearer.

2010-05-23  annulen <annulen@yandex.ru>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Better range for bond radii

  * avogadro/src/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/quantuminput/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Link avogadro-app and plugins to
  modular libraries

2010-05-22  annulen <annulen@yandex.ru>

  * periodictable/src/elementitem_p.cpp, periodictable/src/elementitem_p.h:
  Made periodic table proof to missing elements in OB (cell is skipped)

2010-05-22  annulen <annulen@users.sourceforge.net>

  * CMakeLists.txt, qperiodictable.prf.in, qplotwidget.prf.in: QMake
  integration for periodic table and plot widgets

2010-05-18  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Changing of radii

2010-05-16  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/tools/selectrotatetool.cpp: Support for reading new
  properties from OBAtom

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Added menu items to reset color and
  label

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.h,
  libavogadro/src/tools/selectrotatetool.cpp: Replaced customColor with
  customColorName in Atom  Reasons: 1) there were some crutchy pointers to
  QColor; 2) AvogadroCore shouldn't link with QtGui

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.h: Added new
  overloaded setColor(QString) to Painter class (sets color by name)

2010-05-15  annulen <annulen@users.sourceforge.net>

  * CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Moved condition for RTTI enabling out
  of plugin function definition

  * AvogadroCore.pc.cmake, AvogadroCore.pc.in, AvogadroWidget.pc.cmake,
  AvogadroWidget.pc.in, CMakeLists.txt, QPeriodicTable.pc.in,
  QPlotWidget.pc.in, avogadro.pc.cmake, avogadro.pc.in: Added pkg-config files
  for QPlotWidget and QPeriodicTable

2010-05-13  annulen <annulen@users.sourceforge.net>

  * .../extensions/quantuminput/daltoninputdialog.cpp,
  .../extensions/quantuminput/gamessinputdialog.cpp,
  .../extensions/quantuminput/molproinputdialog.cpp,
  .../extensions/quantuminput/mopacinputdialog.cpp,
  .../extensions/quantuminput/nwcheminputdialog.cpp,
  .../extensions/quantuminput/qcheminputdialog.cpp: quantuminput: removed dead
  code

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, libavogadro/CMakeLists.txt:
  Disable RTTI in plugins, avogadro-app, qperiodictable

  * .../quantuminput/gaussianinputdialog.cpp,
  .../extensions/quantuminput/mopacinputdialog.cpp: Store properties of
  Gaussian and MOPAC in subcategories

  * .../src/extensions/quantuminput/CMakeLists.txt,
  .../extensions/quantuminput/daltoninputdialog.cpp,
  .../extensions/quantuminput/daltoninputdialog.h,
  .../extensions/quantuminput/gamessinputdialog.cpp,
  .../extensions/quantuminput/gamessinputdialog.h,
  .../quantuminput/gaussianinputdialog.cpp,
  .../extensions/quantuminput/gaussianinputdialog.h,
  .../src/extensions/quantuminput/inputdialog.cpp,
  .../src/extensions/quantuminput/inputdialog.h,
  .../extensions/quantuminput/inputfileextension.cpp,
  .../extensions/quantuminput/inputfileextension.h,
  .../extensions/quantuminput/molproinputdialog.cpp,
  .../extensions/quantuminput/molproinputdialog.h,
  .../extensions/quantuminput/mopacinputdialog.cpp,
  .../src/extensions/quantuminput/mopacinputdialog.h,
  .../extensions/quantuminput/nwcheminputdialog.cpp,
  .../extensions/quantuminput/nwcheminputdialog.h,
  .../extensions/quantuminput/qcheminputdialog.cpp,
  .../src/extensions/quantuminput/qcheminputdialog.h: Derived all input dialogs
  from common base, use shared file save function (with exception of Gaussian),
  store dialogs in hash

2010-05-07  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/quantuminput/daltoninputdialog.h,
  libavogadro/src/extensions/quantuminput/gaussianinputdialog.h,
  libavogadro/src/extensions/quantuminput/molproinputdialog.h,
  libavogadro/src/extensions/quantuminput/mopacinputdialog.h,
  libavogadro/src/extensions/quantuminput/nwcheminputdialog.h,
  libavogadro/src/extensions/quantuminput/qcheminputdialog.h: Removed redundant
  headers from input dialogs

  * .../extensions/quantuminput/molproinputdialog.cpp,
  .../extensions/quantuminput/molproinputdialog.h,
  .../extensions/quantuminput/molproinputdialog.ui: Fixed compatibility of
  Molpro dialog with Molpro 2009.1

2010-05-06  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Can change colors of atoms

2010-05-05  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Can change labels

2010-05-03  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Fixed inline declaration

2010-04-28  annulen <annulen@yandex.ru>

  * .../extensions/quantuminput/gamessinputdialog.cpp,
  .../extensions/quantuminput/gamessinputdialog.h: Save path of job export
  directory for Gamess (PR#2883170)

2010-04-27  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/bg.po,
  i18n/avogadro/ca.po, i18n/avogadro/cs.po, i18n/avogadro/da.po,
  i18n/avogadro/de.po, i18n/avogadro/el.po, i18n/avogadro/en_CA.po,
  i18n/avogadro/en_GB.po, i18n/avogadro/es.po, i18n/avogadro/fi.po,
  i18n/avogadro/fr.po, i18n/avogadro/he.po, i18n/avogadro/hr.po,
  i18n/avogadro/hu.po, i18n/avogadro/id.po, i18n/avogadro/it.po,
  i18n/avogadro/ja.po, i18n/avogadro/kn.po, i18n/avogadro/ko.po,
  i18n/avogadro/nb.po, i18n/avogadro/nl.po, i18n/avogadro/oc.po,
  i18n/avogadro/pl.po, i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po,
  i18n/avogadro/ru.po, i18n/avogadro/sk.po, i18n/avogadro/sv.po,
  i18n/avogadro/tr.po, i18n/avogadro/uk.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/ca.po, i18n/libavogadro/cs.po, i18n/libavogadro/da.po,
  i18n/libavogadro/de.po, i18n/libavogadro/el.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/fi.po,
  i18n/libavogadro/fr.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/oc.po,
  i18n/libavogadro/pl.po, i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po,
  i18n/libavogadro/ru.po, i18n/libavogadro/sk.po, i18n/libavogadro/sv.po,
  i18n/libavogadro/tr.po, i18n/libavogadro/uk.po, i18n/libavogadro/zh_CN.po,
  i18n/libavogadro/zh_TW.po, i18n/libqperiodictable/ar.po,
  i18n/libqperiodictable/bg.po, i18n/libqperiodictable/ca.po,
  i18n/libqperiodictable/cs.po, i18n/libqperiodictable/da.po,
  i18n/libqperiodictable/de.po, i18n/libqperiodictable/el.po,
  i18n/libqperiodictable/en_CA.po, i18n/libqperiodictable/en_GB.po,
  i18n/libqperiodictable/es.po, i18n/libqperiodictable/fi.po,
  i18n/libqperiodictable/fr.po, i18n/libqperiodictable/he.po,
  i18n/libqperiodictable/hi.po, i18n/libqperiodictable/hu.po,
  i18n/libqperiodictable/id.po, i18n/libqperiodictable/it.po,
  i18n/libqperiodictable/ja.po, i18n/libqperiodictable/kn.po,
  i18n/libqperiodictable/ko.po, i18n/libqperiodictable/nb.po,
  i18n/libqperiodictable/nl.po, i18n/libqperiodictable/pl.po,
  i18n/libqperiodictable/pt.po, i18n/libqperiodictable/pt_BR.po,
  i18n/libqperiodictable/ru.po, i18n/libqperiodictable/sk.po,
  i18n/libqperiodictable/sv.po, i18n/libqperiodictable/tr.po,
  i18n/libqperiodictable/uk.po, i18n/libqperiodictable/zh_CN.po,
  i18n/libqperiodictable/zh_TW.po: Launchpad update.

2010-04-26  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, cmake/modules/FindLinguist.cmake,
  i18n/avogadro/af.po, i18n/avogadro/ar.po, i18n/avogadro/avogadro-af.po,
  i18n/avogadro/avogadro-ar.po, i18n/avogadro/avogadro-bg.po,
  i18n/avogadro/avogadro-ca.po, i18n/avogadro/avogadro-cs.po,
  i18n/avogadro/avogadro-da.po, i18n/avogadro/avogadro-de.po,
  i18n/avogadro/avogadro-el.po, i18n/avogadro/avogadro-en_CA.po,
  i18n/avogadro/avogadro-en_GB.po, i18n/avogadro/avogadro-es.po,
  i18n/avogadro/avogadro-fi.po, i18n/avogadro/avogadro-fr.po,
  i18n/avogadro/avogadro-he.po, i18n/avogadro/avogadro-hr.po,
  i18n/avogadro/avogadro-hu.po, i18n/avogadro/avogadro-id.po,
  i18n/avogadro/avogadro-it.po, i18n/avogadro/avogadro-ja.po,
  i18n/avogadro/avogadro-kn.po, i18n/avogadro/avogadro-ko.po,
  i18n/avogadro/avogadro-nb.po, i18n/avogadro/avogadro-nl.po,
  i18n/avogadro/avogadro-pl.po, i18n/avogadro/avogadro-pt.po,
  i18n/avogadro/avogadro-pt_BR.po, i18n/avogadro/avogadro-ru.po,
  i18n/avogadro/avogadro-sk.po, i18n/avogadro/avogadro-sv.po,
  i18n/avogadro/avogadro-tr.po, i18n/avogadro/avogadro-uk.po,
  i18n/avogadro/avogadro-zh_CN.po, i18n/avogadro/avogadro-zh_TW.po,
  i18n/avogadro/bg.po, i18n/avogadro/ca.po, i18n/avogadro/cs.po,
  i18n/avogadro/da.po, i18n/avogadro/de.po, i18n/avogadro/el.po,
  i18n/avogadro/en_CA.po, i18n/avogadro/en_GB.po, i18n/avogadro/es.po,
  i18n/avogadro/fi.po, i18n/avogadro/fr.po, i18n/avogadro/he.po,
  i18n/avogadro/hr.po, i18n/avogadro/hu.po, i18n/avogadro/id.po,
  i18n/avogadro/it.po, i18n/avogadro/ja.po, i18n/avogadro/kn.po,
  i18n/avogadro/ko.po, i18n/avogadro/nb.po, i18n/avogadro/nl.po,
  i18n/avogadro/pl.po, i18n/avogadro/pt.po, i18n/avogadro/pt_BR.po,
  i18n/avogadro/ru.po, i18n/avogadro/sk.po, i18n/avogadro/sv.po,
  i18n/avogadro/tr.po, i18n/avogadro/uk.po, i18n/avogadro/zh_CN.po,
  i18n/avogadro/zh_TW.po, i18n/libavogadro/ar.po, i18n/libavogadro/bg.po,
  i18n/libavogadro/ca.po, i18n/libavogadro/cs.po, i18n/libavogadro/da.po,
  i18n/libavogadro/de.po, i18n/libavogadro/el.po, i18n/libavogadro/en_CA.po,
  i18n/libavogadro/en_GB.po, i18n/libavogadro/es.po, i18n/libavogadro/fi.po,
  i18n/libavogadro/fr.po, i18n/libavogadro/he.po, i18n/libavogadro/hi.po,
  i18n/libavogadro/hu.po, i18n/libavogadro/id.po, i18n/libavogadro/it.po,
  i18n/libavogadro/ja.po, i18n/libavogadro/kn.po, i18n/libavogadro/ko.po,
  i18n/libavogadro/libavogadro-ar.po, i18n/libavogadro/libavogadro-bg.po,
  i18n/libavogadro/libavogadro-ca.po, i18n/libavogadro/libavogadro-cs.po,
  i18n/libavogadro/libavogadro-da.po, i18n/libavogadro/libavogadro-de.po,
  i18n/libavogadro/libavogadro-el.po, i18n/libavogadro/libavogadro-en_CA.po,
  i18n/libavogadro/libavogadro-en_GB.po, i18n/libavogadro/libavogadro-es.po,
  i18n/libavogadro/libavogadro-fi.po, i18n/libavogadro/libavogadro-fr.po,
  i18n/libavogadro/libavogadro-he.po, i18n/libavogadro/libavogadro-hi.po,
  i18n/libavogadro/libavogadro-hu.po, i18n/libavogadro/libavogadro-id.po,
  i18n/libavogadro/libavogadro-it.po, i18n/libavogadro/libavogadro-ja.po,
  i18n/libavogadro/libavogadro-kn.po, i18n/libavogadro/libavogadro-ko.po,
  i18n/libavogadro/libavogadro-nb.po, i18n/libavogadro/libavogadro-nl.po,
  i18n/libavogadro/libavogadro-pl.po, i18n/libavogadro/libavogadro-pt.po,
  i18n/libavogadro/libavogadro-pt_BR.po, i18n/libavogadro/libavogadro-ru.po,
  i18n/libavogadro/libavogadro-sk.po, i18n/libavogadro/libavogadro-sv.po,
  i18n/libavogadro/libavogadro-tr.po, i18n/libavogadro/libavogadro-uk.po,
  i18n/libavogadro/libavogadro-zh_CN.po, i18n/libavogadro/libavogadro-zh_TW.po,
  i18n/libavogadro/nb.po, i18n/libavogadro/nl.po, i18n/libavogadro/pl.po,
  i18n/libavogadro/pt.po, i18n/libavogadro/pt_BR.po, i18n/libavogadro/ru.po,
  i18n/libavogadro/sk.po, i18n/libavogadro/sv.po, i18n/libavogadro/tr.po,
  i18n/libavogadro/uk.po, i18n/libavogadro/zh_CN.po, i18n/libavogadro/zh_TW.po,
  i18n/libqperiodictable/ar.po, i18n/libqperiodictable/bg.po,
  i18n/libqperiodictable/ca.po, i18n/libqperiodictable/cs.po,
  i18n/libqperiodictable/da.po, i18n/libqperiodictable/de.po,
  i18n/libqperiodictable/el.po, i18n/libqperiodictable/en_CA.po,
  i18n/libqperiodictable/en_GB.po, i18n/libqperiodictable/es.po,
  i18n/libqperiodictable/fi.po, i18n/libqperiodictable/fr.po,
  i18n/libqperiodictable/he.po, i18n/libqperiodictable/hi.po,
  i18n/libqperiodictable/hu.po, i18n/libqperiodictable/id.po,
  i18n/libqperiodictable/it.po, i18n/libqperiodictable/ja.po,
  i18n/libqperiodictable/kn.po, i18n/libqperiodictable/ko.po,
  i18n/libqperiodictable/libqperiodictable-ar.po,
  i18n/libqperiodictable/libqperiodictable-bg.po,
  i18n/libqperiodictable/libqperiodictable-ca.po,
  i18n/libqperiodictable/libqperiodictable-cs.po,
  i18n/libqperiodictable/libqperiodictable-da.po,
  i18n/libqperiodictable/libqperiodictable-de.po,
  i18n/libqperiodictable/libqperiodictable-el.po,
  i18n/libqperiodictable/libqperiodictable-en_CA.po,
  i18n/libqperiodictable/libqperiodictable-en_GB.po,
  i18n/libqperiodictable/libqperiodictable-es.po,
  i18n/libqperiodictable/libqperiodictable-fi.po,
  i18n/libqperiodictable/libqperiodictable-fr.po,
  i18n/libqperiodictable/libqperiodictable-he.po,
  i18n/libqperiodictable/libqperiodictable-hi.po,
  i18n/libqperiodictable/libqperiodictable-hu.po,
  i18n/libqperiodictable/libqperiodictable-id.po,
  i18n/libqperiodictable/libqperiodictable-it.po,
  i18n/libqperiodictable/libqperiodictable-ja.po,
  i18n/libqperiodictable/libqperiodictable-kn.po,
  i18n/libqperiodictable/libqperiodictable-ko.po,
  i18n/libqperiodictable/libqperiodictable-nb.po,
  i18n/libqperiodictable/libqperiodictable-nl.po,
  i18n/libqperiodictable/libqperiodictable-pl.po,
  i18n/libqperiodictable/libqperiodictable-pt.po,
  i18n/libqperiodictable/libqperiodictable-pt_BR.po,
  i18n/libqperiodictable/libqperiodictable-ru.po,
  i18n/libqperiodictable/libqperiodictable-sk.po,
  i18n/libqperiodictable/libqperiodictable-sv.po,
  i18n/libqperiodictable/libqperiodictable-tr.po,
  i18n/libqperiodictable/libqperiodictable-uk.po,
  i18n/libqperiodictable/libqperiodictable-zh_CN.po,
  i18n/libqperiodictable/libqperiodictable-zh_TW.po,
  i18n/libqperiodictable/nb.po, i18n/libqperiodictable/nl.po,
  i18n/libqperiodictable/pl.po, i18n/libqperiodictable/pt.po,
  i18n/libqperiodictable/pt_BR.po, i18n/libqperiodictable/ru.po,
  i18n/libqperiodictable/sk.po, i18n/libqperiodictable/sv.po,
  i18n/libqperiodictable/tr.po, i18n/libqperiodictable/uk.po,
  i18n/libqperiodictable/zh_CN.po, i18n/libqperiodictable/zh_TW.po,
  libavogadro/src/CMakeLists.txt, periodictable/src/CMakeLists.txt: Moved
  translations to handle Launchpad sync.

  * libavogadro/src/camera.cpp, libavogadro/src/color.cpp,
  libavogadro/src/glpainter_p.cpp: Not sure why GL/gl.h is needed here, it
  should be found through QtOpenGL.

  * i18n/avogadro/avogadro-af.po, i18n/avogadro/avogadro-ar.po,
  i18n/avogadro/avogadro-bg.po, i18n/avogadro/avogadro-ca.po,
  i18n/avogadro/avogadro-cs.po, i18n/avogadro/avogadro-da.po,
  i18n/avogadro/avogadro-de.po, i18n/avogadro/avogadro-el.po,
  i18n/avogadro/avogadro-en_CA.po, i18n/avogadro/avogadro-en_GB.po,
  i18n/avogadro/avogadro-es.po, i18n/avogadro/avogadro-fi.po,
  i18n/avogadro/avogadro-fr.po, i18n/avogadro/avogadro-he.po,
  i18n/avogadro/avogadro-hr.po, i18n/avogadro/avogadro-hu.po,
  i18n/avogadro/avogadro-id.po, i18n/avogadro/avogadro-it.po,
  i18n/avogadro/avogadro-ja.po, i18n/avogadro/avogadro-kn.po,
  i18n/avogadro/avogadro-ko.po, i18n/avogadro/avogadro-nb.po,
  i18n/avogadro/avogadro-nl.po, i18n/avogadro/avogadro-pl.po,
  i18n/avogadro/avogadro-pt.po, i18n/avogadro/avogadro-pt_BR.po,
  i18n/avogadro/avogadro-ru.po, i18n/avogadro/avogadro-sk.po,
  i18n/avogadro/avogadro-sv.po, i18n/avogadro/avogadro-tr.po,
  i18n/avogadro/avogadro-uk.po, i18n/avogadro/avogadro-zh_CN.po,
  i18n/avogadro/avogadro-zh_TW.po, i18n/avogadro/avogadro.pot,
  i18n/libavogadro/libavogadro-ar.po, i18n/libavogadro/libavogadro-bg.po,
  i18n/libavogadro/libavogadro-ca.po, i18n/libavogadro/libavogadro-cs.po,
  i18n/libavogadro/libavogadro-da.po, i18n/libavogadro/libavogadro-de.po,
  i18n/libavogadro/libavogadro-el.po, i18n/libavogadro/libavogadro-en_CA.po,
  i18n/libavogadro/libavogadro-en_GB.po, i18n/libavogadro/libavogadro-es.po,
  i18n/libavogadro/libavogadro-fi.po, i18n/libavogadro/libavogadro-fr.po,
  i18n/libavogadro/libavogadro-he.po, i18n/libavogadro/libavogadro-hi.po,
  i18n/libavogadro/libavogadro-hu.po, i18n/libavogadro/libavogadro-id.po,
  i18n/libavogadro/libavogadro-it.po, i18n/libavogadro/libavogadro-ja.po,
  i18n/libavogadro/libavogadro-kn.po, i18n/libavogadro/libavogadro-ko.po,
  i18n/libavogadro/libavogadro-nb.po, i18n/libavogadro/libavogadro-nl.po,
  i18n/libavogadro/libavogadro-pl.po, i18n/libavogadro/libavogadro-pt.po,
  i18n/libavogadro/libavogadro-pt_BR.po, i18n/libavogadro/libavogadro-ru.po,
  i18n/libavogadro/libavogadro-sk.po, i18n/libavogadro/libavogadro-sv.po,
  i18n/libavogadro/libavogadro-tr.po, i18n/libavogadro/libavogadro-uk.po,
  i18n/libavogadro/libavogadro-zh_CN.po, i18n/libavogadro/libavogadro-zh_TW.po,
  i18n/libavogadro/libavogadro.pot,
  i18n/libqperiodictable/libqperiodictable-ar.po,
  i18n/libqperiodictable/libqperiodictable-bg.po,
  i18n/libqperiodictable/libqperiodictable-ca.po,
  i18n/libqperiodictable/libqperiodictable-cs.po,
  i18n/libqperiodictable/libqperiodictable-da.po,
  i18n/libqperiodictable/libqperiodictable-de.po,
  i18n/libqperiodictable/libqperiodictable-el.po,
  i18n/libqperiodictable/libqperiodictable-en_CA.po,
  i18n/libqperiodictable/libqperiodictable-en_GB.po,
  i18n/libqperiodictable/libqperiodictable-es.po,
  i18n/libqperiodictable/libqperiodictable-fi.po,
  i18n/libqperiodictable/libqperiodictable-fr.po,
  i18n/libqperiodictable/libqperiodictable-he.po,
  i18n/libqperiodictable/libqperiodictable-hi.po,
  i18n/libqperiodictable/libqperiodictable-hu.po,
  i18n/libqperiodictable/libqperiodictable-id.po,
  i18n/libqperiodictable/libqperiodictable-it.po,
  i18n/libqperiodictable/libqperiodictable-ja.po,
  i18n/libqperiodictable/libqperiodictable-kn.po,
  i18n/libqperiodictable/libqperiodictable-ko.po,
  i18n/libqperiodictable/libqperiodictable-nb.po,
  i18n/libqperiodictable/libqperiodictable-nl.po,
  i18n/libqperiodictable/libqperiodictable-pl.po,
  i18n/libqperiodictable/libqperiodictable-pt.po,
  i18n/libqperiodictable/libqperiodictable-pt_BR.po,
  i18n/libqperiodictable/libqperiodictable-ru.po,
  i18n/libqperiodictable/libqperiodictable-sk.po,
  i18n/libqperiodictable/libqperiodictable-sv.po,
  i18n/libqperiodictable/libqperiodictable-tr.po,
  i18n/libqperiodictable/libqperiodictable-uk.po,
  i18n/libqperiodictable/libqperiodictable-zh_CN.po,
  i18n/libqperiodictable/libqperiodictable-zh_TW.po,
  i18n/libqperiodictable/libqperiodictable.pot: Updated translations for
  Launchpad. (Will these be auto-imported?)

  * scripts/extract-application-messages.sh,
  scripts/extract-library-messages.sh,
  scripts/extract-periodictable-messages.sh: Updated scripts to mark obsolete
  messages.

2010-04-23  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/tools/drawtool.cpp, periodictable/src/global.cpp,
  periodictable/src/global.h, periodictable/src/qperiodictable.cpp: Load
  translation of periodic table when used

  * libavogadro/src/CMakeLists.txt, periodictable/src/CMakeLists.txt: Process
  and install periodictable i18n

  * i18n/libqperiodictable/libqperiodictable-ar.po,
  i18n/libqperiodictable/libqperiodictable-bg.po,
  i18n/libqperiodictable/libqperiodictable-ca.po,
  i18n/libqperiodictable/libqperiodictable-cs.po,
  i18n/libqperiodictable/libqperiodictable-da.po,
  i18n/libqperiodictable/libqperiodictable-de.po,
  i18n/libqperiodictable/libqperiodictable-el.po,
  i18n/libqperiodictable/libqperiodictable-en_CA.po,
  i18n/libqperiodictable/libqperiodictable-en_GB.po,
  i18n/libqperiodictable/libqperiodictable-es.po,
  i18n/libqperiodictable/libqperiodictable-fi.po,
  i18n/libqperiodictable/libqperiodictable-fr.po,
  i18n/libqperiodictable/libqperiodictable-he.po,
  i18n/libqperiodictable/libqperiodictable-hi.po,
  i18n/libqperiodictable/libqperiodictable-hu.po,
  i18n/libqperiodictable/libqperiodictable-id.po,
  i18n/libqperiodictable/libqperiodictable-it.po,
  i18n/libqperiodictable/libqperiodictable-ja.po,
  i18n/libqperiodictable/libqperiodictable-kn.po,
  i18n/libqperiodictable/libqperiodictable-ko.po,
  i18n/libqperiodictable/libqperiodictable-nb.po,
  i18n/libqperiodictable/libqperiodictable-nl.po,
  i18n/libqperiodictable/libqperiodictable-pl.po,
  i18n/libqperiodictable/libqperiodictable-pt.po,
  i18n/libqperiodictable/libqperiodictable-pt_BR.po,
  i18n/libqperiodictable/libqperiodictable-ru.po,
  i18n/libqperiodictable/libqperiodictable-sk.po,
  i18n/libqperiodictable/libqperiodictable-sv.po,
  i18n/libqperiodictable/libqperiodictable-tr.po,
  i18n/libqperiodictable/libqperiodictable-uk.po,
  i18n/libqperiodictable/libqperiodictable-zh_CN.po,
  i18n/libqperiodictable/libqperiodictable-zh_TW.po, scripts/clean-po.sh:
  tripped unnecessary strings from periodictable po's

  * i18n/libqperiodictable/libqperiodictable-ar.po,
  i18n/libqperiodictable/libqperiodictable-bg.po,
  i18n/libqperiodictable/libqperiodictable-ca.po,
  i18n/libqperiodictable/libqperiodictable-cs.po,
  i18n/libqperiodictable/libqperiodictable-da.po,
  i18n/libqperiodictable/libqperiodictable-de.po,
  i18n/libqperiodictable/libqperiodictable-el.po,
  i18n/libqperiodictable/libqperiodictable-en_CA.po,
  i18n/libqperiodictable/libqperiodictable-en_GB.po,
  i18n/libqperiodictable/libqperiodictable-es.po,
  i18n/libqperiodictable/libqperiodictable-fi.po,
  i18n/libqperiodictable/libqperiodictable-fr.po,
  i18n/libqperiodictable/libqperiodictable-he.po,
  i18n/libqperiodictable/libqperiodictable-hi.po,
  i18n/libqperiodictable/libqperiodictable-hu.po,
  i18n/libqperiodictable/libqperiodictable-id.po,
  i18n/libqperiodictable/libqperiodictable-it.po,
  i18n/libqperiodictable/libqperiodictable-ja.po,
  i18n/libqperiodictable/libqperiodictable-kn.po,
  i18n/libqperiodictable/libqperiodictable-ko.po,
  i18n/libqperiodictable/libqperiodictable-nb.po,
  i18n/libqperiodictable/libqperiodictable-nl.po,
  i18n/libqperiodictable/libqperiodictable-pl.po,
  i18n/libqperiodictable/libqperiodictable-pt.po,
  i18n/libqperiodictable/libqperiodictable-pt_BR.po,
  i18n/libqperiodictable/libqperiodictable-ru.po,
  i18n/libqperiodictable/libqperiodictable-sk.po,
  i18n/libqperiodictable/libqperiodictable-sv.po,
  i18n/libqperiodictable/libqperiodictable-tr.po,
  i18n/libqperiodictable/libqperiodictable-uk.po,
  i18n/libqperiodictable/libqperiodictable-zh_CN.po,
  i18n/libqperiodictable/libqperiodictable-zh_TW.po,
  i18n/libqperiodictable/libqperiodictable.pot: i18n for periodictable - taken
  from libavogadro, updated with script

2010-04-22  Konstantin Annulen Tokarev <kostya@localhost.localdomain>

  * avogadro/src/CMakeLists.txt, cmake/modules/PythonDeps.cmake,
  libavogadro/src/camera.cpp, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/color.cpp,
  libavogadro/src/python/elementtranslator.cpp,
  libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/periodictableview.cpp,
  libavogadro/src/python/qlist.cpp: Fixed compilation with Python and GLEW
  (gl.h must always go after glew.h)

2010-04-22  annulen <annulen@yandex.ru>

  * libavogadro/src/glwidget.h, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Removed unnecessary
  <avogadro/glhit.h> from glwidget.h

  * AvogadroCore.pc.cmake, AvogadroWidget.pc.cmake, CMakeLists.txt,
  avogadro.pc.cmake: Pkg-config files

  * CMakeLists.txt, avogadro.prf.in, avopkg.in: Use @prefix@ instead of
  $prefix$, use it in .prf too (for superpackage)

2010-04-22  annulen <annulen@users.sourceforge.net>

  * i18n/libqperiodictable/libqperiodictable.pot,
  scripts/extract-periodictable-messages.sh: Added i18n files for periodictable

  * cmake/modules/AvogadroUse.cmake, cmake/modules/FindAvogadro.cmake: Use new
  modules for linking of 3rd party extensions

  * cmake/modules/PythonDeps.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt: Fixed build with Python

2010-04-21  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.h: Draw text only
  through painter

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Fix headers

  * libavogadro/src/glpainter_p.cpp, libavogadro/src/glpainter_p.h: Inlines

  * libavogadro/src/CMakeLists.txt, periodictable/src/CMakeLists.txt: Separated
  libAvogadroCore; new header directories

  * CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Moved dependencies to correct places

2010-04-20  Konstantin Annulen Tokarev <kostya@localhost.localdomain>

  * CMakeLists.txt, avopkg.in: Set "$prefix$" as AVOPKG_PREFIX in bundle
  installation

  * CMakeLists.txt, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/spectra/abstract_ir.h,
  libavogadro/src/extensions/spectra/cd.h,
  libavogadro/src/extensions/spectra/dos.h,
  libavogadro/src/extensions/spectra/nmr.h,
  .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  .../src/extensions/spectra/spectradialog.ui,
  libavogadro/src/extensions/spectra/spectratype.cpp,
  libavogadro/src/extensions/spectra/spectratype.h,
  libavogadro/src/extensions/spectra/uv.h, libavogadro/src/tools/drawtool.cpp,
  periodictable/src/CMakeLists.txt, periodictable/src/elementtranslator.h,
  periodictable/src/global.h, periodictable/src/periodictableexport.h,
  periodictable/src/periodictableview.h, periodictable/src/qperiodictable.cpp,
  periodictable/src/qperiodictable.h, plotwidget/src/CMakeLists.txt,
  plotwidget/src/global.h, plotwidget/src/plotaxis.h,
  plotwidget/src/plotexport.h, plotwidget/src/plotobject.h,
  plotwidget/src/plotpoint.h, plotwidget/src/plotwidget.h: Moved headers of
  plotwidget and periodictable to separate directories; preserved copies in
  /avogadro for compatibility

2010-04-20  annulen <annulen@yandex.ru>

  * periodictable/src/elementtranslator.h,
  periodictable/src/periodictableexport.h,
  periodictable/src/periodictableview.h, periodictable/src/qperiodictable.cpp:
  Replaced global.h in periodictable

  * plotwidget/src/plotaxis.h, plotwidget/src/plotexport.h,
  plotwidget/src/plotobject.h, plotwidget/src/plotwidget.h: Unbinded plotwidget
  from avogadro's global.h

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: propextension: Fixed highlight in
  localized versions  Made atom/bond/angle/... numbers the last fields in table
  headers

2010-04-20  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectra/abstract_ir.cpp,
  libavogadro/src/extensions/spectra/abstract_ir.h,
  libavogadro/src/extensions/spectra/ir.cpp,
  libavogadro/src/extensions/spectra/raman.cpp,
  libavogadro/src/extensions/spectra/spectratype.cpp,
  libavogadro/src/extensions/spectra/spectratype.h,
  libavogadro/src/extensions/spectra/tab_ir_raman.ui: Threshold for peal labels

  * libavogadro/src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  libavogadro/src/extensions/spectra/spectradialog.ui:
  s/push_customize/push_advanced

  * libavogadro/src/extensions/spectra/abstract_ir.cpp,
  libavogadro/src/extensions/spectra/abstract_ir.h,
  libavogadro/src/extensions/spectra/ir.cpp,
  libavogadro/src/extensions/spectra/raman.cpp,
  libavogadro/src/extensions/spectra/spectratype.cpp: Refactored IR and Raman:
  merged line/gaussian generation, gaussian labeling

2010-04-19  annulen <annulen@users.sourceforge.net>

  * plotwidget/CMakeLists.txt, plotwidget/src/CMakeLists.txt: CMake files for
  plotwidget

2010-04-18  annulen <annulen@users.sourceforge.net>

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/plotaxis.cpp, libavogadro/src/plotaxis.h,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.cpp, libavogadro/src/plotpoint.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h,
  plotwidget/src/plotaxis.cpp, plotwidget/src/plotaxis.h,
  plotwidget/src/plotobject.cpp, plotwidget/src/plotobject.h,
  plotwidget/src/plotpoint.cpp, plotwidget/src/plotpoint.h,
  plotwidget/src/plotwidget.cpp, plotwidget/src/plotwidget.h: Separated
  libQPlotWidget

  * libavogadro/src/extensions/spectra/ir.cpp,
  .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: PlotWidget:
  somewhat improved placement of labels

2010-04-17  annulen <annulen@users.sourceforge.net>

  * avopkg.in, doc/avopkg.1: Avopkg: query mode

  * avopkg.in, doc/avopkg.1: Avopkg: manpage, exit code

  * CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Used -fvisibility=hidden for Intel
  compiler with exception of forcefield-related files

2010-04-13  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt:
  Added link libraries necessary to link.  The Avogadro library needs to link
  to the OpenGL library as it uses OpenGL symbols, also the shader extension
  must link to the GLEW library as functions from that library are used in it.
  These issues caused link failures on my Linux system at least.

2010-04-12  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/CMakeLists.txt, periodictable/src/elementdetail_p.cpp,
  periodictable/src/elementitem_p.cpp,
  periodictable/src/periodictablescene_p.cpp,
  periodictable/src/qperiodictable.cpp, periodictable/src/qperiodictable.h:
  Fixed compile errors on Mac.

  * libavogadro/src/extensions/insertpeptidedialog.ui,
  libavogadro/src/extensions/insertpeptideextension.cpp: Added 3-10 and pi
  helices

2010-04-06  annulen <annulen@users.sourceforge.net>

  * scripts/cc, scripts/cxx: Added "compilers" for use gcc with ccache

  * CMakeLists.txt, cmake/modules/FindLinguist.cmake: Make possible choice of
  one language for i18n to be build and installed

2010-04-05  Konstantin Annulen Tokarev <kostya@localhost.localdomain>

  * CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  periodictable/src/CMakeLists.txt: Fixed superpackage build

2010-04-05  annulen <annulen@users.sourceforge.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  cmake/modules/FindLinguist.cmake, libavogadro/src/CMakeLists.txt:
  FindLinguist: don't fail if not required

2010-04-04  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/extensions/surfaces/surfacedialog.cpp: Fixed broken connects
  on stratup

  * periodictable/src/CMakeLists.txt, periodictable/src/config.h.in,
  periodictable/src/qperiodictable.cpp, periodictable/src/qperiodictable.h:
  Added qperiodictable executable to the main build system

2010-04-03  annulen <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectra/ir.cpp,
  libavogadro/src/extensions/spectra/nmr.cpp,
  libavogadro/src/extensions/spectra/raman.cpp,
  libavogadro/src/extensions/spectra/spectratype.cpp,
  libavogadro/src/extensions/spectra/spectratype.h: Moved Gaussian widening
  algorithm to spectratype base class

2010-04-03  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/qtiocompressor/qtiocompressor.cpp,
  libavogadro/qtiocompressor/qtiocompressor.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/molpro.cpp, libavogadro/src/extensions/molpro.h,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h,
  libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfacedialog.ui,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/extensions/surfaceextension.h,
  libavogadro/src/extensions/surfaces/CMakeLists.txt,
  libavogadro/src/extensions/surfaces/basisset.cpp,
  libavogadro/src/extensions/surfaces/basisset.h,
  .../src/extensions/surfaces/gaussianfchk.cpp,
  libavogadro/src/extensions/surfaces/gaussianfchk.h,
  libavogadro/src/extensions/surfaces/molpro.cpp,
  libavogadro/src/extensions/surfaces/molpro.h,
  libavogadro/src/extensions/surfaces/mopacaux.cpp,
  libavogadro/src/extensions/surfaces/mopacaux.h,
  .../surfaces/qtiocompressor/qtiocompressor.cpp,
  .../surfaces/qtiocompressor/qtiocompressor.h,
  libavogadro/src/extensions/surfaces/slaterset.cpp,
  libavogadro/src/extensions/surfaces/slaterset.h,
  .../src/extensions/surfaces/surfacedialog.cpp,
  .../src/extensions/surfaces/surfacedialog.h,
  .../src/extensions/surfaces/surfacedialog.ui,
  .../src/extensions/surfaces/surfaceextension.cpp,
  .../src/extensions/surfaces/surfaceextension.h,
  libavogadro/src/extensions/surfaces/vdwsurface.cpp,
  libavogadro/src/extensions/surfaces/vdwsurface.h,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vdwsurface.h: Separated surfaces, moved
  qtiocompressor there

  * libavogadro/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt, periodictable/src/CMakeLists.txt:
  Excessive linking

  * avogadro/gl2ps/COPYING.GL2PS, avogadro/gl2ps/COPYING.LGPL,
  avogadro/gl2ps/README.txt, avogadro/gl2ps/TODO.txt, avogadro/gl2ps/gl2ps.c,
  avogadro/gl2ps/gl2ps.h, avogadro/gl2ps/gl2ps.pdf, avogadro/gl2ps/gl2psTest.c,
  avogadro/gl2ps/gl2psTestSimple.c, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, libavogadro/gl2ps/COPYING.GL2PS,
  libavogadro/gl2ps/COPYING.LGPL, libavogadro/gl2ps/README.txt,
  libavogadro/gl2ps/TODO.txt, libavogadro/gl2ps/gl2ps.c,
  libavogadro/gl2ps/gl2ps.h, libavogadro/gl2ps/gl2ps.pdf,
  libavogadro/gl2ps/gl2psTest.c, libavogadro/gl2ps/gl2psTestSimple.c,
  libavogadro/src/CMakeLists.txt: Moved gl2ps into libavogadro; some excessive
  linking fixes

2010-04-02  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/quantuminput/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt: Removed some excessive
  linking

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: labelengine: restored font
  button, polished ui

2010-04-01  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * .../extensions/quantuminput/gaussianinputdialog.ui,
  .../extensions/quantuminput/molproinputdialog.ui,
  .../extensions/quantuminput/mopacinputdialog.ui,
  .../extensions/quantuminput/nwcheminputdialog.ui,
  .../extensions/quantuminput/qcheminputdialog.ui: Killed translation of some
  basis set combos

2010-04-01  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Improved labels settings

  * periodictable/examples/Makefile, periodictable/examples/main.cpp,
  periodictable/examples/qperiodictable.cpp,
  periodictable/examples/qperiodictable.h,
  periodictable/examples/qperiodictable.pro: Improved periodic table
  (standalone)

2010-03-31  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avogadro.prf.in, cmake/modules/AvogadroUse.cmake: Integrated avopkg into
  build system of 3rd party plugin (targets manifest, package, install)

  * periodictable/examples/Makefile, periodictable/examples/main.cpp,
  periodictable/examples/periodictable: Standalone periodic table (prototype)

  * examples/c++/CMakeLists.txt, examples/c++/templateextension.cpp,
  examples/c++/templateextension.h, examples/c++/templateextension.pro,
  examples/python/extensiontemplate.py, examples/python/proteinextension.py,
  examples/python/standalone.py, examples/python/tooltemplate.py,
  libavogadro/examples/c++/CMakeLists.txt,
  libavogadro/examples/c++/templateextension.cpp,
  libavogadro/examples/c++/templateextension.h,
  libavogadro/examples/c++/templateextension.pro,
  libavogadro/examples/python/extensiontemplate.py,
  libavogadro/examples/python/proteinextension.py,
  libavogadro/examples/python/standalone.py,
  libavogadro/examples/python/tooltemplate.py: C++ and Python examples belong
  to libavogadro => moved to its directory

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/elementdetail_p.cpp, libavogadro/src/elementdetail_p.h,
  libavogadro/src/elementitem_p.cpp, libavogadro/src/elementitem_p.h,
  libavogadro/src/elementtranslator.cpp, libavogadro/src/elementtranslator.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/periodictablescene_p.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/tools/CMakeLists.txt, periodictable/CMakeLists.txt,
  periodictable/src/CMakeLists.txt, periodictable/src/elementdetail_p.cpp,
  periodictable/src/elementdetail_p.h, periodictable/src/elementitem_p.cpp,
  periodictable/src/elementitem_p.h, periodictable/src/elementtranslator.cpp,
  periodictable/src/elementtranslator.h,
  periodictable/src/periodictablescene_p.cpp,
  periodictable/src/periodictablescene_p.h,
  periodictable/src/periodictableview.cpp,
  periodictable/src/periodictableview.h: Separated periodic table into library
  (libperiodictable)

2010-03-29  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro/avogadro-af.po, i18n/avogadro/avogadro-ar.po,
  i18n/avogadro/avogadro-bg.po, i18n/avogadro/avogadro-ca.po,
  i18n/avogadro/avogadro-cs.po, i18n/avogadro/avogadro-da.po,
  i18n/avogadro/avogadro-de.po, i18n/avogadro/avogadro-el.po,
  i18n/avogadro/avogadro-en_CA.po, i18n/avogadro/avogadro-en_GB.po,
  i18n/avogadro/avogadro-es.po, i18n/avogadro/avogadro-fi.po,
  i18n/avogadro/avogadro-fr.po, i18n/avogadro/avogadro-he.po,
  i18n/avogadro/avogadro-hr.po, i18n/avogadro/avogadro-hu.po,
  i18n/avogadro/avogadro-id.po, i18n/avogadro/avogadro-it.po,
  i18n/avogadro/avogadro-ja.po, i18n/avogadro/avogadro-kn.po,
  i18n/avogadro/avogadro-ko.po, i18n/avogadro/avogadro-nb.po,
  i18n/avogadro/avogadro-nl.po, i18n/avogadro/avogadro-pl.po,
  i18n/avogadro/avogadro-pt.po, i18n/avogadro/avogadro-pt_BR.po,
  i18n/avogadro/avogadro-ru.po, i18n/avogadro/avogadro-sk.po,
  i18n/avogadro/avogadro-sv.po, i18n/avogadro/avogadro-tr.po,
  i18n/avogadro/avogadro-uk.po, i18n/avogadro/avogadro-zh_CN.po,
  i18n/avogadro/avogadro-zh_TW.po, i18n/avogadro/avogadro.pot,
  i18n/libavogadro/libavogadro-ar.po, i18n/libavogadro/libavogadro-bg.po,
  i18n/libavogadro/libavogadro-ca.po, i18n/libavogadro/libavogadro-cs.po,
  i18n/libavogadro/libavogadro-da.po, i18n/libavogadro/libavogadro-de.po,
  i18n/libavogadro/libavogadro-el.po, i18n/libavogadro/libavogadro-en_CA.po,
  i18n/libavogadro/libavogadro-en_GB.po, i18n/libavogadro/libavogadro-es.po,
  i18n/libavogadro/libavogadro-fi.po, i18n/libavogadro/libavogadro-fr.po,
  i18n/libavogadro/libavogadro-he.po, i18n/libavogadro/libavogadro-hi.po,
  i18n/libavogadro/libavogadro-hu.po, i18n/libavogadro/libavogadro-id.po,
  i18n/libavogadro/libavogadro-it.po, i18n/libavogadro/libavogadro-ja.po,
  i18n/libavogadro/libavogadro-kn.po, i18n/libavogadro/libavogadro-ko.po,
  i18n/libavogadro/libavogadro-nb.po, i18n/libavogadro/libavogadro-nl.po,
  i18n/libavogadro/libavogadro-pl.po, i18n/libavogadro/libavogadro-pt.po,
  i18n/libavogadro/libavogadro-pt_BR.po, i18n/libavogadro/libavogadro-ru.po,
  i18n/libavogadro/libavogadro-sk.po, i18n/libavogadro/libavogadro-sv.po,
  i18n/libavogadro/libavogadro-tr.po, i18n/libavogadro/libavogadro-uk.po,
  i18n/libavogadro/libavogadro-zh_CN.po, i18n/libavogadro/libavogadro-zh_TW.po,
  i18n/libavogadro/libavogadro.pot: Updated translation templates for
  trunk/Launchpad.

  * libavogadro/src/colors/smartscolor.cpp,
  libavogadro/src/colors/smartscolor.h: Implemented arbitrary match coloring
  and custom color settings.

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/smartscolor.cpp, libavogadro/src/colors/smartscolor.h:
  Color by SMARTS -- currently uses [#7] as static example string. Just needs
  an options widget.

2010-03-28  Konstantin Tokarev <kostya@SpringStar.(none)>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt: Made linguis dependency optional (only show
  warning)

  * scripts/installer/installer_languages/russian.nsh,
  scripts/installer/setup.nsi: Russian for NSIS

  * examples/c++/CMakeLists.txt, examples/c++/templateextension.pro: Added
  CMake template project

  * examples/c++/templateextension.cpp, examples/c++/templateextension.h,
  examples/c++/templateextension.pro: Fixed c++ template for extension, added
  QMake project

  * examples/c++/templateextension.cpp, examples/c++/templateextension.h,
  examples/python/extensiontemplate.py, examples/python/proteinextension.py,
  examples/python/standalone.py, examples/python/tooltemplate.py,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h, python/extensiontemplate.py,
  python/proteinextension.py, python/standalone.py, python/tooltemplate.py:
  Reorganized examples for python and c++

2010-03-27  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h,
  libavogadro/src/extensions/daltoninputdialog.ui,
  .../src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessefpmatchdialog.ui,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamesshighlighter.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui,
  libavogadro/src/extensions/inputfileextension.cpp,
  libavogadro/src/extensions/inputfileextension.h,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/molproinputdialog.h,
  libavogadro/src/extensions/molproinputdialog.ui,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h,
  libavogadro/src/extensions/mopacinputdialog.ui,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.h,
  libavogadro/src/extensions/nwcheminputdialog.ui,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui,
  .../src/extensions/quantuminput/CMakeLists.txt,
  .../extensions/quantuminput/daltoninputdialog.cpp,
  .../extensions/quantuminput/daltoninputdialog.h,
  .../extensions/quantuminput/daltoninputdialog.ui,
  .../quantuminput/gamessefpmatchdialog.cpp,
  .../extensions/quantuminput/gamessefpmatchdialog.h,
  .../quantuminput/gamessefpmatchdialog.ui,
  .../extensions/quantuminput/gamessextension.cpp,
  .../src/extensions/quantuminput/gamessextension.h,
  .../extensions/quantuminput/gamesshighlighter.cpp,
  .../extensions/quantuminput/gamesshighlighter.h,
  .../extensions/quantuminput/gamessinputdata.cpp,
  .../src/extensions/quantuminput/gamessinputdata.h,
  .../extensions/quantuminput/gamessinputdialog.cpp,
  .../extensions/quantuminput/gamessinputdialog.h,
  .../extensions/quantuminput/gamessinputdialog.ui,
  .../quantuminput/gaussianinputdialog.cpp,
  .../extensions/quantuminput/gaussianinputdialog.h,
  .../extensions/quantuminput/gaussianinputdialog.ui,
  .../extensions/quantuminput/inputfileextension.cpp,
  .../extensions/quantuminput/inputfileextension.h,
  .../extensions/quantuminput/molproinputdialog.cpp,
  .../extensions/quantuminput/molproinputdialog.h,
  .../extensions/quantuminput/molproinputdialog.ui,
  .../extensions/quantuminput/mopacinputdialog.cpp,
  .../src/extensions/quantuminput/mopacinputdialog.h,
  .../extensions/quantuminput/mopacinputdialog.ui,
  .../extensions/quantuminput/nwcheminputdialog.cpp,
  .../extensions/quantuminput/nwcheminputdialog.h,
  .../extensions/quantuminput/nwcheminputdialog.ui,
  .../extensions/quantuminput/qcheminputdialog.cpp,
  .../src/extensions/quantuminput/qcheminputdialog.h,
  .../extensions/quantuminput/qcheminputdialog.ui: Moved quantum input
  extensions to subdirectory

2010-03-27  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/extensions/spectra/abstract_ir.cpp,
  libavogadro/src/extensions/spectra/abstract_ir.h,
  libavogadro/src/extensions/spectra/cd.cpp,
  libavogadro/src/extensions/spectra/cd.h,
  libavogadro/src/extensions/spectra/dos.cpp,
  libavogadro/src/extensions/spectra/dos.h,
  libavogadro/src/extensions/spectra/ir.cpp,
  libavogadro/src/extensions/spectra/ir.h,
  libavogadro/src/extensions/spectra/nmr.cpp,
  libavogadro/src/extensions/spectra/nmr.h,
  libavogadro/src/extensions/spectra/raman.cpp,
  libavogadro/src/extensions/spectra/raman.h,
  .../extensions/spectra/spectratype_abstract_ir.cpp,
  .../extensions/spectra/spectratype_abstract_ir.h,
  .../src/extensions/spectra/spectratype_cd.cpp,
  .../src/extensions/spectra/spectratype_cd.h,
  .../src/extensions/spectra/spectratype_dos.cpp,
  .../src/extensions/spectra/spectratype_dos.h,
  .../src/extensions/spectra/spectratype_ir.cpp,
  .../src/extensions/spectra/spectratype_ir.h,
  .../src/extensions/spectra/spectratype_nmr.cpp,
  .../src/extensions/spectra/spectratype_nmr.h,
  .../src/extensions/spectra/spectratype_raman.cpp,
  .../src/extensions/spectra/spectratype_raman.h,
  .../src/extensions/spectra/spectratype_uv.cpp,
  .../src/extensions/spectra/spectratype_uv.h,
  libavogadro/src/extensions/spectra/uv.cpp,
  libavogadro/src/extensions/spectra/uv.h: Refactor spectra: more file renames
  (keep it simple)

  * libavogadro/src/extensions/spectra/CMakeLists.txt,
  .../src/extensions/spectra/spectratab_ir_raman.ui,
  libavogadro/src/extensions/spectra/spectratabcd.ui,
  .../src/extensions/spectra/spectratabdos.ui,
  .../src/extensions/spectra/spectratabnmr.ui,
  libavogadro/src/extensions/spectra/spectratabuv.ui,
  .../extensions/spectra/spectratype_abstract_ir.h,
  .../src/extensions/spectra/spectratype_cd.h,
  .../src/extensions/spectra/spectratype_dos.h,
  .../src/extensions/spectra/spectratype_nmr.h,
  .../src/extensions/spectra/spectratype_uv.h,
  libavogadro/src/extensions/spectra/tab_cd.ui,
  libavogadro/src/extensions/spectra/tab_dos.ui,
  libavogadro/src/extensions/spectra/tab_ir_raman.ui,
  libavogadro/src/extensions/spectra/tab_nmr.ui,
  libavogadro/src/extensions/spectra/tab_uv.ui: Refactor spectra: renamed uis
  to match class names and make them shorter

  * libavogadro/src/extensions/spectra/CMakeLists.txt,
  libavogadro/src/extensions/spectra/spectratype.cpp,
  libavogadro/src/extensions/spectra/spectratype.h,
  .../extensions/spectra/spectratype_abstract_ir.cpp,
  .../extensions/spectra/spectratype_abstract_ir.h,
  .../src/extensions/spectra/spectratype_ir.cpp,
  .../src/extensions/spectra/spectratype_ir.h,
  .../src/extensions/spectra/spectratype_raman.h: Refactorization of
  spectraextension

2010-03-26  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * avopkg.in, doc/avopkg.1: Avopkg: check arch and OS, add this information to
  manifest automatically

2010-03-26  Konstantin Tokarev <annulen@users.sourceforge.net>

  * .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Jailed spectra
  plot in default limits (containig all data points)

2010-03-23  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectra/spectratype_ir.cpp,
  libavogadro/src/extensions/spectra/spectratype_raman.cpp: IR&Raman limits,
  0.97

  * libavogadro/src/extensions/spectra/spectratype_ir.cpp,
  libavogadro/src/extensions/spectra/spectratype_raman.cpp: Get rid of 0.97
  multiplier, changed default limits for IR and Raman  (plot will enlarge if
  they are too small)

  * .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Fit default
  limits of spectra plot to data

2010-03-20  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Right click outside molecule clears
  selection

2010-03-20  Konstantin Tokarev <annulen@users.sourceforge.net>

  * .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  .../src/extensions/spectra/spectradialog.ui: Show coordinates of PlotWidget
  in spectra dialog

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Enhanced label settings
  dialog

2010-03-19  Konstantin Annulen Tokarev <kostya@localhost.localdomain>

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/extensions/spectra/spectratype_ir.cpp: Fixed building with
  Intel Compiler

2010-03-19  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added new text renderer

2010-03-18  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Change default of "atom
  radius" to be consistent with prev. releases. Users can change to covalent,
  but it should be their choice.

2010-03-16  Konstantin Tokarev <annulen@users.sourceforge.net>

  * Doxyfile, README, doc/CMakeLists.txt, doc/avogadro.1, doc/avopkg.1,
  doc/mainpage.dox: Updated docs, added man pages

2010-03-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro/avogadro-af.po, i18n/avogadro/avogadro-ar.po,
  i18n/avogadro/avogadro-bg.po, i18n/avogadro/avogadro-ca.po,
  i18n/avogadro/avogadro-cs.po, i18n/avogadro/avogadro-da.po,
  i18n/avogadro/avogadro-de.po, i18n/avogadro/avogadro-el.po,
  i18n/avogadro/avogadro-en_CA.po, i18n/avogadro/avogadro-en_GB.po,
  i18n/avogadro/avogadro-es.po, i18n/avogadro/avogadro-fi.po,
  i18n/avogadro/avogadro-fr.po, i18n/avogadro/avogadro-he.po,
  i18n/avogadro/avogadro-hr.po, i18n/avogadro/avogadro-hu.po,
  i18n/avogadro/avogadro-id.po, i18n/avogadro/avogadro-it.po,
  i18n/avogadro/avogadro-ja.po, i18n/avogadro/avogadro-kn.po,
  i18n/avogadro/avogadro-ko.po, i18n/avogadro/avogadro-nb.po,
  i18n/avogadro/avogadro-nl.po, i18n/avogadro/avogadro-pl.po,
  i18n/avogadro/avogadro-pt.po, i18n/avogadro/avogadro-pt_BR.po,
  i18n/avogadro/avogadro-ru.po, i18n/avogadro/avogadro-sk.po,
  i18n/avogadro/avogadro-sv.po, i18n/avogadro/avogadro-tr.po,
  i18n/avogadro/avogadro-uk.po, i18n/avogadro/avogadro-zh_CN.po,
  i18n/avogadro/avogadro-zh_TW.po, i18n/avogadro/avogadro.pot,
  i18n/libavogadro/libavogadro-ar.po, i18n/libavogadro/libavogadro-bg.po,
  i18n/libavogadro/libavogadro-ca.po, i18n/libavogadro/libavogadro-cs.po,
  i18n/libavogadro/libavogadro-da.po, i18n/libavogadro/libavogadro-de.po,
  i18n/libavogadro/libavogadro-el.po, i18n/libavogadro/libavogadro-en_CA.po,
  i18n/libavogadro/libavogadro-en_GB.po, i18n/libavogadro/libavogadro-es.po,
  i18n/libavogadro/libavogadro-fi.po, i18n/libavogadro/libavogadro-fr.po,
  i18n/libavogadro/libavogadro-he.po, i18n/libavogadro/libavogadro-hi.po,
  i18n/libavogadro/libavogadro-hu.po, i18n/libavogadro/libavogadro-id.po,
  i18n/libavogadro/libavogadro-it.po, i18n/libavogadro/libavogadro-ja.po,
  i18n/libavogadro/libavogadro-kn.po, i18n/libavogadro/libavogadro-ko.po,
  i18n/libavogadro/libavogadro-nb.po, i18n/libavogadro/libavogadro-nl.po,
  i18n/libavogadro/libavogadro-pl.po, i18n/libavogadro/libavogadro-pt.po,
  i18n/libavogadro/libavogadro-pt_BR.po, i18n/libavogadro/libavogadro-ru.po,
  i18n/libavogadro/libavogadro-sk.po, i18n/libavogadro/libavogadro-sv.po,
  i18n/libavogadro/libavogadro-tr.po, i18n/libavogadro/libavogadro-uk.po,
  i18n/libavogadro/libavogadro-zh_CN.po, i18n/libavogadro/libavogadro-zh_TW.po,
  i18n/libavogadro/libavogadro.pot: Bumped translations to force Launchpad
  re-import.

2010-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/FindNumpy.cmake, cmake/modules/PythonDeps.cmake: Another
  update to cmake files for numpy (wasn't working before)

  * cmake/modules/FindNumpy.cmake, cmake/modules/PythonDeps.cmake: Fix bug
  where cmake incorrectly detects numpy when it is not there. (Fixes: #2886558)

2010-03-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, i18n/avogadro-af.po, i18n/avogadro-ar.po,
  i18n/avogadro-bg.po, i18n/avogadro-ca.po, i18n/avogadro-cs.po,
  i18n/avogadro-da.po, i18n/avogadro-de.po, i18n/avogadro-el.po,
  i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po, i18n/avogadro-es.po,
  i18n/avogadro-fi.po, i18n/avogadro-fr.po, i18n/avogadro-he.po,
  i18n/avogadro-hu.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/avogadro/avogadro-af.po, i18n/avogadro/avogadro-ar.po,
  i18n/avogadro/avogadro-bg.po, i18n/avogadro/avogadro-ca.po,
  i18n/avogadro/avogadro-cs.po, i18n/avogadro/avogadro-da.po,
  i18n/avogadro/avogadro-de.po, i18n/avogadro/avogadro-el.po,
  i18n/avogadro/avogadro-en_CA.po, i18n/avogadro/avogadro-en_GB.po,
  i18n/avogadro/avogadro-es.po, i18n/avogadro/avogadro-fi.po,
  i18n/avogadro/avogadro-fr.po, i18n/avogadro/avogadro-he.po,
  i18n/avogadro/avogadro-hr.po, i18n/avogadro/avogadro-hu.po,
  i18n/avogadro/avogadro-id.po, i18n/avogadro/avogadro-it.po,
  i18n/avogadro/avogadro-ja.po, i18n/avogadro/avogadro-kn.po,
  i18n/avogadro/avogadro-ko.po, i18n/avogadro/avogadro-nb.po,
  i18n/avogadro/avogadro-nl.po, i18n/avogadro/avogadro-pl.po,
  i18n/avogadro/avogadro-pt.po, i18n/avogadro/avogadro-pt_BR.po,
  i18n/avogadro/avogadro-ru.po, i18n/avogadro/avogadro-sk.po,
  i18n/avogadro/avogadro-sv.po, i18n/avogadro/avogadro-tr.po,
  i18n/avogadro/avogadro-uk.po, i18n/avogadro/avogadro-zh_CN.po,
  i18n/avogadro/avogadro-zh_TW.po, i18n/avogadro/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-da.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-he.po, i18n/libavogadro-hi.po, i18n/libavogadro-hu.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot,
  i18n/libavogadro/libavogadro-ar.po, i18n/libavogadro/libavogadro-bg.po,
  i18n/libavogadro/libavogadro-ca.po, i18n/libavogadro/libavogadro-cs.po,
  i18n/libavogadro/libavogadro-da.po, i18n/libavogadro/libavogadro-de.po,
  i18n/libavogadro/libavogadro-el.po, i18n/libavogadro/libavogadro-en_CA.po,
  i18n/libavogadro/libavogadro-en_GB.po, i18n/libavogadro/libavogadro-es.po,
  i18n/libavogadro/libavogadro-fi.po, i18n/libavogadro/libavogadro-fr.po,
  i18n/libavogadro/libavogadro-he.po, i18n/libavogadro/libavogadro-hi.po,
  i18n/libavogadro/libavogadro-hu.po, i18n/libavogadro/libavogadro-id.po,
  i18n/libavogadro/libavogadro-it.po, i18n/libavogadro/libavogadro-ja.po,
  i18n/libavogadro/libavogadro-kn.po, i18n/libavogadro/libavogadro-ko.po,
  i18n/libavogadro/libavogadro-nb.po, i18n/libavogadro/libavogadro-nl.po,
  i18n/libavogadro/libavogadro-pl.po, i18n/libavogadro/libavogadro-pt.po,
  i18n/libavogadro/libavogadro-pt_BR.po, i18n/libavogadro/libavogadro-ru.po,
  i18n/libavogadro/libavogadro-sk.po, i18n/libavogadro/libavogadro-sv.po,
  i18n/libavogadro/libavogadro-tr.po, i18n/libavogadro/libavogadro-uk.po,
  i18n/libavogadro/libavogadro-zh_CN.po, i18n/libavogadro/libavogadro-zh_TW.po,
  i18n/libavogadro/libavogadro.pot, libavogadro/src/CMakeLists.txt,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh:
  Moved translations to allow automatic import of templates and translations
  from Git into Launchpad.

  * avogadro/gl2ps/README.txt, avogadro/gl2ps/TODO, avogadro/gl2ps/TODO.txt,
  avogadro/gl2ps/gl2ps.c, avogadro/gl2ps/gl2ps.h, avogadro/gl2ps/gl2ps.pdf,
  avogadro/gl2ps/gl2psTest.c, avogadro/gl2ps/gl2psTestSimple.c: Import of gl2ps
  1.3.5

2010-03-07  Konstantin Tokarev <annulen@users.sourceforge.net>

  * CMakeLists.txt, avogadro.prf.in: Added avogadro.prf generation and
  installation

2010-03-06  Konstantin Tokarev <annulen@users.sourceforge.net>

  * CMakeLists.txt, avopkg.in: Added avopkg tool

2010-03-03  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp: Fixes to accomodate new
  OBUnitCell behavior

2010-03-03  Konstantin Tokarev <annulen@users.sourceforge.net>

  * .../src/extensions/spectra/vibrationextension.cpp,
  .../src/extensions/spectra/vibrationextension.h,
  .../src/extensions/spectra/vibrationwidget.cpp,
  .../src/extensions/spectra/vibrationwidget.h,
  .../src/extensions/spectra/vibrationwidget.ui: Added normalization of
  vibrational displacements

2010-03-02  Konstantin Tokarev <annulen@users.sourceforge.net>

  * .../src/extensions/spectra/vibrationextension.cpp,
  .../src/extensions/spectra/vibrationwidget.cpp,
  .../src/extensions/spectra/vibrationwidget.h,
  .../src/extensions/spectra/vibrationwidget.ui: Added filter to vibration
  widget; stop animation if dock closed

2010-02-28  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/unitcellparamdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Change color of
  unit cell (feature request #...)

  * libavogadro/src/extensions/spectra/vibrationwidget.cpp,
  libavogadro/src/extensions/spectra/vibrationwidget.ui: Added icons to
  vibrationwidget, fixed pause/continue button state on stop

2010-02-26  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * .../src/extensions/spectra/vibrationextension.cpp,
  libavogadro/src/extensions/spectra/vibrationextension.h: Try to save position
  of dock, seems not to work, but doesn't break anything

2010-02-26  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Added sorting to Cartesian
  Editor

  * libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Read&write settings of
  CartesianEnditor

2010-02-25  Konstantin Tokarev <annulen@users.sourceforge.net>

  * i18n/avogadro-ru.po, i18n/libavogadro-ru.po: Russian

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui: Added choice of Covalen/VdW
  radii

2010-02-24  Konstantin Tokarev <annulen@users.sourceforge.net>

  * i18n/avogadro-ru.po, i18n/libavogadro-ru.po: Russian

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Fixed angles and torsions highlight

2010-02-23  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/dockextension.cpp,
  libavogadro/src/dockextension.h,
  libavogadro/src/extensions/spectra/vibrationextension.cpp: Respect
  preferredDockArea in dock placement

2010-02-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/pythonextension_p.cpp,
  libavogadro/src/pythonextension_p.h: * avogadro/src/mainwindow.cpp: Call
  GLWidget::setExtensions(...) at the appropriate points.  *
  libavogadro/src/glwidget.[h/cpp]: Add GLWidget::setExtensions(...). Call
  PythonExtension::paint(...) for all python extensions.  *
  libavogadro/src/pythonextension_p.[h/cpp]: Add PythonExtension::paint(...).
  In future versions (when we break ABI) we can add the virtual
  Extension::paint function.

2010-02-22  Konstantin Tokarev <annulen@users.sourceforge.net>

  * .../src/extensions/spectra/vibrationdialog.ui,
  .../src/extensions/spectra/vibrationwidget.ui: Small change in vibration UI

  * libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h: Ported PythonTerminal to
  DockExtension

  * libavogadro/src/CMakeLists.txt, libavogadro/src/dockextension.cpp,
  libavogadro/src/dockextension.h,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  .../src/extensions/spectra/vibrationextension.cpp,
  .../src/extensions/spectra/vibrationextension.h: Added DockExtension class
  and ported VibrationExtension to it (build in fresh directory!)

2010-02-21  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectra/CMakeLists.txt,
  .../src/extensions/spectra/spectradialog.cpp,
  libavogadro/src/extensions/spectra/spectradialog.h,
  .../src/extensions/spectra/spectradialog.ui,
  .../src/extensions/spectra/spectraextension.cpp,
  .../src/extensions/spectra/spectraextension.h,
  .../src/extensions/spectra/spectratab_ir_raman.ui,
  libavogadro/src/extensions/spectra/spectratabcd.ui,
  .../src/extensions/spectra/spectratabdos.ui,
  .../src/extensions/spectra/spectratabnmr.ui,
  libavogadro/src/extensions/spectra/spectratabuv.ui,
  libavogadro/src/extensions/spectra/spectratype.cpp,
  libavogadro/src/extensions/spectra/spectratype.h,
  .../src/extensions/spectra/spectratype_cd.cpp,
  .../src/extensions/spectra/spectratype_cd.h,
  .../src/extensions/spectra/spectratype_dos.cpp,
  .../src/extensions/spectra/spectratype_dos.h,
  .../src/extensions/spectra/spectratype_ir.cpp,
  .../src/extensions/spectra/spectratype_ir.h,
  .../src/extensions/spectra/spectratype_nmr.cpp,
  .../src/extensions/spectra/spectratype_nmr.h,
  .../src/extensions/spectra/spectratype_raman.cpp,
  .../src/extensions/spectra/spectratype_raman.h,
  .../src/extensions/spectra/spectratype_uv.cpp,
  .../src/extensions/spectra/spectratype_uv.h,
  .../src/extensions/spectra/vibrationdialog.ui,
  .../src/extensions/spectra/vibrationextension.cpp,
  .../src/extensions/spectra/vibrationextension.h,
  .../src/extensions/spectra/vibrationwidget.cpp,
  .../src/extensions/spectra/vibrationwidget.h,
  .../src/extensions/spectra/vibrationwidget.ui,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/spectraextension.h,
  libavogadro/src/extensions/spectratab_ir_raman.ui,
  libavogadro/src/extensions/spectratabcd.ui,
  libavogadro/src/extensions/spectratabdos.ui,
  libavogadro/src/extensions/spectratabnmr.ui,
  libavogadro/src/extensions/spectratabuv.ui,
  libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h,
  libavogadro/src/extensions/spectratype_uv.cpp,
  libavogadro/src/extensions/spectratype_uv.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationwidget.cpp,
  libavogadro/src/extensions/vibrationwidget.h,
  libavogadro/src/extensions/vibrationwidget.ui: Moved spectraextension and
  vibrationextension to subdirectory

2010-02-20  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationwidget.cpp,
  libavogadro/src/extensions/vibrationwidget.h: changed filenames
  vibrationdialog.* to vibrationwidget.*

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Blocked old CartesianType code in
  propextension

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h: Fixed impossibility to run one
  vibration animation twice; Pause button fix

2010-02-19  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Show spectra connections

2010-02-17  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Removed Vibrations from menu
  since now it's dock

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_raman.h,
  libavogadro/src/extensions/spectratype_uv.h: Fixed build on Debian 5

2010-02-17  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationwidget.ui: Fixed segfault on Forces;
  added Pause button

2010-02-15  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt, CTestConfig.cmake, avogadro/src/CMakeLists.txt,
  libavogadro/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/tests/CMakeLists.txt:
  Changes to the build system to support subprojects.  These changes add labels
  to the source, targets and tests. They also add some custom targets named
  after the subprojects for the engines, tools, extensions and colors. You can
  now type 'make engines' in order to build all engines. The add plugin
  function takes a couple of extra (optional) variables to accomplish this.

2010-02-15  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationwidget.ui: Made vibrationDock displaying
  correctly (may crash!)

2010-02-14  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Fixed couple of segfaults in
  propextension

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Improved look&feel of Properties
  Extension

2010-02-13  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectratabir.ui,
  libavogadro/src/extensions/spectratabraman.ui,
  libavogadro/src/extensions/spectratype_raman.cpp: Removed unnecessary uis

  * libavogadro/src/extensions/spectratab_ir_raman.ui,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_raman.cpp: Small improvements in IR
  and Raman

2010-02-12  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectratab_ir_raman.ui,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h: Calculation of Raman
  intensities (not tested)

2010-02-11  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h: Some code cleanups

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectratab_ir_raman.ui,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h: Derived IR and Raman from
  AbstractIRSpectra

  * libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratype_uv.cpp: Some code cleanups

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationwidget.ui: Transformed VibrationalDialog
  into dock

2010-02-09  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Added a coordinate only
  output, e.g. for VASP.

  * libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Add fractional editor to
  coordinate editor, clean up indention.

2010-01-31  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Eleminated possibility of
  segfault in CartesianExtension

2010-02-10  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h: Automatic change of current
  spectrum if current tab has changed

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: Replaced 'noscale' with 'orig'

2010-02-09  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectratabraman.ui,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h: Added new UI elements to
  Raman tab

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: dataTable displays scaled
  fequencies

2010-02-07  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_dos.h: Disabled updateDataTable for
  DOS spectra

  * libavogadro/src/extensions/spectratabir.ui,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: Interactive sliders for scale
  and Gaussian width for IR; relative scaling

2010-02-05  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: Added scale(double) function

  * libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_uv.cpp,
  libavogadro/src/extensions/spectratype_uv.h: Some code cleanups

  * i18n/avogadro-ru.po, i18n/libavogadro-ru.po: Russian translation

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated po files

2010-02-04  Константин Токарев <kostya@localhost.localdomain>

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_raman.cpp: Fix for scaling of
  gaussians in IR and Raman

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectratype_raman.h: Fixed build with OB 2.2.3

2010-02-04  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui: Improved look of
  vibrationdialog

  * libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h,
  libavogadro/src/extensions/spectratype_uv.cpp,
  libavogadro/src/extensions/spectratype_uv.h: Refactorization of SpectraType
  and subclasses

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui,
  libavogadro/src/extensions/spectratabraman.ui: Raman support and data table
  in spectradialog

2010-02-02  David C. Lonie <loniedavid@gmail.com>

  * testfiles/VASP-DOS/CONTCAR, testfiles/VASP-DOS/DOSCAR,
  testfiles/VASP-DOS/POTCAR: Added VASP test directory with DOS info to
  testfiles/ -- Open CONTCAR in avogadro to load

  * testfiles/cdspectrum, testfiles/spectrum: Added Turbomol CD and UV output
  to testfiles (must be loaded manually in the Spectra extension.

2010-01-31  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Eleminated possibility of
  segfault in CartesianExtension

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratabraman.ui,
  libavogadro/src/extensions/spectratype_raman.cpp,
  libavogadro/src/extensions/spectratype_raman.h: Initial support for Raman
  spectra

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h,
  libavogadro/src/extensions/spectratype_uv.h,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h: Added pathes to some Qt
  includes (following KDE coding style)

2010-01-29  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui: Display Raman activities in
  VibrationDialog

2010-01-26  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/cartesianextension.cpp: Added the new cartesian
  editor back in to dlonie/master

2010-01-19  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-he.po, i18n/avogadro-hu.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-da.po, i18n/libavogadro-de.po, i18n/libavogadro-el.po,
  i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-he.po,
  i18n/libavogadro-hi.po, i18n/libavogadro-hu.po, i18n/libavogadro-id.po,
  i18n/libavogadro-it.po, i18n/libavogadro-ja.po, i18n/libavogadro-ko.po,
  i18n/libavogadro-nb.po, i18n/libavogadro-nl.po, i18n/libavogadro-pl.po,
  i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po,
  i18n/libavogadro-sk.po, i18n/libavogadro-sv.po, i18n/libavogadro-tr.po,
  i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po,
  i18n/libavogadro.pot: Update with latest Launchpad translations.

2009-10-30  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h: Blocked old cartesian editor in
  propextension

2009-11-29  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp, libavogadro/src/molecule.cpp:
  Improved label style "Symbol & Number in Group" - now "1" isn't displayed if
  there is only one atom of certain element

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Re-ordered types of atom
  labels in labelsettinswidget

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui, libavogadro/src/molecule.cpp:
  Moved new numbering scheme from OB to Avogadro - eliminated dependence on
  non-accepted patch to OB

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Eleminated segfault by
  removing label preview

2009-11-24  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Size of properties dialog now
  depends on rows and columns number; made it resizable under Fluxbox

2009-11-23  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui, libavogadro/src/molecule.cpp:
  Added support for changing of labels font color, but still can't change font

2009-11-22  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_uv.cpp,
  libavogadro/src/extensions/spectratype_uv.h, libavogadro/src/molecule.cpp:
  Add ifdefs to select available spectra based on OB version.

2009-11-22  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Improved UI of
  labelsettingswidget; now will compile with unmodified OB (without new label
  type)

2009-11-19  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h: New Label type: Symbol & Number in group
  (requires patch for OB which wasn't accepted yet)

2009-11-17  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Labels can be moved from
  atoms on arbitrary vector

2009-11-16  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Added annulen's
  default heuristics for pasting coordinates.

2009-11-16  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Improved dipole engine:
  vector points outside molecule; origin can be changed

2009-11-15  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h:
  Added settings widget for Axes engine

2009-11-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/daltoninputdialog.cpp,
  .../src/extensions/daltoninputdialog.cpp.disabled,
  libavogadro/src/extensions/daltoninputdialog.h,
  .../src/extensions/daltoninputdialog.h.disabled,
  libavogadro/src/extensions/daltoninputdialog.ui,
  .../src/extensions/daltoninputdialog.ui.disabled: Re-enabled Cyanat's dalton
  code.

2009-11-13  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avogadro/src/pluginlistview.cpp, avogadro/src/pluginlistview.h: Added
  copyright information

  * avogadro/src/pluginlistview.cpp, avogadro/src/pluginlistview.h,
  avogadro/src/pluginsettings.cpp: Fixed improper behavior of PluginListView
  (plugin info didn't change on keyboard movements)

2009-11-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/tools/autoopttool.cpp: Ignore dummy atoms for force field
  calcs. (Includes some debugging info.)

2009-11-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_nmr.cpp: Move connections to
  constructors for spectra tabs.

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_nmr.cpp: Move connections to
  constructors for spectra tabs.

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_nmr.cpp: Move connections to
  constructors for spectra tabs.

  * libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_uv.cpp: DOS only: move connections to
  ctors

2009-11-06  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, scripts/extract-application-messages.sh: Updated
  template -- main.cpp messages were not properly processed by
  extract-application-messages.sh.

2009-11-05  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp: Changed font size in
  editor from 10 to value, relative to default

  * libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Code style: fixed braces
  placement, replaced tabs with spaces, changed Qt headers

2009-11-05  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h,
  .../src/extensions/icons/document-revert.png,
  libavogadro/src/extensions/icons/edit-clear.png,
  libavogadro/src/extensions/icons/edit-copy.png,
  libavogadro/src/extensions/icons/edit-cut.png,
  libavogadro/src/extensions/icons/edit-paste.png: Backout new Cartesian editor
  extension from 1.0 branch.

2009-11-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h,
  libavogadro/src/extensions/edit.qrc,
  libavogadro/src/extensions/icons/amarok_back.png,
  libavogadro/src/extensions/icons/amarok_next.png,
  libavogadro/src/extensions/icons/amarok_pause.png,
  libavogadro/src/extensions/icons/amarok_play.png,
  libavogadro/src/extensions/icons/amarok_stop.png,
  .../src/extensions/icons/document-revert.png,
  libavogadro/src/extensions/icons/edit-clear.png,
  libavogadro/src/extensions/icons/edit-copy.png,
  libavogadro/src/extensions/icons/edit-cut.png,
  libavogadro/src/extensions/icons/edit-paste.png: Re-merge annulen's cartesian
  editor.

2009-11-03  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POT and PO files (with fewer messages)

  * avogadro/src/macchempasteboard.cpp.disabled,
  avogadro/src/macchempasteboard.h.disabled,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/daltoninputdialog.cpp.disabled,
  .../src/extensions/daltoninputdialog.h.disabled,
  .../src/extensions/daltoninputdialog.ui.disabled,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/liganddialog.ui,
  libavogadro/src/extensions/linmorph.qrc,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphdialog.h,
  libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/pocketdialog.ui,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h: Remove unused source files --
  these are still used for translations!

2009-10-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h: PythonTerminal extension: Allow
  selections in the python terminal widget without allowing to edit (i.e.
  delete) already processed commands

2009-10-30  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h: Blocked old cartesian editor in
  propextension

  * libavogadro/src/extensions/icons/document-revert.png,
  libavogadro/src/extensions/icons/edit-clear.png,
  libavogadro/src/extensions/icons/edit-copy.png,
  libavogadro/src/extensions/icons/edit-cut.png,
  libavogadro/src/extensions/icons/edit-paste.png: Added icons for Cartesian
  Editor - copied form avogadro/src/icons

  * libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Added extension "Cartesian
  Editor"

2009-10-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h: PythonTerminal extension: Allow
  selections in the python terminal widget without allowing to edit (i.e.
  delete) already processed commands

2009-10-28  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POTs and translations.

  * scripts/find-po-email.py, scripts/find-translators.sh: Update scripts --
  used to grab contributors for Avo 1.0.

  * i18n/avogadro-ar.po, i18n/avogadro-ca.po, i18n/avogadro-cs.po,
  i18n/avogadro-de.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po, scripts/clean-po.sh: Stripped PO files -- fixes
  bugs noted by Benoit and Annulen about untranslated messages (i.e., lupdate
  gets confused by obsolete translations).

2009-10-26  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  scripts/extract-application-messages.sh: Updated with translation suggestions
  from annulen

2009-10-25  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/updatecheck.cpp,
  libavogadro/src/extensions/networkfetchextension.cpp: Changed all deletes on
  the network reply to deleteLater() calls.

  * avogadro/src/updatecheck.cpp,
  libavogadro/src/extensions/networkfetchextension.cpp: Changed all deletes on
  the network reply to deleteLater() calls.

2009-10-24  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile: Bumped build files in master to 1.1.0 -
  development versions.

2009-10-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile: Bumped the version number in preparation for the
  1.0.0 release.

2009-10-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Final import of translations before 1.0.

2009-10-22  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/enginecolorswidget.h, libavogadro/src/config.h.in,
  libavogadro/src/glwidget.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h: Added versioned plugin directories - fixes
  bug 2882816.  I added versioned plugin directories on all architectures. This
  can be disabled, but it should not do any harm being left on. This
  necessitated soem changes to the plugin manager class. I removed the static
  and const methods and ported affected classes to get an instance of the
  singleton.

2009-10-22  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h,
  libavogadro/src/extensions/daltoninputdialog.ui: Added option for multiply
  augmented cc basis sets.

2009-10-20  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/molecule.cpp, libavogadro/src/residue.cpp,
  libavogadro/src/residue.h: When element changes with Atom::setAtomicNumber,
  issue an updated() signal from the atom. Residues will now listen for this
  signal and invalidate atom IDs accordingly. When saving residue information
  with molecules, check for invalid atom ids. Addresses PR#2855789.

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Latest Launchpad Translations.

2009-10-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POTs. Will merge Launchpad shortly.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  .../src/extensions/daltoninputdialog.cpp.disabled,
  libavogadro/src/extensions/daltoninputdialog.h,
  .../src/extensions/daltoninputdialog.h.disabled,
  libavogadro/src/extensions/daltoninputdialog.ui,
  .../src/extensions/daltoninputdialog.ui.disabled,
  libavogadro/src/extensions/inputfileextension.cpp,
  libavogadro/src/extensions/inputfileextension.h: Disable Dalton generation --
  not enough time for translations.

  * libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/gamessinputdialog.ui: Update disambiguation of
  "loop" translations suggested by Konstantin Tokarev.

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Modified patch from Patch
  PR#2799140.

2009-10-19  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h: Added keyword "nosymm" when
  asking for excitation energies.

2009-10-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt: WIN32: Don't
  attempt to create QM files on windows -- these should be copied from a linux
  build to avoid unicode problems with the translations [just place the QM
  files in avogadro/src and libavogadro/src] We could add the QM files to git
  but since there are only a handful of people building on windows, the
  downsides seem to outweigh the benefits. If not copied, Avogadro still build
  but will be untranslated.

2009-10-18  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/plugin.h: Bumped the plugin
  version number and config file versions - make clean required.

2009-10-17  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile: Bumped the version number to 0.9.9 in preparation
  for tagging.

2009-10-17  Kristof Bal <kristof.bal@gmail.com>

  * avogadro/src/engineitemdelegate.h,
  libavogadro/qtiocompressor/qtiocompressor.cpp,
  libavogadro/src/python/swig.cpp: Fix spelling errors (Krazy).  Spelling
  errors in comments and strings should be fixed as they may show up later in
  API documentation, handbooks, etc.

2009-10-16  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Latest Launchpad Translations.

2009-10-16  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltonextension.cpp,
  libavogadro/src/extensions/daltonextension.h,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h,
  libavogadro/src/extensions/daltoninputdialog.ui,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/inputfileextension.cpp,
  libavogadro/src/extensions/inputfileextension.h: Extended the Dalton input
  file plugin and renamed the gaussian extension to inputfile extension to make
  it more general.  All the input file generators, except GAMESS, were added to
  the Gaussian extension and therefore it makes sense to rename the extension
  to make it more general. Maybe also merge it with the GAMESS extension if
  possible.

2009-10-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp: Fix more vibration bugs. Now
  arrow keys work correctly, and old vibrations don't reappear.x

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/tools/autoopttool.cpp: Convert all energies to kJ/mol for
  consistency.

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Fix vibration crash
  in recent versions -- don't always free conformer memory. We save it for
  vibrations.

  * .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: Disable updating the properties
  window if it's not visible.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Fix bug with
  "extra" window when opening files. Now checks for default filename.

2009-10-11  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/updatecheck.cpp,
  avogadro/src/updatecheck.h: Made UpdateCheck a singleton, fixed segfault with
  Qt 4.5.3.  Fixed the segfault with Qt 4.5.3 - use reply->deleteLater()
  instead of deleting the object directly in the slot once finished. Also made
  this class into a singleton - there is no point in checking for an update
  more than once in any given instance of Avogadro!

2009-10-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: More debugging looking for
  vibration crash.

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: First step for debugging
  vibration & animation. Attempt to lock Molecule more.

2009-10-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro.pot, i18n/libavogadro.pot: Updated with recent translatable
  strings, including formal charges.

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/extensions/propmodel.cpp: Add support for formal charges. You
  can set them using the Atom Properties, show them using atom labels, or draw
  appropriate bonding patterns to have them interpreted.

2009-10-09  Geoff Hutchison <babel@geoffhutchison.net>

  * .../src/extensions/molecularpropextension.cpp,
  libavogadro/src/molecule.cpp: Use MMFF94 to estimate dipole moment when
  available. On set of ~1000 molecules, correlation is R^2 = 0.769!

2009-10-06  Casper Steinmann <casper.steinmann@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltonextension.cpp: Placed the Dalton extension
  in the appropriate menu by renaming the .so file generated

2009-10-01  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltonextension.cpp,
  libavogadro/src/extensions/daltonextension.h,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h,
  libavogadro/src/extensions/daltoninputdialog.ui: First basic implementation
  of Dalton Input File generator extension

2009-09-30  Casper Steinmann <casper.steinmann@gmail.com>

  * libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui: Fixed bug "Error in GAMESS
  advanced setup menu - ID: 2836316"  Also: * Updated the input to use MWORDS
  instead of the old MEMORY keywork. * There are still minor issues with the
  input preview not updating when one selects a different unit of time, but no
  apparent fix was found.

2009-09-22  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Updated with Launchpad translations.

2009-09-09  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/molecule.cpp: Fixed some
  issues with file modification and saving.  Issue 2854213 should now be fixed,
  modification of the molecule is more accurately reflected now. Specifically
  when closing a molecule the empty window will not be marked as modified, when
  saving a molecule the window will be reset to reflect it was not modified
  since save and unsaved new files will prompt for a file name.

  * CMakeLists.txt, Doxyfile: Bumped version number to 0.9.8 in preparation for
  new release.

  * libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/glpainter_p.cpp, libavogadro/src/glpainter_p.h,
  libavogadro/src/mesh.cpp, libavogadro/src/mesh.h,
  libavogadro/src/python/mesh.cpp: Use Color3f to store colors in Mesh, port
  other classes.  The Mesh class now uses Color3f to store color information
  for colored meshes. Other classes were ported to work with this new class.

  * libavogadro/src/CMakeLists.txt, libavogadro/src/color3f.h: Added simple
  color class that uses 3 floats to store color.  This is a very simple color
  class that uses 3 floats to store the red, green and blue components of
  color. It is designed to be used with OpenGL calls (OpenGL stores colors as
  floats normally), but can also be used with other display types. It allows
  vectors of color objects to be passed directly to OpenGL functions as GLfloat
  pointers.

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Added
  some locking back into the draw tool.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Removed the
  function level locks in the Molecule class.  The locks have been causing
  performance issues due to multiple locks/unlocks in tight loops, along with
  some deadlocks. Migrating code to use tryLock* gets rid of deadlocks and has
  improved performance in some of the tight loops.  The Python bindings could
  do with some extra logic to take care of locking, or the documentation should
  make it clear that scripts need to take care of this.

2009-09-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated translations from Launchpad.

2009-09-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/tests/moleculefiletest.cpp, libavogadro/tests/moleculetest.cpp,
  testfiles/fail1.drawlog, testfiles/fail1.drawlog.ignore,
  testfiles/fail2.drawlog, testfiles/fail2.drawlog.ignore: Fix setAllConformers
  to just replace all conformers (and make sure there is always at least one
  conformer). See doxygen comments for more info. There is also a unit test for
  this in moleculetest.cpp.

2009-09-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/color.cpp, libavogadro/src/color.h: Just use float, rather
  than GLFloat for colors.

2009-09-01  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratabdos.ui,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h: Added integration scaling as an
  option, and the option to plot density per valence electron.

2009-08-31  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratabdos.ui,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_ir.cpp: Add integrated DOS plotting.

2009-08-22  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: More clean ups for
  the recent file list.  Cleaned up the recent file list code to ensure it is
  called on first load. Also removed a duplicate function and replaced with a
  default parameter.

  * libavogadro/src/engines/dipoleengine.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h: Fixed bug 2823931 - memory corruption on molecule
  close.  This bug was caused by a dangling pointer, updateGeomInfo was
  deleting the dipole moment pointer every time, but not setting the pointer to
  zero. I have cleaned up the dipole moment code, but it is still not doing
  anything useful as far as I can tell right now.

2009-08-21  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: Hide the dipole moment for now,
  some clean ups and GLWidget signal fix.

2009-08-21  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h: Update NMR plots to reflect
  changes to spectratype.*

  * libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: Added a function to generate a
  list of sampling points so that long flat stretches aren't sampled at high
  resolution.

  * libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h,
  libavogadro/src/extensions/spectratype_uv.cpp,
  libavogadro/src/extensions/spectratype_uv.h: Modify DOS, CD, and UV plots to
  reflect the changes to spectratype.*

  * libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: Added a function to generate a
  list of sampling points so that long flat stretches aren't sampled at high
  resolution.

2009-08-21  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp: Added an option to
  reset display types to default for a view.  This was a long standing bug that
  caused issues for many users. I had to add a new string to the view menu, but
  I think it is worth it to improve the user experience. In addition to
  previous improvements to saving/loading display type settings, the user can
  now reset the display types. We should probably add a more global option to
  reset Avogadro to defaults without requiring users to manually delete the
  configuration file.

2009-08-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Changed the
  energy function to take a signed int, works as expected now.

2009-08-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h: Removed the lock from the base Primitive class,
  added to classes that need it.

2009-08-15  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_uv.cpp, libavogadro/src/molecule.cpp:
  Update to reflect name change in OB trunk.

2009-08-13  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectratype_uv.cpp: Added turbomole CD as a
  loadable spectra type.

2009-08-12  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratabcd.ui,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h,
  libavogadro/src/extensions/spectratype_uv.cpp: Changes to CD/UV plotting.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratabcd.ui,
  libavogadro/src/extensions/spectratype_cd.cpp,
  libavogadro/src/extensions/spectratype_cd.h: Added CD spectra

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratabuv.ui,
  libavogadro/src/extensions/spectratype_uv.cpp,
  libavogadro/src/extensions/spectratype_uv.h, libavogadro/src/molecule.cpp:
  Added in UV spectra

2009-08-11  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectratabdos.ui,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h: Added some options for
  visualizing DOS plots.

2009-08-11  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h, libavogadro/src/molecule.cpp:
  Remove leaked DOS code from master branch...

2009-08-11  root <root@dl-laptop.localdomain>

  * libavogadro/src/extensions/spectratabdos.ui,
  libavogadro/src/extensions/spectratype_dos.cpp,
  libavogadro/src/extensions/spectratype_dos.h: Forgot to include the DOS files
  earlier....

2009-08-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/drawcommandtest.cpp, testfiles/basic1.drawlog,
  testfiles/basic2.drawlog, testfiles/basic3.drawlog, testfiles/basic4.drawlog,
  testfiles/basic5.drawlog, testfiles/basic6.drawlog, testfiles/fail1.drawlog,
  testfiles/fail2.drawlog: * Fix various draw tool bugs * Update draw command
  unit tests: If you uncomment the DEBUG_COMMANDS define in drawcommand.cpp,
  all information needed to replay the commands are output using qDebug().
  Capturing this output and placing moving it to testfiles/*.drawlog will make
  the drawcommandtest replay the commands. Each command is undone/redone before
  executing the next command. At the end, all commands in the stack are
  undone/redone 10 times. Various values are veryfied while doing all this.
  There are still some cases for which the replay fails but these don't cause a
  segfault. In short, the draw commands are in better shape than ever before.

2009-08-06  David Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h, libavogadro/src/molecule.cpp: DOS
  plotting

2009-08-05  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/main.cpp, i18n/avogadro-af.po, i18n/avogadro-ar.po,
  i18n/avogadro-bg.po, i18n/avogadro-ca.po, i18n/avogadro-cs.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-el.po,
  i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-id.po,
  i18n/libavogadro-it.po, i18n/libavogadro-ja.po, i18n/libavogadro-ko.po,
  i18n/libavogadro-nb.po, i18n/libavogadro-nl.po, i18n/libavogadro-pl.po,
  i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po,
  i18n/libavogadro-sk.po, i18n/libavogadro-sv.po, i18n/libavogadro-tr.po,
  i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po,
  i18n/libavogadro.pot: Updated POT and Launchpad translations.

2009-07-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Update geometry
  also needs to be called in order to render the whole molecule.

2009-07-19  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added a function
  to change an arbitrary conformer's energy.

2009-07-18  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile, INSTALL: Bumping to version 0.9.7 in preparation
  for the release.

2009-07-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h: Improved handling of loaded cube
  files, default for loaded cubes.

2009-07-17  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po, i18n/avogadro-es.po,
  i18n/avogadro-fi.po, i18n/avogadro-fr.po, i18n/avogadro-id.po,
  i18n/avogadro-it.po, i18n/avogadro-ja.po, i18n/avogadro-ko.po,
  i18n/avogadro-nb.po, i18n/avogadro-nl.po, i18n/avogadro-pl.po,
  i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po,
  i18n/avogadro-sk.po, i18n/avogadro-sv.po, i18n/avogadro-tr.po,
  i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po: Translations updates
  before 0.9.7

2009-07-17  Sergey Smirnov <sasmir@gmail.com>

  * avogadro/src/application.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/pythonwhenidle.cpp, libavogadro/src/pythonwhenidle.h: Release
  the python's GIL when Avogadro is idle (waiting for new events).

2009-07-11  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po, i18n/avogadro-es.po,
  i18n/avogadro-fi.po, i18n/avogadro-fr.po, i18n/avogadro-id.po,
  i18n/avogadro-it.po, i18n/avogadro-ja.po, i18n/avogadro-ko.po,
  i18n/avogadro-nb.po, i18n/avogadro-nl.po, i18n/avogadro-pl.po,
  i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po,
  i18n/avogadro-sk.po, i18n/avogadro-sv.po, i18n/avogadro-tr.po,
  i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po: Launchpad export of
  current translations.

2009-07-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: The non const slot is the one that
  is generally used.

2009-07-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h: Change
  PlotObject::addPoint() to return a reference to the added PlotPoint.

  * libavogadro/src/plotpoint.cpp, libavogadro/src/plotpoint.h: Added a
  customData property to PlotPoint -- this can be used to store extra
  information to help identify the point.

2009-07-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/surfaceextension.cpp: Removed the old orbital
  extension, now replaced by the surface extension.

  * libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/molecule.cpp: Added ability to use loaded cube files in the
  surface extension too.

2009-07-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/extensions/surfaceextension.h: Ported to use the enum in the
  Cube class to denote cube types.

2009-07-02  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/surfaceextension.cpp: Some fixes for slater type
  basis sets.

2009-07-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/extensions/surfacedialog.cpp: Moved the orbital engine to the
  surface engine, made necessary changes for move.

2009-06-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: Removed the surface engine
  - the orbital engine will take its place.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: A few minor cleanups to the orbitals
  engine - it is a general surface engine now.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Renamed function for drawing boxes,
  made it private and inline.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Cleaned up the mesh combo update
  code, made the color combo work correctly again.

2009-06-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/cube.h, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/extensions/surfaceextension.cpp, libavogadro/src/mesh.h,
  libavogadro/src/primitive.h: Updates to the orbital engine, soon to be the
  surface engine...  Added a cubeType property to cubes, allows for easy
  enumeration of cubes/meshes. Made the surface mesh selection work again in
  the orbital engine. Still needs some more fix ups but it is looking a lot
  better.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfacedialog.ui,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/extensions/surfaceextension.h: The new, improved surface
  extension/dialog - simpler and more intuitive.  This is the first working
  version of the new, improved surface dialog. Not everything is finished yet,
  and it is basically a rewrite of the orbital extension/dialog. I think that
  most of the logic is in there now, need to add a little more for color
  mapping cubes onto each other, showing progress dialogs for mesh calculations
  and fixing a few remaining crashers. It is much simpler and allows users to
  accomplish calculations using a single form.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Added a new signal, improved debug
  output. These classes need an overhaul - common base.

2009-06-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Display unit cell axes by default if present. Add
  a signal/slot for updating the unit cell axes menu item when changed in
  glwidget.

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Make sure to
  remove deleted primitives from the selected list.

2009-06-23  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h: Add virtual to
  indicate if certain actions use the network. Currently unused.

2009-06-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/icons/AvoDocument.png, avogadro/src/icons/avogadro.png,
  avogadro/src/icons/avogadro.svg, avogadro/src/mac/AvogadroDocument.icns,
  avogadro/src/mac/avogadro.icns: Fix Avogadro icon slightly -- layering of one
  "orbit" was off. (Sorry, I'm obsessive compulsive about these things.)

2009-06-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/bond.h, libavogadro/src/camera.h, libavogadro/src/color.h,
  libavogadro/src/glwidget.h, libavogadro/src/molecule.h,
  libavogadro/src/moleculefile.h, libavogadro/src/painter.h,
  libavogadro/src/plugin.h, libavogadro/src/pluginmanager.h,
  libavogadro/src/primitive.h, libavogadro/src/primitivelist.h,
  libavogadro/src/surfacemeshgenerator.h, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.h: Some header documentation changes resulting from
  updating python bindings.

  * libavogadro/src/animation.cpp, libavogadro/src/bond.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/python/Avogadro.py,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/TODO,
  libavogadro/src/python/animation.cpp, libavogadro/src/python/atom.cpp,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/python/cube.cpp,
  libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/elementtranslator.cpp,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/extension.cpp,
  libavogadro/src/python/fragment.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/mesh.cpp, libavogadro/src/python/meshgenerator.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/molecule.h,
  libavogadro/src/python/moleculefile.cpp,
  libavogadro/src/python/moleculelist.cpp, libavogadro/src/python/navigate.cpp,
  libavogadro/src/python/neighborlist.cpp, libavogadro/src/python/painter.cpp,
  libavogadro/src/python/painterdevice.cpp, libavogadro/src/python/plugin.cpp,
  libavogadro/src/python/pluginmanager.cpp,
  libavogadro/src/python/primitive.cpp,
  libavogadro/src/python/primitivelist.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/residue.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/std_vector.cpp, libavogadro/src/python/tool.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/camera.py,
  libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/mesh.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/tool.py,
  libavogadro/src/python/unittest/toolgroup.py,
  libavogadro/src/python/unittest/util.py: Update python, cleanup & added
  docstrings (copied from doxygen docs). Also checked function overloading &
  default arguments.  Minor code changes in cpp files: Animation: implement
  dynamicBonds() Bond: initialize m_aromaticity to false in ctor.
  Molecule::calculateAromaticity(): prevent crash (use OBMol::NumBonds()
  instead of numBonds() when accessing bonds from an OBMol.)

2009-06-17  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po, i18n/avogadro-es.po,
  i18n/avogadro-fi.po, i18n/avogadro-fr.po, i18n/avogadro-id.po,
  i18n/avogadro-it.po, i18n/avogadro-ja.po, i18n/avogadro-ko.po,
  i18n/avogadro-nb.po, i18n/avogadro-nl.po, i18n/avogadro-pl.po,
  i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po,
  i18n/avogadro-sk.po, i18n/avogadro-sv.po, i18n/avogadro-tr.po,
  i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po: Updated launchpad
  translations.

2009-06-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h: Handle VASP files as a special case in
  MoleculeFile

2009-06-17  David Lonie <loniedavid@gmail.com>

  * testfiles/VASP-8LiH/INCAR, testfiles/VASP-8LiH/KPOINTS,
  testfiles/VASP-8LiH/POSCAR, testfiles/VASP-8LiH/POTCAR,
  testfiles/VASP-8LiH/readme: Added VASP input set to testfiles.

2009-06-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/PythonDeps.cmake, libavogadro/src/python/sip.cpp: Add support
  for sip 4.8.0

2009-06-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/tests/moleculefiletest.cpp:
  CartoonEngine: remove debug output MoleculeFile: bug fix, make sure streampos
  contains the correct number of positions (was causing an endless loop in
  replaceMolecule)

2009-06-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/directorytreemodel.cpp,
  libavogadro/src/extensions/directorytreemodel.h,
  .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.ui,
  libavogadro/src/filetreeitem.cpp, libavogadro/src/filetreeitem.h: Fix
  PR#2663883 -- switch fragment window to QFileSystemModel. The downside is
  that we only can have the default set of fragments, not a list of
  directories, but this should be fine for 1.0. Evidently the best way to
  handle multiple root directories is with a proxy model.

2009-06-12  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot,
  libavogadro/src/extensions/gamessinputdialog.ui: Updated typo in GAMESS input
  builder.

  * libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/molecule.cpp: Add back feature to add hydrogens by pH. Fixes
  PR#2799259.

2009-06-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-ar.po, i18n/avogadro-bg.po, i18n/avogadro-ca.po,
  i18n/avogadro-cs.po, i18n/avogadro-de.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot,
  libavogadro/src/extensions/surfacedialog.ui: One more -- disambiguation of
  "In Display Type:"

  * avogadro/src/mainwindow.cpp, libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/spectratabnmr.ui: Translation corrections from
  Louis Ricard.

  * i18n/avogadro-ar.po, i18n/avogadro-bg.po, i18n/avogadro-ca.po,
  i18n/avogadro-cs.po, i18n/avogadro-de.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot,
  libavogadro/src/elementtranslator.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/tools/aligntool.h: Spelling corrections on translatable
  strings.

2009-06-11  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-ar.po, i18n/avogadro-bg.po, i18n/avogadro-ca.po,
  i18n/avogadro-cs.po, i18n/avogadro-de.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot,
  scripts/create-translations.sh: Latest translations from Launchpad plus
  updated POT files.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Fix prop model to handle numeric
  sorting. Solves PR#2803874

  * libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/numbertableitem.cpp, libavogadro/src/numbertableitem.h: Qt
  doesn't have a numeric QTableWidgetItem because it you can't subclass it
  correctly.

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  cmake/modules/FindLinguist.cmake, libavogadro/src/CMakeLists.txt: Switch PO
  translations to a new QT_WRAP_PO macro in FindLinguist. Works much, much
  better -- only updates when needed.

  * libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/numbertableitem.h, libavogadro/src/undosequence.h: Update
  documentation for NumberTableItem

  * libavogadro/src/numbertableitem.cpp, libavogadro/src/numbertableitem.h:
  Small class to handle numeric sorting -- surprused Qt doesn't have one.

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/zmatrixtool.cpp: Added some work and debugging messages
  to find parentless widgets. There's a bug on Mac where the program won't quit
  correctly.

2009-06-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, scripts/create-translations.sh: Improve
  translation creation & updating. The replacing of "-" with "_" caused some
  problems here since my build directory contains a "-" character.

2009-06-10  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: Fix bugs with "animate
  speed based on frequency" now works smoothly. Thanks to Jan Jensen for the
  suggestion.

  * libavogadro/src/python/moleculefile.cpp,
  libavogadro/src/python/openbabelwrapper.cpp, libavogadro/src/python/sip.cpp:
  Finish merge of OpenbabelWrapper -- didn't get Python code.

2009-06-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/src/openbabelwrapper.h:
  Merge OBwrapper & MOleculeFile. Now one class.

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/overlaysettingswidget.ui: Remove overlay settings
  widget -- confusing carbon copy of label engine.

  * i18n/avogadro-ar.po, i18n/avogadro-bg.po, i18n/avogadro-ca.po,
  i18n/avogadro-cs.po, i18n/avogadro-de.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot,
  libavogadro/src/extensions/surfacedialog.ui: Added some translation context,
  particularly for surfacedialog.ui

  * i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POT and PO files.

  * avogadro/src/avogadro.qrc, avogadro/src/icons/configure.png,
  avogadro/src/icons/document-open-recent.png,
  avogadro/src/icons/document-open-remote.png,
  libavogadro/src/tools/autoopttool.png, libavogadro/src/tools/measure.png:
  More icon updates. Now with an auto-opt icon (E with arrow)

2009-06-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, scripts/create-translations.sh: Probably the
  last PO translation update. Seems to work smoothly now. I *HATE*
  add_custom_target -- it re-runs all the time. If someone knows Cmake magic,
  let's fix this.

  * i18n/avogadro-ar.po, i18n/avogadro-bg.po, i18n/avogadro-ca.po,
  i18n/avogadro-cs.po, i18n/avogadro-de.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po:
  Launchpad PO files -- something modifies them in CMake scripts? I'll check.

  * i18n/avogadro-ar.po, i18n/avogadro-bg.po, i18n/avogadro-ca.po,
  i18n/avogadro-cs.po, i18n/avogadro-de.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Add PO files from Launchpad.

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, i18n/avogadro_ar.ts,
  i18n/avogadro_bg.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_CA.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_id.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sk.ts, i18n/avogadro_sv.ts,
  i18n/avogadro_tr.ts, i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts,
  i18n/avogadro_zh_TW.ts, i18n/libavogadro_ar.ts, i18n/libavogadro_bg.ts,
  i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts, i18n/libavogadro_de.ts,
  i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts, i18n/libavogadro_es.ts,
  i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts, i18n/libavogadro_id.ts,
  i18n/libavogadro_it.ts, i18n/libavogadro_ja.ts, i18n/libavogadro_ko.ts,
  i18n/libavogadro_nb.ts, i18n/libavogadro_nl.ts, i18n/libavogadro_pl.ts,
  i18n/libavogadro_pt.ts, i18n/libavogadro_pt_BR.ts, i18n/libavogadro_ru.ts,
  i18n/libavogadro_sk.ts, i18n/libavogadro_sv.ts, i18n/libavogadro_tr.ts,
  i18n/libavogadro_uk.ts, i18n/libavogadro_zh_CN.ts, i18n/libavogadro_zh_TW.ts,
  libavogadro/src/CMakeLists.txt, scripts/create-translations.sh: Switch to use
  PO files and lconvert for building translations. (Ideally,
  avogadro/src/CMakeLists.txt and libavogadro/src/CMakeLists.txt won't wrap TS
  files until translations are built.) CMake help here would be appreciated.
  Right now, it's a race condition.

2009-06-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/main.cpp:
  Ommit python module wrapper for now (wasn't working)

2009-06-08  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Added feature for faster
  vibration animations for high-frequency modes. Currently crashes for unknown
  reason.

  * libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/qcheminputdialog.ui: Add "Compute..." buttons for
  local calculations.

  * avogadro/src/avogadro.qrc, avogadro/src/engineitemmodel.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/autoopttool.png,
  libavogadro/src/tools/measure.png, libavogadro/src/tools/zmatrixtool.cpp,
  libavogadro/src/tools/zmatrixtool.qrc: Updated icons.

  * avogadro/src/avogadro.qrc, avogadro/src/engineitemdelegate.cpp,
  avogadro/src/engineitemmodel.cpp, avogadro/src/engineprimitiveswidget.ui,
  avogadro/src/icons/application-exit.png, avogadro/src/icons/arrow-down.png,
  avogadro/src/icons/arrow-left.png, avogadro/src/icons/arrow-right.png,
  avogadro/src/icons/arrow-up.png, avogadro/src/icons/avogadro-icon.png,
  avogadro/src/icons/avogadro_icon.png, avogadro/src/icons/back.png,
  avogadro/src/icons/colorize.png, avogadro/src/icons/configure.png,
  avogadro/src/icons/copy.png, avogadro/src/icons/cut.png,
  avogadro/src/icons/document-close.png,
  avogadro/src/icons/document-export.png,
  avogadro/src/icons/document-import.png, avogadro/src/icons/document-new.png,
  avogadro/src/icons/document-open.png, avogadro/src/icons/document-print.png,
  avogadro/src/icons/document-revert.png,
  avogadro/src/icons/document-save-as.png,
  avogadro/src/icons/document-save.png, avogadro/src/icons/down.png,
  avogadro/src/icons/edit-add-child.png, avogadro/src/icons/edit-add.png,
  avogadro/src/icons/edit-clear.png, avogadro/src/icons/edit-copy.png,
  avogadro/src/icons/edit-cut.png, avogadro/src/icons/edit-paste.png,
  avogadro/src/icons/edit-redo.png, avogadro/src/icons/edit-remove.png,
  avogadro/src/icons/edit-select-all.png, avogadro/src/icons/edit-undo.png,
  avogadro/src/icons/edit_add.png, avogadro/src/icons/edit_remove.png,
  avogadro/src/icons/exit.png, avogadro/src/icons/fileclose.png,
  avogadro/src/icons/fileexport.png, avogadro/src/icons/filenew.png,
  avogadro/src/icons/fileopen.png, avogadro/src/icons/filesave.png,
  avogadro/src/icons/filesaveas.png, avogadro/src/icons/fill-color.png,
  avogadro/src/icons/forward.png, avogadro/src/icons/minus.png,
  avogadro/src/icons/paste.png, avogadro/src/icons/plus.png,
  avogadro/src/icons/preferences-plugin.png, avogadro/src/icons/rebuild.png,
  avogadro/src/icons/redo.png, avogadro/src/icons/revert.png,
  avogadro/src/icons/tab-close.png, avogadro/src/icons/tab-detach.png,
  avogadro/src/icons/tab-duplicate.png, avogadro/src/icons/tab-new.png,
  avogadro/src/icons/tab_new.png, avogadro/src/icons/tab_remove.png,
  avogadro/src/icons/tools-report-bug.png, avogadro/src/icons/undo.png,
  avogadro/src/icons/up.png, avogadro/src/icons/view-fullscreen.png,
  avogadro/src/icons/view-list-tree.png, avogadro/src/icons/view-restore.png,
  avogadro/src/icons/window_fullscreen.png,
  avogadro/src/icons/window_nofullscreen.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui, avogadro/src/projecttreeeditor.qrc,
  avogadro/src/projecttreeeditor.ui, avogadro/src/settingsdialog.ui,
  libavogadro/src/tools/autoopttool.png, libavogadro/src/tools/autorotate.png,
  libavogadro/src/tools/manipulate.png, libavogadro/src/tools/measure.png,
  libavogadro/src/tools/zmatrix.png: Icon update, including new icons from KDE
  Oxygen theme.

2009-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/openbabelwrapper.cpp: Ported
  the bug fixes to file saving from MainWindow.  I ported the changes I made in
  MainWindow to fix the file saving bugs. I also added back in some error
  checking for normal saves of single molecules. Actual file saving seems to be
  working OK, but Avogadro does not register the changes have been saved and so
  prompts the user when closing - this needs fixing. We also need to do a lot
  of testing on these functions on all three platforms to ensure we have not
  had any regressions, such as the zero length file bug.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added in some extra
  logic to figure out which widget is active.

  * avogadro/src/detachedview.cpp, avogadro/src/detachedview.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Bring back the
  detached view functionality I have been missing so much!  This is me bringing
  back a detached GLWidget view. This is now mostly working, with the main
  remaining issue being how to set the active display to change the settings of
  the GLWidget. I have a few ideas, please take a look and see if you can see
  any more issues with it.

2009-06-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.h, libavogadro/src/python/glgraphicsview.cpp,
  libavogadro/src/python/main.cpp: Merge + remove GLGraphicsView python binding

2009-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/glgraphicsview.cpp, avogadro/src/glgraphicsview.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/glgraphicsview.cpp,
  libavogadro/src/glgraphicsview.h: Moved the GLGraphicsView classes into
  avogadro and out of our API.

  * avogadro/src/engineitemdelegate.cpp, avogadro/src/engineitemmodel.cpp:
  Improvements to the model and delegate - background comes out right now too.

  * libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/hbondengine.h, libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h: Implemented hasSettings virtual to
  speed up engine tree view display.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Removed settings
  button, added new engine view. Need icon for settings!  I removed the
  settings button, the grey boxes can now be used to get the settings dialog. I
  need a picture, but it works very nicely here. I would appreciate feedback
  and testing. I will look for an image to put in there too, but am open to
  suggestions.

  * avogadro/src/engineitemdelegate.cpp, avogadro/src/engineitemdelegate.h,
  avogadro/src/engineviewwidget.cpp, avogadro/src/engineviewwidget.h: New
  engine tree view with inline settings buttons.  First pass at a mew engine
  tree view with inline settings buttons. We could extend this to have inline
  duplicate and remove buttons in the future. I really need some images for
  settings (tools?). Remove and duplicate images would be useful too. They can
  be drawn by the item delegate if I can find/draw some icons.

  * avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h: Additions
  and improvements to the engine item model, facilitates inline settings now.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Added a new signal
  for engines to indicate whether they have a settings dialog.

2009-06-07  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp: Allow "always
  build" 3D coordinates for multi-molecule file. Prevent saving to gzip files.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Switch to table
  widget for selecting molecules. Looks great.

2009-06-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Keep the spectra plot widget the
  same size on toggleCustomize(). Fixes PR#2801471

2009-06-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Finally got rid
  of the two argument moleculeChanged signal.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Some changes and
  improvements to the Engine base class.  The default implementation only pays
  attention to Atom and Bond objects. If your engine handles other types the
  virtual functions can be reimplemented.

2009-06-06  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Added "view all molecules" -- need to debug, but
  heading out for errands.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Use MoleculeFile.
  Ready to use a QListWidget for selecting slices.

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp: Update to use titlesRef and
  streamposRef()

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h: Add
  filename parameters (currently unused) for replaceMolecule methods.

2009-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/mainwindow.cpp,
  avogadro/src/primitiveitemmodel.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molecule.cpp,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/glwidget.cpp:
  Getting rid of all the primitive caching in GLWidget.  This is the first part
  of my attempt to get rid of all the primitive caching in GLWidget. This works
  and compiles, but the PrimitiveItemModel is totally broken. Should be able to
  fix that up with a little work.

2009-06-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp: Add QStringList& MoleculeFile::titles()
  again as titles_p()

2009-06-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/plugin.cpp, libavogadro/src/plugin.h: Added a license
  virtual function to plugin, so that plugins can declare their license.

  * CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt: Find and link to
  zlib, qiocompressor implicitly links to zlib anyway.

2009-06-06  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/importdialog.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h, libavogadro/src/openbabelwrapper.cpp,
  libavogadro/src/python/openbabelwrapper.cpp: First pass at migrating
  MainWindow to OpenbabelWrapper & MoleculeFile. NOT ready for "prime-time"

2009-06-05  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/tools/autoopttool.cpp: Add
  energy of the molecule when doing forcefield or autoopt interactions. Fixes
  PR#1976211.

  * scripts/find-po-email.py, scripts/find-translators.sh: Add scripts to pull
  e-mail addresses (or names) from Launchpad PO files.

2009-06-05  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile, cmake/modules/AvoCPack.cmake: Bumped version
  number to 0.9.6 in preparation for release.

2009-06-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h: Fix bug in vibration dialog
  sorting. Closes PR#2801711

2009-06-05  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Track the current
  conformer (e.g., for setting current energy). Track whether we're using an
  estimated dipole moment -- if so, delete the cache when the geometry changes.

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.h: Add ellipsoid
  placeholder for ORTEP diagrams.

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Minor warning fix.

2009-06-04  Geoff Hutchison <babel@geoffhutchison.net>

  * builder/amino/l-ala.zmat,
  libavogadro/src/extensions/insertpeptideextension.cpp: Fix some peptide
  builder bugs. Now ensures all amino acids will have bonds.

2009-06-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/orbitalextension.cpp: Added support for reading
  .fchk.gz Gaussian output.

2009-06-03  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Finish addition of local
  Gaussian runs. Now works cleanly and will try to run formchk.

  * libavogadro/qtiocompressor/qtiocompressor.cpp,
  libavogadro/qtiocompressor/qtiocompressor.h: Added LGPL QtIOCompressor for
  reading compressed streams.

  * fragments/cyclic sugars/alpha-D-allopyranose.cml, .../cyclic
  sugars/alpha-D-arabinopyranose.cml, fragments/cyclic
  sugars/alpha-D-fucopyranose.cml, .../cyclic
  sugars/alpha-D-galactopyranose.cml, .../cyclic
  sugars/alpha-D-galacturonopyranose.cml, fragments/cyclic
  sugars/alpha-D-glucopyranose.cml, .../cyclic
  sugars/alpha-D-glucuronopyranose.cml, fragments/cyclic
  sugars/alpha-D-gulopyranose.cml, fragments/cyclic
  sugars/alpha-D-idopyranose.cml, fragments/cyclic
  sugars/alpha-D-lyxopyranose.cml, fragments/cyclic
  sugars/alpha-D-mannopyranose.cml, fragments/cyclic
  sugars/alpha-D-psicopyranose.cml, fragments/cyclic
  sugars/alpha-D-rhamnopyranose.cml, fragments/cyclic
  sugars/alpha-D-ribopyranose.cml, fragments/cyclic
  sugars/alpha-D-tagatopyranose.cml, fragments/cyclic
  sugars/alpha-D-talopyranose.cml, fragments/cyclic
  sugars/alpha-D-xylopyranose.cml, .../cyclic
  sugars/alpha-L-arabinopyranose.cml, fragments/cyclic
  sugars/alpha-L-fucopyranose.cml, .../cyclic
  sugars/alpha-L-galactopyranose.cml, fragments/cyclic
  sugars/alpha-L-lyxopyranose.cml, fragments/cyclic
  sugars/alpha-L-rhamnopyranose.cml, fragments/cyclic
  sugars/alpha-L-ribopyranose.cml, fragments/cyclic
  sugars/alpha-L-sorbopyranose.cml, fragments/cyclic
  sugars/alpha-L-xylopyranose.cml, fragments/cyclic
  sugars/beta-D-allopyranose.cml, fragments/cyclic
  sugars/beta-D-arabinopyranose.cml, fragments/cyclic
  sugars/beta-D-fructopyranose.cml, fragments/cyclic
  sugars/beta-D-fucopyranose.cml, fragments/cyclic
  sugars/beta-D-galactopyranose.cml, fragments/cyclic
  sugars/beta-D-glucopyranose.cml, fragments/cyclic
  sugars/beta-D-gulopyranose.cml, fragments/cyclic
  sugars/beta-D-idopyranose.cml, fragments/cyclic
  sugars/beta-D-lyxopyranose.cml, fragments/cyclic
  sugars/beta-D-mannopyranose.cml, fragments/cyclic
  sugars/beta-D-rhamnopyranose.cml, fragments/cyclic
  sugars/beta-D-ribopyranose.cml, fragments/cyclic
  sugars/beta-D-tagatopyranose.cml, fragments/cyclic
  sugars/beta-D-talopyranose.cml, fragments/cyclic
  sugars/beta-D-xylopyranose.cml, fragments/cyclic
  sugars/beta-L-arabinopyranose.cml, fragments/cyclic
  sugars/beta-L-lyxopyranose.cml, fragments/cyclic
  sugars/beta-L-ribopyranose.cml, fragments/cyclic
  sugars/beta-L-xylopyranose.cml,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Added cyclic sugars from
  Klotho repository, suggested by Magnus Lundborg

2009-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile, INSTALL, cmake/modules/AvoCPack.cmake,
  libavogadro/src/glwidget.h: Bumped version number in Doxyfile, few small
  updates to build files and docs.

2009-06-02  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, i18n/libavogadro.pot: POT files for 0.9.5.

  * i18n/avogadro_ar.ts, i18n/avogadro_bg.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_CA.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts, i18n/avogadro_fi.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_id.ts, i18n/avogadro_it.ts,
  i18n/avogadro_ja.ts, i18n/avogadro_ko.ts, i18n/avogadro_nb.ts,
  i18n/avogadro_nl.ts, i18n/avogadro_pl.ts, i18n/avogadro_pt.ts,
  i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts, i18n/avogadro_sk.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts, i18n/libavogadro_ar.ts,
  i18n/libavogadro_bg.ts, i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts,
  i18n/libavogadro_de.ts, i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts,
  i18n/libavogadro_es.ts, i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts,
  i18n/libavogadro_id.ts, i18n/libavogadro_it.ts, i18n/libavogadro_ja.ts,
  i18n/libavogadro_ko.ts, i18n/libavogadro_nb.ts, i18n/libavogadro_nl.ts,
  i18n/libavogadro_pl.ts, i18n/libavogadro_pt.ts, i18n/libavogadro_pt_BR.ts,
  i18n/libavogadro_ru.ts, i18n/libavogadro_sk.ts, i18n/libavogadro_sv.ts,
  i18n/libavogadro_tr.ts, i18n/libavogadro_uk.ts, i18n/libavogadro_zh_CN.ts,
  i18n/libavogadro_zh_TW.ts: Last pile of up-to-date translations.

2009-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/engineprimitiveswidget.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/primitivetreeview.cpp: Fixed primitiveitemmodel.h includes for
  new location.

  * avogadro/src/primitiveitemmodel.cpp, avogadro/src/primitiveitemmodel.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/primitiveitemmodel.h: Moved primitiveitemmodel - only used by
  the engine widget.

2009-06-01  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/molecularpropdialog.ui,
  .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h,
  libavogadro/src/extensions/propextension.cpp: New molecular property window
  with formula, number of atoms, etc.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Add parameter to
  test if dipole moments are estimated or known accurately.

2009-06-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added a default
  file name for new molecules.  Added a default file name for new molecules,
  this should make handling of molecules without a name easier for plugins.
  Fixes part of bug 2786154 for example.

2009-06-01  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/primitiveitemmodel.cpp: Add more krazy ignore comments

2009-06-01  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/settingsdialog.ui, i18n/avogadro.pot, i18n/libavogadro.pot,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh:
  Update POT to give contexts to messages.

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_bg.ts,
  i18n/avogadro_ca.ts, i18n/avogadro_cs.ts, i18n/avogadro_de.ts,
  i18n/avogadro_en_CA.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fi.ts, i18n/avogadro_fr.ts, i18n/avogadro_id.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sk.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts,
  i18n/libavogadro.pot, i18n/libavogadro_ar.ts, i18n/libavogadro_bg.ts,
  i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts, i18n/libavogadro_de.ts,
  i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts, i18n/libavogadro_es.ts,
  i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts, i18n/libavogadro_id.ts,
  i18n/libavogadro_it.ts, i18n/libavogadro_ja.ts, i18n/libavogadro_ko.ts,
  i18n/libavogadro_nb.ts, i18n/libavogadro_nl.ts, i18n/libavogadro_pl.ts,
  i18n/libavogadro_pt.ts, i18n/libavogadro_pt_BR.ts, i18n/libavogadro_ru.ts,
  i18n/libavogadro_sk.ts, i18n/libavogadro_sv.ts, i18n/libavogadro_tr.ts,
  i18n/libavogadro_uk.ts, i18n/libavogadro_zh_CN.ts, i18n/libavogadro_zh_TW.ts,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh:
  Updated translations for 0.9.5 from Launchpad.

2009-06-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/moleculefiletest.cpp: Update OpenbabelWrapper &
  MoleculeFile + unit tests

2009-05-31  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/colors/customcolor.cpp,
  libavogadro/src/colors/customcolor.h,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/tools/eyecandy.cpp: Revised
  syntax for Color class. No shadowed methods anymore.

  * avogadro/src/aboutdialog.cpp, avogadro/src/application.cpp,
  avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/updatecheck.cpp,
  libavogadro/src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertpeptideextension.cpp,
  libavogadro/src/extensions/pythonterminal.cpp, libavogadro/src/global.cpp,
  libavogadro/src/global.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/primitiveitemmodel.cpp: Krazy fixes (and comments for krazy
  ignore).

2009-05-30  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/updatedialog.cpp: Few small clean
  ups, added the option to disable the update checker at compile time.

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/updatecheck.cpp,
  avogadro/src/updatecheck.h, avogadro/src/updatedialog.cpp,
  avogadro/src/updatedialog.h: Added a class to check for an updated Avogadro
  version.  This is the first pass at a tool to check for an updated version of
  Avogadro. Feedback would be appreciated. It checks a file on the web server,
  parses it and displays the release notes if the version is greater than that
  installed. It will only prompt once for any given version update, and should
  provide a link to our updates page.

2009-05-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/src/openbabelwrapper.h,
  libavogadro/src/python/fileio.cpp,
  libavogadro/src/python/openbabelwrapper.cpp: Add support for error messages
  to OpenbabelWrapper and MoleculeFile

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/tools/autoopttool.cpp: Extract forces from OBMol to set
  Atom::forceVector() (AutoOptTool & ForceFieldExtension)

2009-05-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/python/template.py, python/extensiontemplate.py,
  python/proteinextension.py, python/standalone.py, python/tooltemplate.py:
  Move the python tool template to an example folder. (Fixes #2795303, bug
  about "('paint(', <Avogadro.GLWidget object at 0x10adf30>, ')')")

  * libavogadro/src/protein.cpp, libavogadro/src/protein.h: Update
  documentation & remove some obsolete methods (were used by old cartoon
  engine)

  * libavogadro/src/python/Avogadro.py, libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/main.cpp: Rename Avogadro.[so/pyd] to
  _Avogadro.[so/pyd] and create Avogadro.py to ensure standalone scripts can
  load OB formats.

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/neighborlist.cpp, libavogadro/src/neighborlist.h,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h,
  libavogadro/src/python/neighborlist.cpp,
  libavogadro/tests/neighborlisttest.cpp: NeighborList: Add constructor taking
  QList<Atom*> HBondEngine: respect engine's primitives (draw H-bonds only to
  atoms in the engine's primitive list) Protein: Add some documentation
  OrbitalExtension: update for NeighborList changes

  * libavogadro/src/CMakeLists.txt, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/boxcontrol.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/line.cpp, libavogadro/src/line.h,
  libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/python/glwidget.cpp: Remove BoxControl, Point & Line classes

2009-05-28  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/colors/customcolor.cpp: Save
  and read settings for colors.

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/pluginmanager.cpp: Add usefulness for extensions. Sort tools,
  extensions and colors before returning.

2009-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/elementdetail_p.cpp, libavogadro/src/elementitem_p.cpp:
  Fixed include, got rid of etab instantiations.

2009-05-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/chargecolor.h, libavogadro/src/colors/customcolor.cpp,
  libavogadro/src/colors/customcolor.h, libavogadro/src/colors/distancecolor.h,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.h,
  libavogadro/src/colors/residuecolor.h: Added custom color plugin. This should
  be statically linked.

2009-05-27  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added
  scaleLimits(PlotObject*) slot to plot widget. Automatically sets the limits
  of the plot based on the extremes of the passed PlotObject reference. The
  PlotObject can be omitted to look at all PlotObjects added to the widget.

2009-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/highlighter.h,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h,
  libavogadro/src/extensions/pythonterminalwidget.ui: Improve python terminal,
  now a single widget like a real terminal...

2009-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/trajvideomaker.h: Few minor clean ups, looking for
  the source of Windows linking issues.

2009-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/cartoonmeshgenerator.cpp,
  libavogadro/src/cartoonmeshgenerator.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.h: Move CartoonMeshGenerator
  ouside libavogadro's API

2009-05-27  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/insertpeptidedialog.ui,
  .../src/extensions/insertpeptideextension.cpp,
  .../src/extensions/insertpeptideextension.h: Add chain numbering, plus
  terminal modifications.

  * builder/amino/l-arg.zmat, builder/amino/l-ser.zmat: Fix bonding in ARG and
  SER residues.

2009-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/cartoonmeshbench.cpp:
  Remove CartoonMeshBench (obsolete)

2009-05-27  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Added element symbol + atom
  number for PR#2781947.

2009-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/elementdetail_p.cpp, libavogadro/src/elementdetail_p.h,
  libavogadro/src/elementitem_p.cpp, libavogadro/src/elementitem_p.h,
  libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/periodictablescene_p.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h:
  Separated private PeriodicTableView classes out into their own files.  Only
  the periodic table view class is exported, and so the rest did not belong in
  a public header. There are some issues with the global etab that should be
  looked at, but they are in private classes.

2009-05-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/python/painter.cpp: First pass at
  cleaning up the Painter API ready for 1.0.  I think most of the changes made
  are quite conservative. Made the API a little more consistent, removed the
  QObject as I do not see any need for this to be a QObject. Added a couple of
  placeholder functions.

2009-05-26  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/openbabelwrapper.cpp: Track
  down all remainin filenames needing QFile::encodeName.

  * avogadro/src/mainwindow.cpp, libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_nmr.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/periodictableview.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp: More localized numbers. This
  should be all of them.

2009-05-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/tools/bondcentrictool.cpp: Better localizations of numbers.

2009-05-25  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratabir.ui,
  libavogadro/src/extensions/spectratabnmr.ui,
  libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h: Separated out the different
  spectra types to make it easier to add more and reduce clutter.

2009-05-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: Fix PR#2728372. Sync force
  engine and display force vector in dialog.

  * CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/insertpeptidedialog.ui,
  .../src/extensions/insertpeptideextension.cpp,
  .../src/extensions/insertpeptideextension.h: Peptide builder, including
  fragments. Still needs end-group modification.

2009-05-24  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Moved spectra tabs to separate
  ui files.

  * libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added
  PlotWidget::setPointFollowMouse(bool), which places a small blue dot on the
  point nearest the cursor.

  * libavogadro/src/plotobject.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Added some slots for selecting points  The
  following slots will draw or clear (or both!) yellow circles at indicated
  points:  selectPoint(PlotPoint*) Draw circle at indicated PlotPoint
  selectPoints(QList<PlotPoint*>) Draw a circle at each PlotPoint in the list 
  clearAndSelectPoints(PlotPoint*) Same as selectPoint(PlotPoint*), but clears
  the selection first. clearAndSelectPoint(QList<PlotPoint*>) Same as
  selectPoints(QList<PlotPoint*>), but clears the selection first. 
  clearSelection() Clears all selected points.

2009-05-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added a
  mouseover signal with the x, y coords in data units.

2009-05-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/cartoonmeshgenerator.cpp,
  libavogadro/src/cartoonmeshgenerator.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/cartoonsettingswidget.ui, libavogadro/src/mesh.h,
  libavogadro/tests/CMakeLists.txt, libavogadro/tests/cartoonmeshbench.cpp:
  CartoonMeshGenerator: put the mesh generating code in a thread, clean it up
  and fix a some performance problems. For some reason I was calling
  Mesh::setVertices (and setNormals/setColors) after generating mesh parts for
  each residue inside one of the inner loop functions. The mesh is now
  generated in a few msec.  CartoonEngine: Add settings dialog with shape &
  color settings.  Mesh: Add numVertices() & numNormals(), calling
  mesh->vertices.size() always copies the whole list right?  CartoonMeshBench:
  Add benchmark for generating protein meshes. (not really needed anymore
  though)

2009-05-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added three
  new signals to PlotWidget to retrieve points from a left click. 
  pointClicked(double x, double y)	x and y coordinates of click in data units.
  pointClicked(QList<PlotPoint*> pl)	List of PlotPoints within 4 pixels of
  click. pointClicked(PlotPoint*)		PlotPoint nearest click. NULL if no points
  nearby.

2009-05-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/directorytreemodel.cpp,
  libavogadro/src/extensions/directorytreemodel.h,
  libavogadro/src/extensions/insertcommand.cpp,
  libavogadro/src/extensions/insertcommand.h,
  .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.h,
  libavogadro/src/extensions/insertfragmentdialog.ui,
  .../src/extensions/insertfragmentextension.cpp,
  .../src/extensions/insertfragmentextension.h,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/insertfragmentdialog.ui: Move insert fragment into an
  extension (out of the draw tool).

2009-05-22  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/extension.h: Add new signal for extensions with "delayed"
  undo commands (e.g., show a window) Should work well for property extension
  and others.

2009-05-22  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Small clean up of
  old classes no longer used/included.

2009-05-22  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/back.png, avogadro/src/down.png, avogadro/src/forward.png,
  avogadro/src/icons/back.png, avogadro/src/icons/down.png,
  avogadro/src/icons/forward.png, avogadro/src/icons/minus.png,
  avogadro/src/icons/plus.png, avogadro/src/icons/up.png,
  avogadro/src/minus.png, avogadro/src/plus.png, avogadro/src/up.png: Moved
  icons for project tree editor to be internally consistent.

  * avogadro/src/flowlayout.cpp, avogadro/src/flowlayout.h,
  avogadro/src/icontabwidget.cpp, avogadro/src/icontabwidget.h,
  avogadro/src/mainwindow.cpp: Removed flow layout in icon widget.

  * CMakeLists.txt, avogadro/src/mac/CompleteBundle.cmake.in,
  avogadro/src/mac/CreateBundle.sh.in: Attemping to get Qt plugins working for
  the Mac relocatable package.

  * i18n/avogadro.pot, i18n/libavogadro.pot: Current PO templates for
  Launchpad.

2009-05-20  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/extension.h,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  .../src/extensions/networkfetchextension.cpp: Added a new parameter to the
  Extension moleculeChanged signal.  This is still experimental, especially the
  naming of the enums. This allows the extension to specify how the new and old
  Molecule objects should be treated. So you can request a new window if the
  old molecule has been modified, prevent the old molecule from being deleted
  etc.

  * libavogadro/src/CMakeLists.txt, libavogadro/src/glhit.cpp,
  libavogadro/src/glhit.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Moved GLHit to its own header/implementation.

2009-05-20  Geoff Hutchison <babel@geoffhutchison.net>

  * builder/amino/d-ala.zmat, builder/amino/d-arg.zmat,
  builder/amino/d-asn.zmat, builder/amino/d-asp.zmat, builder/amino/d-cys.zmat,
  builder/amino/d-gln.zmat, builder/amino/d-glu.zmat, builder/amino/d-his.zmat,
  builder/amino/d-ile.zmat, builder/amino/d-leu.zmat, builder/amino/d-lys.zmat,
  builder/amino/d-met.zmat, builder/amino/d-phe.zmat, builder/amino/d-pro.zmat,
  builder/amino/d-ser.zmat, builder/amino/d-thr.zmat, builder/amino/d-trp.zmat,
  builder/amino/d-tyr.zmat, builder/amino/d-val.zmat, builder/amino/gly.zmat,
  builder/amino/l-ala.zmat, builder/amino/l-arg.zmat, builder/amino/l-asn.zmat,
  builder/amino/l-asp.zmat, builder/amino/l-cys.zmat, builder/amino/l-gln.zmat,
  builder/amino/l-glu.zmat, builder/amino/l-his.zmat, builder/amino/l-ile.zmat,
  builder/amino/l-leu.zmat, builder/amino/l-lys.zmat, builder/amino/l-met.zmat,
  builder/amino/l-phe.zmat, builder/amino/l-pro.zmat, builder/amino/l-pyl.zmat,
  builder/amino/l-sec.zmat, builder/amino/l-ser.zmat, builder/amino/l-thr.zmat,
  builder/amino/l-trp.zmat, builder/amino/l-tyr.zmat, builder/amino/l-val.zmat:
  Rename builder files to lowercase.

  * builder/amino/D-Ala.zmat, builder/amino/D-Arg.zmat,
  builder/amino/D-Asn.zmat, builder/amino/D-Asp.zmat, builder/amino/D-Cys.zmat,
  builder/amino/D-Gln.zmat, builder/amino/D-Glu.zmat, builder/amino/D-His.zmat,
  builder/amino/D-Ile.zmat, builder/amino/D-Leu.zmat, builder/amino/D-Lys.zmat,
  builder/amino/D-Met.zmat, builder/amino/D-Phe.zmat, builder/amino/D-Pro.zmat,
  builder/amino/D-Ser.zmat, builder/amino/D-Thr.zmat, builder/amino/D-Trp.zmat,
  builder/amino/D-Tyr.zmat, builder/amino/D-Val.zmat, builder/amino/Gly.zmat,
  builder/amino/L-Ala.zmat, builder/amino/L-Arg.zmat, builder/amino/L-Asn.zmat,
  builder/amino/L-Asp.zmat, builder/amino/L-Cys.zmat, builder/amino/L-Gln.zmat,
  builder/amino/L-Glu.zmat, builder/amino/L-His.zmat, builder/amino/L-Ile.zmat,
  builder/amino/L-Leu.zmat, builder/amino/L-Lys.zmat, builder/amino/L-Met.zmat,
  builder/amino/L-Phe.zmat, builder/amino/L-Pro.zmat, builder/amino/L-Pyl.zmat,
  builder/amino/L-Sec.zmat, builder/amino/L-Ser.zmat, builder/amino/L-Thr.zmat,
  builder/amino/L-Trp.zmat, builder/amino/L-Tyr.zmat, builder/amino/L-Val.zmat:
  Renaming builder files to lowercase.

2009-05-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/navigatesettingswidget.ui,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  New navigate settings widget - first phase - make Noel happier ;-)  Added a
  new settings widget to allow control of whether the eye candy (visual cues)
  are displayed. This is a long requested feature from a few users and closes
  feature request 2349900.

2009-05-20  Geoff Hutchison <geoff@geoffhutchison.net>

  * builder/amino/D-Ala.zmat, builder/amino/D-Arg.zmat,
  builder/amino/D-Asn.zmat, builder/amino/D-Asp.zmat, builder/amino/D-Cys.zmat,
  builder/amino/D-Gln.zmat, builder/amino/D-Glu.zmat, builder/amino/D-His.zmat,
  builder/amino/D-Ile.zmat, builder/amino/D-Leu.zmat, builder/amino/D-Lys.zmat,
  builder/amino/D-Met.zmat, builder/amino/D-Phe.zmat, builder/amino/D-Pro.zmat,
  builder/amino/D-Ser.zmat, builder/amino/D-Thr.zmat, builder/amino/D-Trp.zmat,
  builder/amino/D-Tyr.zmat, builder/amino/D-Val.zmat, builder/amino/Gly.zmat,
  builder/amino/L-Ala.zmat, builder/amino/L-Arg.zmat, builder/amino/L-Asn.zmat,
  builder/amino/L-Asp.zmat, builder/amino/L-Cys.zmat, builder/amino/L-Gln.zmat,
  builder/amino/L-Glu.zmat, builder/amino/L-His.zmat, builder/amino/L-Ile.zmat,
  builder/amino/L-Leu.zmat, builder/amino/L-Lys.zmat, builder/amino/L-Met.zmat,
  builder/amino/L-Phe.zmat, builder/amino/L-Pro.zmat, builder/amino/L-Pyl.zmat,
  builder/amino/L-Sec.zmat, builder/amino/L-Ser.zmat, builder/amino/L-Thr.zmat,
  builder/amino/L-Trp.zmat, builder/amino/L-Tyr.zmat, builder/amino/L-Val.zmat:
  Amino acid builder files.

2009-05-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/zmatrixtool.h: Fix
  some compile warnings.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/modeltest.cpp,
  libavogadro/tests/modeltest.h, libavogadro/tests/primitivemodeltest.cpp: Add
  test for QAbstractItemModels. Currently doesn't link.

2009-05-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h, libavogadro/src/protein.cpp,
  libavogadro/src/protein.h: Improve protein rendering (ported cartoon-like
  mesh generation from Zodiac www.zeden.org).

2009-05-19  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, i18n/avogadro.pot, i18n/libavogadro.pot,
  libavogadro/src/CMakeLists.txt, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/global.cpp, libavogadro/src/openbabelwrapper.cpp,
  scripts/create-translations.sh, scripts/extract-application-messages.sh,
  scripts/extract-library-messages.sh: More translation fixes.

  * libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/propmodel.cpp: Krazy fixes.

  * i18n/avogadro_ar.ts, i18n/avogadro_bg.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_CA.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts, i18n/avogadro_fi.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sk.ts, i18n/avogadro_sv.ts,
  i18n/avogadro_tr.ts, i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts,
  i18n/avogadro_zh_TW.ts, i18n/libavogadro.pot, i18n/libavogadro_ar.ts,
  i18n/libavogadro_bg.ts, i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts,
  i18n/libavogadro_de.ts, i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts,
  i18n/libavogadro_es.ts, i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts,
  i18n/libavogadro_it.ts, i18n/libavogadro_ja.ts, i18n/libavogadro_ko.ts,
  i18n/libavogadro_nb.ts, i18n/libavogadro_nl.ts, i18n/libavogadro_pl.ts,
  i18n/libavogadro_pt.ts, i18n/libavogadro_pt_BR.ts, i18n/libavogadro_ru.ts,
  i18n/libavogadro_sk.ts, i18n/libavogadro_sv.ts, i18n/libavogadro_tr.ts,
  i18n/libavogadro_uk.ts, i18n/libavogadro_zh_CN.ts, i18n/libavogadro_zh_TW.ts,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh,
  scripts/extract-messages.sh: Split translations into libavogadro and avogadro
  templates.

  * libavogadro/src/animation.h, libavogadro/src/atom.h,
  libavogadro/src/bond.h, libavogadro/src/boxcontrol.h,
  libavogadro/src/camera.h, libavogadro/src/color.h,
  libavogadro/src/colorbutton.h, libavogadro/src/cube.h,
  libavogadro/src/global.h: Update some copyright lines based on automated
  copyright.py script from Carsten.

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/pythontool_p.cpp, libavogadro/src/pythontool_p.h,
  libavogadro/src/tool.h, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/zmatrixtool.h: Translation fixes. Use QString::arg()
  more often, and add new Tool::settingsTitle() to improve context.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/molpro.cpp,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp: Fix additional
  QString/QChar krazy warnings.

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Add support for running
  local g03 jobs.

2009-05-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotwidget.cpp,
  libavogadro/src/tools/zmatrixtool.cpp: More krazy & compile warnings fixes.

2009-05-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/gl2ps/TODO, avogadro/gl2ps/gl2ps.c, avogadro/gl2ps/gl2ps.h,
  avogadro/gl2ps/gl2ps.pdf, avogadro/gl2ps/gl2psTest.c,
  avogadro/gl2ps/gl2psTestSimple.c: Import of GL2PS 1.3.3 -- latest stable
  release.

  * avogadro/src/aboutdialog.cpp, avogadro/src/addenginedialog.cpp,
  avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/pluginsettings.h, avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/selectiondelegate.h,
  avogadro/src/projecttreeitem.h, avogadro/src/savedialog.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/openbabelwrapper.cpp,
  libavogadro/src/plotwidget.cpp, libavogadro/src/protein.cpp,
  libavogadro/src/pythonengine_p.h, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonextension_p.h, libavogadro/src/pythontool_p.h,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/zmatrixdialog.h: A
  whole pile of Krazy fixes. Still a bunch of GCC warnings to clean up too.

2009-05-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/skeletontree.cpp,
  libavogadro/src/tools/skeletontree.h: Use const reference function arguments,
  rather than passing by value.

2009-05-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h,
  avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/mainwindow.cpp: Avogadro: connect the
  PluginManager::reloadPlugins() signal to the new GLWidget::reloadEngines()
  method and properly repopulate the EngineListView (EngineItemModel)

2009-05-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Check visibility
  of toolbars before fullscreen/normal mode. Added shortcut of escape key to
  Full Screen / normal mode.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Make sure tool
  settings and engine settings buttons are synced with visibility of the docks.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.h: Move most "properties" to the "View"
  menu -- hopefully it will be more intuitive to find them there.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: More GUI changes. New toolbar adds QPushButtons
  to hide/show tool and display settings.

2009-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/pythonengine_p.cpp,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythonthread_p.h,
  libavogadro/src/pythontool_p.cpp: Fix python Global Interpreter Lock (GIL)
  usage. (note: when running standalone python scripts, the Qt event loop seems
  to run in another thread which means we have to obtain the GIL. The
  pythonthread_p.h header contains a simple class which calls
  PyGILState_Ensure() in the constructor and PyStateGIL_Release in the
  destructor.

  * libavogadro/src/pythonengine_p.cpp, libavogadro/src/pythonengine_p.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythonextension_p.h,
  libavogadro/src/pythontool_p.cpp, libavogadro/src/pythontool_p.h: Remove d
  pointer from private classes (PythonTool, PythonExtension, PythonEngine).

  * avogadro/src/mainwindow.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/std_vector.cpp, libavogadro/src/pythonengine_p.cpp,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/pythontool_p.cpp: Some changes to the way python is
  initialized.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Add
  Molecule::conformers() & fix for Molecule::clearConformers (set m_atomPos to
  m_atomConformers[0] after deleting all other conformers)

2009-05-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/settingsdialog.cpp,
  avogadro/src/settingsdialog.ui, libavogadro/src/toolgroup.cpp: Move tools
  into a standard QToolBar with extra shortcuts (Ctrl+1, Ctrl+2, etc.) Still
  need to add buttons for toggling the toolSettings and displaySettings to the
  toolbar.

2009-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h, libavogadro/src/openbabelwrapper.cpp,
  libavogadro/src/openbabelwrapper.h: Add support for reading multiple
  molecules to OpenbabelWrapper. A file is read in a separate thread. By
  default, OpenbabelWrapper::readFile(...) waits for the thread to finish. It
  is also possible to connect to the returned object and a signal will be
  emitted when the file is read. (For reading large files +10000 molecules).
  Conformers are automatically detected which allows us to use any OBFormat
  with support for multiple molecules as conformer files.

  * libavogadro/src/animation.cpp, libavogadro/src/animation.h,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/python/animation.cpp: Some improvements to the Animation
  class. Remove duplicated code from the animation extension and use Animation
  class. Also added optional "dynamic bonds" for animating QM reactions. TODO:
  add a plot widget to display the energy

2009-05-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianinputdialog.ui,
  libavogadro/src/extensions/orbitaldialog.ui: Fix warnings from duplicate
  horizontal spacer names. Addresses PR#2786502.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/bondcentrictool.cpp: Fix bugs with editing angle and
  torsion values. Now you can set them as you wish.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/quaternion.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h:
  Remove home-grown Quaternions from BondCentric tool and port to
  Eigen/Geometry classes. Much cleaner and appears to give a nice speed boost
  too.

  * libavogadro/src/animation.cpp, libavogadro/src/animation.h: Start on
  animation class documentation.

  * libavogadro/src/colorbutton.cpp,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfacesettingswidget.ui: Switch ColorButton to the
  Avogadro namespace.

2009-05-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfacesettingswidget.ui: Fixed to bring all the way
  into Avogadro namespace. Ported UI files.

2009-05-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colorbutton.h, libavogadro/src/glwidget.h,
  libavogadro/src/line.h, libavogadro/src/neighborlist.h,
  libavogadro/src/plotaxis.h, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.h, libavogadro/src/plotwidget.h,
  libavogadro/src/point.h, libavogadro/src/protein.h,
  libavogadro/src/pythoninterpreter.h, libavogadro/src/zmatrix.h: Documentation
  fixes.

  * CMakeLists.txt, avogadro/src/mac/CompleteBundle.cmake.in,
  avogadro/src/mac/CreateBundle.sh.in, libavogadro/src/CMakeLists.txt: Fixes
  for Cmake builds with Mac .app package.

2009-05-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/src/openbabelwrapper.h:
  Openbabel wrapper class to open and save files.  This class takes care of
  opening and saving files using Openbabel. It could use some finer grained
  error control possibly, it does take care of preserving UTF8 file names and
  allows for simple calls that can read and write molecule data files.

2009-05-14  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui: Remove
  "smooth animations option." Always use smooth animations, unless the system
  is large (> 1000 atoms). We can debate the "large" threshold, but why
  wouldn't we want some eyecandy?

2009-05-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/CMakeLists.txt, libavogadro/src/colors/chargecolor.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/basisset.cpp,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  .../src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/skeletontree.cpp,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixmodel.cpp,
  libavogadro/src/tools/zmatrixtool.cpp: Migrated plugins to use qt4_wrap_cpp
  to generate MOC files.  All plugins, apart from the few static ones, now use
  qt4_wrap_cpp macro to generate moc files, these are then built and linked to
  the plugin rather than directly included. Some extra logic has been
  introduced into the avogadro_plugin function to deal with grc and ui files
  more gracefully too.

2009-05-14  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Add a "slop" to make it easier to pick
  atoms.

2009-05-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/molpro.cpp, libavogadro/src/extensions/molpro.h:
  Patch from Michael Banck (PR#2786157) Update for the molpro molecular orbital
  code. Now can parse and display cc-pVDZ basis set based MOs. Cartesian basis
  sets still not implemented (but they are not default in MOLPRO anyway).

2009-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, cmake/modules/AvogadroConfigVersion.cmake.in: Added
  versioning to the AvogadroConfig logic.  Now added versioning to the
  AvogadroConfig logic, see the documentation to find_package for more details.
  In CMakeLists.txt files simply add a line such as find_package(Avogadro 0.9.4
  REQUIRED) to only accept Avogadro versions greater than or equal to 0.9.4. As
  a side effect this will also stop Mac installed AvogadroConfig.cmake files
  from being used, if the config file has no accompanying version file is will
  be rejected when a version is requested.

2009-05-13  Marcus Hanwell <mhanwell@cobalt.chem.pitt.edu>

  * CMakeLists.txt, libavogadro/src/pluginmanager.cpp: Mac changes, default to
  installing in /Applications/Avogadro.app, load plugins relative to location
  only.

  * CMakeLists.txt, avogadro/src/CMakeLists.txt: Added a new option to make
  packages, initially just affects the make install for Mac.

2009-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/tests/CMakeLists.txt: Improved the handling of library
  dependencies for Avogadro.  Renamed the avogadro-lib target to avogadro, this
  allows CMake to automatically assemble the library dependencies for the
  Avogadro library. This fixes link issues seen on the Mac.

2009-05-13  Marcus Hanwell <mhanwell@cobalt.chem.pitt.edu>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/mac/CompleteBundle.cmake.in,
  avogadro/src/mac/CreateBundle.sh.in, avogadro/src/main.cpp,
  cmake/modules/AvoCPack.cmake, cmake/modules/AvoCPackOptions.cmake.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/pluginmanager.cpp:
  Relocatable Apple Mac package as part of a super project.  This is the first
  merge of work I have been doing to make a relocatable Mac application bundle
  with all libraries included. Currently this works if you run make install, I
  have been using Avogadro0.9.app as that can be installed in parallel to the
  default Avogadro.app directory. Initial testing looks pretty good, but some
  more work is needed to automate the actual building of a package.

2009-05-13  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: General appearance and code cleanup
  of properties tables.

2009-05-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h: First pass at editing bond, angle,
  and dihedral properties. Changing bond length now works.

2009-05-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/animation.cpp, libavogadro/src/python/atom.cpp,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/python/cube.cpp,
  libavogadro/src/python/elementtranslator.cpp,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/extension.cpp,
  libavogadro/src/python/fragment.cpp,
  libavogadro/src/python/glgraphicsview.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/mesh.cpp, libavogadro/src/python/meshgenerator.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/navigate.cpp,
  libavogadro/src/python/neighborlist.cpp,
  libavogadro/src/python/periodictableview.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/pluginmanager.cpp,
  libavogadro/src/python/primitive.cpp,
  libavogadro/src/python/primitivelist.cpp, libavogadro/src/python/residue.cpp,
  libavogadro/src/python/std_vector.cpp, libavogadro/src/python/tool.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/mesh.py: Update python bindings for recent
  changes

2009-05-12  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/cube.cpp, libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h, libavogadro/src/meshgenerator.cpp,
  libavogadro/src/navigate.cpp, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h: Fix a variety of minor compiler errors.

2009-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/primitive.h,
  libavogadro/src/residue.cpp, libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/drawcommand.cpp: Use templated C++ function to find max
  unsigned long value.

2009-05-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Added
  a timer-based key handler. Now accepts multi-character element symbols.

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h:
  Handle one-character elements. You can now type "c" or "o" to switch to
  carbon and oxygen.

2009-05-11  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h:
  Add simple QWidget::event handlers for future expansion, as suggested by Qt
  coding conventions: http://qt.gitorious.org/qt/pages/CodingConventions

  * avogadro/src/engineitemmodel.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/pluginsettings.cpp, avogadro/src/settingsdialog.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/indexcolor.cpp, libavogadro/src/toolgroup.cpp: Don't
  use dynamic casts unless necessary. Even on Mac, qobject_cast works great.

  * libavogadro/src/atom.cpp, libavogadro/src/primitive.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/drawcommand.cpp: Fix use of -1 with unsigned int/long.
  Instead use UINT_MAX or ULONG_MAX.

2009-05-10  marcus <marcus@eeepc.(none)>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/cylinder_p.cpp, libavogadro/src/cylinder_p.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glpainter_p.cpp, libavogadro/src/glpainter_p.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h,
  libavogadro/src/pythonengine_p.cpp, libavogadro/src/pythonengine_p.h,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonextension.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythonextension_p.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h,
  libavogadro/src/pythontool_p.cpp, libavogadro/src/pythontool_p.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/sphere_p.cpp, libavogadro/src/sphere_p.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/textrenderer_p.cpp, libavogadro/src/textrenderer_p.h: Moved
  private headers to classname_p.h header flies.  All private headers should be
  placed in a classname_p.h style file name in order to make it clear that
  these are private classes not exposed in our API. Private classes do not need
  d-pointers etc as their symbols are not exported and no external programs
  should be referencing them.

2009-05-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginsettings.cpp, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonscript.cpp,
  libavogadro/src/pythonscript.h, libavogadro/src/pythontool.cpp:
  libavogadro/src/pythonscript.*: Add identifier method. Use the Sha1 of
  script's content as identifier. (Fixes: 
  libavogadro/src/python[tool,engine,extension].cpp: Use the new
  PythonScript::identifier() method.

2009-05-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamesshighlighter.h: Added some more logic to the
  syntax highlighting, experimenting with the rules.

  * .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/networkfetchextension.h: Added function to fetch a
  file from any URL.

2009-05-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added support for loading
  calculated spectra that may not be included in molecule, e.g. PWSCF output. 
  PWSCF output does not contain geometries, and a user requested the ability to
  load the IR data that it outputs.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Peak labeling for NMR

2009-05-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added gaussian widths to NMR
  spectra.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Cleaned up signals and added a
  reference offset to NMR plots.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp: Allow inspection of
  vibrational frequencies when there are no intensities.  Spectra extension
  uses an arbitrary intensity and warns the user, vibration extension uses "-"
  in place of the intensity on the table.

2009-05-04  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added inital support for
  visualizing NMR data stored as "NMR Isotropic Shift" per OBAtom.

2009-05-04  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts,
  libavogadro/src/elementtranslator.h: Update translations.

2009-05-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/glwidget.cpp: Fixed the engine list view when plugins are
  removed.  This fixes the case where an engine plugin is removed and the names
  got messed up. It still does not handle the case where new engine plugins are
  added but not added automatically.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamesshighlighter.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h: Initial support for syntax
  highlighting in GAMESS input generator.  This is still quite early stage, and
  needs many more rules. It already demonstrates the basic concepts after
  talking to Albert DeFusco about GAMESS syntax highlighting and some of the
  work he has done with vim.

2009-05-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.h, scripts/cmake-msvc2008.bat:
  libavogadro/src/extensions/pythonterminal.h: fix header issue.

2009-05-02  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile, avogadro/CMakeLists.txt,
  avogadro/src/config.h.in, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/config.h.in: Bumped the
  version number to 0.9.4 in preparation for tagging.  Centralised the version
  numbering - only needs changing in TWO places now!

  * CMakeLists.txt, avogadro/src/CMakeLists.txt: Added an option to use RPath
  at install tiem. Can cause issues on some distros if installed in /usr.

2009-05-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotaxis.cpp, libavogadro/src/plotaxis.h,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Cleaned up whitespace with QtCreator.

2009-05-01  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated translations for
  0.9.4.

2009-05-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonengine.h, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythonextension.h, libavogadro/src/pythonscript.cpp,
  libavogadro/src/pythonscript.h, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h: Some changes to python includes to compile with
  cryos' recent changes

  * libavogadro/src/python/engine.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/pluginmanager.cpp, libavogadro/src/python/tool.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/toolgroup.py: Some updates to the python
  bindings and python unit tests. All tests should pass again.

  * scripts/cmake-msvc2008.bat, scripts/cmake-vs2005.bat: Rename
  scripts/cmake-vs2005.bat to scripts/cmake-msvc2008.bat

  * cmake/modules/AvoCPack.cmake, cmake/modules/FindNumpy.cmake,
  libavogadro/src/python/CMakeLists.txt, scripts/cmake-vs2005.bat:
  cmake/modules/AvoCPack.cmake: Changes to correctly include all python stuff 
  cmake/modules/FindNumpy.cmake: Small bug fix, wasen't working here 
  libavogadro/src/python/CMakeLists.txt: Set library SUFFIX property to ".pyd"
  on WIN32  scripts/cmake-vs2005.bat: update for python & GLSL support

2009-04-30  Michael Banck <michael.banck@ch.tum.de>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/molproinputdialog.h,
  libavogadro/src/extensions/molproinputdialog.ui: New Molpro input file
  generator.

2009-04-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/networkfetchextension.h: First network aware
  extension - direct PDB downloads.  This is the first network aware extension.
  I added QtNetwork to the Avogadro library as I think we will want to use the
  network more and more in the future. This extension is a very simple proof of
  concept - it attempts to download the named PDB from the PDB site.

  * avogadro/src/CMakeLists.txt, libavogadro/include/avogadro/animation.h,
  libavogadro/include/avogadro/atom.h, libavogadro/include/avogadro/bond.h,
  libavogadro/include/avogadro/boost.h,
  libavogadro/include/avogadro/boxcontrol.h,
  libavogadro/include/avogadro/camera.h, libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/colorbutton.h,
  libavogadro/include/avogadro/cube.h, libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/elementtranslator.h,
  libavogadro/include/avogadro/engine.h,
  libavogadro/include/avogadro/extension.h,
  libavogadro/include/avogadro/filetreeitem.h,
  libavogadro/include/avogadro/fragment.h,
  libavogadro/include/avogadro/glgraphicsview.h,
  libavogadro/include/avogadro/global.h,
  libavogadro/include/avogadro/glpainter.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/idlist.h, libavogadro/include/avogadro/line.h,
  libavogadro/include/avogadro/mesh.h,
  libavogadro/include/avogadro/meshgenerator.h,
  libavogadro/include/avogadro/molecule.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/navigate.h,
  libavogadro/include/avogadro/neighborlist.h,
  libavogadro/include/avogadro/painter.h,
  libavogadro/include/avogadro/painterdevice.h,
  libavogadro/include/avogadro/periodictableview.h,
  libavogadro/include/avogadro/plotaxis.h,
  libavogadro/include/avogadro/plotobject.h,
  libavogadro/include/avogadro/plotpoint.h,
  libavogadro/include/avogadro/plotwidget.h,
  libavogadro/include/avogadro/plugin.h,
  libavogadro/include/avogadro/pluginmanager.h,
  libavogadro/include/avogadro/point.h,
  libavogadro/include/avogadro/povpainter.h,
  libavogadro/include/avogadro/primitive.h,
  libavogadro/include/avogadro/primitiveitemmodel.h,
  libavogadro/include/avogadro/primitivelist.h,
  libavogadro/include/avogadro/protein.h,
  libavogadro/include/avogadro/pythonerror.h,
  libavogadro/include/avogadro/pythoninterpreter.h,
  libavogadro/include/avogadro/pythonscript.h,
  libavogadro/include/avogadro/residue.h,
  libavogadro/include/avogadro/sphere.h,
  libavogadro/include/avogadro/textrenderer.h,
  libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h,
  libavogadro/include/avogadro/undosequence.h,
  libavogadro/include/avogadro/zmatrix.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp, libavogadro/src/protein.cpp: Use CMake to
  generate the include directory at build time.  This is all part of my evil
  plan to have CMake do all the mundane tasks so that you have no excuse but to
  implement cool new features. The Avogadro headers are now copied at CMake
  time into the build directory, this is used to build against and those same
  headers are installed.

2009-04-28  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/plotwidget.cpp: Added an extra include that is needed for
  Open Babel 2.2.1.

  * avogadro/src/engineitemmodel.cpp, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/boxcontrol.h, libavogadro/src/color.h,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molecule.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h, libavogadro/src/textrenderer.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixdialog.h,
  libavogadro/src/tools/zmatrixdialog.ui,
  libavogadro/src/tools/zmatrixtool.cpp, libavogadro/src/tools/zmatrixtool.h:
  Removed several includes from glwidget.h, less global includes.

  * CMakeLists.txt, cmake/modules/CTestCustom.cmake.in: GCC flags tweaked and
  CTestCustom.cmake added for CDash submission  I removed -Wundef from the GCC
  flags for now, too many warnings from the Boost headers are generated to be
  useful. I also added a CTestCustomConfig.cmake.in to ignore some warnings on
  Windows and for eigen.cpp which has a massive number of warnings (this should
  be looked at separately).

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/moleculebench.cpp:
  Added some initial Molecule benchmarking code.

2009-04-24  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, cmake/modules/AvogadroConfig.cmake.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Modifications to build system to allow
  including in a super project.

2009-04-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Major code changes to
  spectradialog.*  * Added many more comments * Organized functions a bit more
  logically * Separated out and identified all spectra-specific var, functions,
  etc * Rewrote import function to be much smaller.

2009-04-23  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Update
  to prevent Python breakage. Use an overloaded parameter for loadFactories().

2009-04-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, cmake/modules/AvogadroConfig.cmake.in,
  cmake/modules/AvogadroUse.cmake: Install an AvogadroConfig.cmake file and
  supporting files.  Changes to install an AvogadroConfig.cmake file, along
  with several supporting files. This negates the need for a FindAvogadro.cmake
  file and also introduces an AvogadroUse.cmake file which makes building
  against the installed Avogadro library much simpler. Supporting example
  project will be added to GitHub shortly.

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Tweaks
  to the plugin loading code  Addded the contrib directory to the list of
  default searched paths. Also added a new void
  PluginManager::loadFactories(const QString& dir) to load plugins from a
  supplied directory path.

  * avogadro/src/aboutdialog.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp,
  libavogadro/src/boxcontrol.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/color.cpp, libavogadro/src/colors/chargecolor.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/idlist.cpp, libavogadro/src/plugin.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/primitivelist.cpp,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythontool.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/undosequence.cpp: Fixing up config.h includes - many places
  where it was not needed.

2009-04-22  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, CTestConfig.cmake, cmake/modules/AvoCTestConfig.cmake: The
  CTestConfig.cmake was moved, some small changes to the build system.

2009-04-21  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h: Renamed member var and fixed
  segfault in Qt 4.4 work around.  schemes --> m_schemes QHashIterator in
  writeSettings() never advanced to allow data to be accessed, resulting in
  non-persistent schemes and assertion problems.

2009-04-20  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h: Cleanup and put in frame work to
  begin thinking about other sorts of spectra.

2009-04-17  Michael Banck <michael.banck@ch.tum.de>

  * testfiles/methane.g03, testfiles/methane.inp, testfiles/methane.mp,
  testfiles/methane.mpo, testfiles/methane.nwo: Added some new test files for
  quantum output processing.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/molpro.cpp, libavogadro/src/extensions/molpro.h,
  libavogadro/src/extensions/orbitalextension.cpp: Added support for reading
  Molpro output files in.

2009-04-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added a new signal
  to the Molecule, used in the properties extensions. Still needs work.

2009-04-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/include/avogadro/elementtranslator.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/elementtranslator.cpp,
  libavogadro/src/elementtranslator.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/simplewireengine.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/python/TODO,
  libavogadro/src/tools/drawtool.cpp: Moved the ElementTranslator class to be
  consistent with the class name.

2009-04-14  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.ui: Add multiplicity options
  back in to nwchem generator (only for DFT)

2009-04-12  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.ui: Cleaned up nwchem input
  generator.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.h,
  libavogadro/src/extensions/nwcheminputdialog.ui: Initial addition of NWChem
  input generator.

2009-04-09  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectraextension.cpp: Cleaned up whitespace with
  qt creator

2009-04-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/simplewireengine.h: Added a new engine - super simple
  wire frame engine. Mainly for testing purposes and as an example of a very
  simple engine.

2009-04-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Added an option to optimize the font size of
  exported images to spectradialog.*, and the necessary code to plotwidget.*.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui, libavogadro/src/plotwidget.cpp:
  Fixed some font and spacing issues in image export.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui, libavogadro/src/plotobject.cpp,
  libavogadro/src/plotobject.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: * Fixed up image export with some new options.
  * Added file output to the plot widget

2009-04-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Added a new CMake function -
  avogadro_plugin. Migrated plugins to it.  The avogadro_plugin function allows
  developers to easily add new plugins, makes our build files more concise.
  Allows for global changes in the way plugins are built in the future.

2009-04-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Moved spectra image export to a
  tab.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added a spectra tsv export
  feature.

2009-04-06  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, avogadro/src/aboutdialog.cpp, avogadro/src/config.h.in,
  avogadro/src/main.cpp, libavogadro/src/config.h.in,
  libavogadro/src/global.cpp, libavogadro/src/global.h: Updates to the handling
  of builds from Git clones - now report the hash the build was made against.

2009-04-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Restructure GUI to use tabs in
  the spectra extension

2009-04-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Spectra now use persistent,
  customizable color schemes.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/spectraextension.h: * Added persistant settings to
  spectra extension * Cleaned up debugging output * Started framework for color
  schemes

2009-04-03  David Lonie <loniedavid@gmail.com>

  * testfiles/methanol.jdx, testfiles/methanol.nwo: Added two testfiles: an
  NWChem out with IR data, and a .jdx for JCAMP-DX spectrum tests.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Better handling in spectra
  extension for files without valid data.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Fixed some bugs in the spectra
  extension

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/spectraextension.h,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Moved spectra plotting to its
  own extension.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added a gaussian superposition
  of peaks to vibrationplot.*.

2009-04-01  Geoff Hutchison <babel@geoffhutchison.net>

  * CMakeLists.txt, scripts/create-translations.sh: Added custom command for
  "create-translations" -- use lconvert from PO -> TS

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Update translations from
  Launchpad.

  * libavogadro/src/tools/zmatrixmodel.cpp,
  libavogadro/src/tools/zmatrixmodel.h: Added Q_OBJECT macro and moc output.

2009-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Improvements to orbital
  engine handling of colored meshes.

  * CMakeLists.txt, avogadro/CMakeLists.txt, cmake/modules/AvoCPack.cmake,
  libavogadro/CMakeLists.txt: Version bump in preparation for tagging the 0.9.3
  release.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Enable configuration of plot
  font in vibrationplot.*..

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Options to
  get font are nice too :)

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added code to
  change font in plot widget.

2009-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixdialog.h,
  libavogadro/src/tools/zmatrixdialog.ui,
  libavogadro/src/tools/zmatrixmodel.cpp, libavogadro/src/tools/zmatrixmodel.h,
  libavogadro/src/tools/zmatrixtool.cpp, libavogadro/src/zmatrix.cpp,
  libavogadro/src/zmatrix.h: Lots of changes to the z matrix tool. It actually
  does stuff now, disabling by default. It is far from ready to be used yet.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added support for absorbances in
  vibrationplot.*

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Replaced vibrationplot.* scaling
  slider/text edit with spin box

2009-03-31  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: plotwidgets
  can zoom with scroll wheel now.

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Allow a
  default limit to be set and reapplied by a doubleclick. Also change the
  click-and-drag to use the right mouse button for consistancy with the gl
  canvas.

2009-03-31  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h: Initial fixes for bug 2723686,
  create dialogs for the views. I am not sure that the logic is correct for the
  views created here.

2009-03-31  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added simple
  click-and-drag plot movement.

2009-03-30  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added option to toggle off the
  calculated spectra, just for completeness sake.

2009-03-29  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.ui: Fixed some git-merging
  conflicts...

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added options to vibrationplot.*
  for color, font size, etc...

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added options to vibrationplot.*
  for color, font size, etc...

2009-03-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/molecule.cpp: Do not do ring perception on load - terrible
  performance for big systems. Also blocked signals for performance reasons and
  updated the super cell extension a little.

2009-03-28  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Grouped customization options
  together.

2009-03-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/include/avogadro/zmatrix.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixdialog.h,
  libavogadro/src/tools/zmatrixdialog.ui,
  libavogadro/src/tools/zmatrixmodel.cpp, libavogadro/src/tools/zmatrixmodel.h,
  libavogadro/src/tools/zmatrixtool.cpp, libavogadro/src/tools/zmatrixtool.h,
  libavogadro/src/zmatrix.cpp, libavogadro/src/zmatrix.h: Initial work on a new
  z matrix editor. Far from complete just yet. Questionable whether it belongs
  with the other tools, but does need mouse interaction.

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Some
  improvements to the drawing tool, lazy initialization, clean ups.

2009-03-27  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added simple image output to
  vibrationplot.*.

2009-03-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h:
  Reduced the number of includes massively.

2009-03-26  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added in an import function to
  vibrationplot.* that can overlay experimental spectra. General retooling of
  plotobject handling. GUI changes.

2009-03-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h: Small changes to indentation
  and variable names.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/molecule.cpp: Inlined a few functions that are called
  a lot.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Moved the atom
  and bond storage into the class, should allow some inlining.

2009-03-25  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationplot.ui: GUI changes for vibrationplot.*

2009-03-25  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt: Second thoughts - relative
  RPATH is only needed for executables.

2009-03-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glpainter.cpp: A
  few small adjustments to use the correct colour transparency when rendering
  using colorMesh.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Fixed up the orbital
  selection, previously had bugs when several meshes were present.

2009-03-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added labels to the peaks and
  changed the font so that it would actually be legible. Removed debug output
  and unnecessary credits.

  * libavogadro/src/plotaxis.cpp, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Removed debug output and added the ability to
  change font size through PlotWidget::setFontSize(int pointSize).

2009-03-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h: Removed #warning - it is a GCC
  extension. Removed unimplemented slot - caused link issues on Windows.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Added the D5 type orbitals for
  electron density calculations.

  * libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/tools/navigatetool.cpp: Only do space group transformations
  when there is a space group. Otherwise duplicate the unit cell to make a
  supercell.

2009-03-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Cleaned up vibration plot a
  bit..

2009-03-22  David Lonie <loniedavid@gmail.com>

  * libavogadro/include/avogadro/plotaxis.h,
  libavogadro/include/avogadro/plotobject.h,
  libavogadro/include/avogadro/plotpoint.h,
  libavogadro/include/avogadro/plotwidget.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui, libavogadro/src/plotaxis.cpp,
  libavogadro/src/plotaxis.h, libavogadro/src/plotobject.cpp,
  libavogadro/src/plotobject.h, libavogadro/src/plotpoint.cpp,
  libavogadro/src/plotpoint.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Added plotting widget based off of KPlotWidget
  as <avogadro/plotwidget.h> and added a dialog to plot mock IR spectra to the
  vibrations extension..

2009-03-22  David Lonie <dl@david-laptop.(none)>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Initial working vibration
  plotting (Has hack to get around bug in qchem files).

  * libavogadro/include/avogadro/plotaxis.h,
  libavogadro/include/avogadro/plotobject.h,
  libavogadro/include/avogadro/plotpoint.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Fixed some issues in the plotwidget.

  * libavogadro/include/avogadro/plotwidget.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/kplotaxis.cpp, libavogadro/src/kplotaxis.h,
  libavogadro/src/kplotobject.cpp, libavogadro/src/kplotobject.h,
  libavogadro/src/kplotpoint.cpp, libavogadro/src/kplotpoint.h,
  libavogadro/src/kplotwidget.cpp, libavogadro/src/kplotwidget.h,
  libavogadro/src/plotaxis.cpp, libavogadro/src/plotaxis.h,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.cpp, libavogadro/src/plotpoint.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Completed
  integrating kde's KPlotWidget to Avogadro::PlotWidget.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui, libavogadro/src/kplotaxis.cpp,
  libavogadro/src/kplotaxis.h, libavogadro/src/kplotobject.h,
  libavogadro/src/kplotpoint.cpp, libavogadro/src/kplotpoint.h,
  libavogadro/src/kplotwidget.cpp, libavogadro/src/kplotwidget.h: Initial
  attempt to create a plot of the vibrations.

2009-03-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/shaders/vmd.frag,
  libavogadro/src/extensions/shaders/vmd.vert, testfiles/icsd_83086.cif,
  testfiles/icsd_83086.res: Removed files, Daniel Leidert pointed out possible
  copyright issues.

2009-03-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui: Fixed segfault when starting
  vibration animation with no mode selected. 

  * avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp: Fixed shortcut collision in
  menubar. 

2009-03-04  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui: Fixed segfault when starting
  vibration animation with no mode selected.

  * avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp: Fixed shortcut collision in
  menubar.

2009-03-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp: Changed from David Lonie
  for an "export" feature.

2009-03-03  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Updates to Q-Chem input
  builder. Now offers new DFT functionals and basis sets.

  * libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Update Q-Chem -- no AM1 or
  PM3, and we should always output a FCHK file.

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated translations and POT
  template.

2009-03-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Added support for colored
  MOs and electron density in the orbital engine.

2009-03-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h, testfiles/methane.FChk,
  testfiles/methane.out: Added example files (methane.out for vibrations) and
  minor cleanups.

2009-03-02  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: More fixes. Still has a
  double free, and a slight hitch in the frames.

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.cpp: Better vibrational
  implementation. Now smoother animation and you can use the arrow keys in the
  dialog.

  * libavogadro/src/animation.cpp, libavogadro/src/animation.h,
  libavogadro/src/extensions/vibrationextension.cpp: Set up continual loopback
  for vibration animations. Still needs testing.

  * libavogadro/include/avogadro/animation.h, libavogadro/src/animation.cpp,
  libavogadro/src/animation.h,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Initial effort at
  an animation framework, including animation for vibrations.

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: First pass at signals/slots
  for animations and other options.

2009-03-01  David Lonie <loniedavid@gmail.com>

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts,
  libavogadro/src/extensions/animationdialog.cpp: Fixed typo in the animation
  file dialog.

2009-03-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/neighborlist.h: Do a little of that optimization I mentioned
  on the supercell builder...

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercelldialog.h,
  libavogadro/src/extensions/supercelldialog.ui,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/supercellextension.h: Added a new super cell
  builder extension. Still a little rough but can already build large zeolite
  super cells.

  * libavogadro/src/atom.cpp, libavogadro/src/extensions/qcheminputdialog.cpp:
  Emit a signal when atom positions are modified, and also improve the update
  logic a little in the Q-Chem input dialog.

2009-02-28  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/avogadro.desktop, avogadro/src/icons/avogadro_icon.png: Added
  a .desktop file and icon for Linux, improves the end user experience.

  * CMakeLists.txt, avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  cmake/modules/AvoCPack.cmake, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/config.h.in, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Build system improvements, handle
  installation locations more logically, some rpath logic and bumped our
  version number in preparation for release.

  * libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp: Fixed some compiler warnings.

2009-02-28  Simon Ochsenreither <soc@desktop06.(none)>

  * i18n/avogadro_de_AT.ts, i18n/avogadro_de_CH.ts, i18n/avogadro_de_DE.ts:
  Symlinks aren't needed. Qt falls back to de if it doesn't find de_DE.

  * i18n/avogadro_de_AT.ts, i18n/avogadro_de_CH.ts, i18n/avogadro_de_DE.ts:
  Symlinked de_DE, de_AT and de_CH to de because we use a single translation
  file for all german-speaking countries at the moment.

2009-02-28  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp: Use QDir::homePath() as the
  default location if we have an untitled file.

2009-02-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/molecule.cpp, libavogadro/src/python/qlist.cpp: Fix
  compile error in the python bindings (include glwidget.h sicne extension.h no
  longer includes it) + add some missing functions for Molecule

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/tests/drawcommandtest.cpp:
  DrawCommands: You can now drag (with C selected for example) from a hydrogen
  to an empty space (or another atom) which will result in a ChangeElement,
  AddBond and/or AddAtom command. This used to "steal" the hydrogen from the
  atom it was attached to. The new behaviour is much more intuitive and
  probably what most people would expect to happen.

2009-02-27  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Add suport for showing/hiding unit cell axes. By
  default, this will be disabled on PDB files -- matching most users'
  expectations.

2009-02-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/tests/drawcommandtest.cpp: DrawCommands: Replace the int
  adjustHydrogens with QFlags for more control

2009-02-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/painter.h: Removed the triangle
  windings hack as it is not needed anymore. Fixed a bug in transparency in
  coloured meshes in POV-Ray output too.

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp: Reduced the verbosity of
  the debug output.

2009-02-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Use "Window" menu
  on all platforms, not just Mac.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Merge from Cryos.

2009-02-27  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Add configuration
  file versioning, reject unversioned configuration with the option to bump in
  the future. Should address issues with stale configuration files.

2009-02-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp: Sorted out some of the
  parenting issues and updates on destruction - quantum codes only care about
  atoms!

  * libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h: Updates to the MOPAC dialog,
  respect cancel for job submission, plugged a small memory leak in the
  z-matrix code and save whether preview is shown or not.

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h: Fixed parenting issues in these
  extensions.

  * libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp: Small fixes to destruction
  of extensions and parenting of dialogs.

  * libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h: Few small improvements to
  the plugin and tool classes.

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp: Removed the GLWidget
  include and replaced with some forward declarations. Added includes to
  extensions missing them.

2009-02-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Updated surface engine -- uses
  single color mesh for renderQuick. Solves PR# 2619826.

2009-02-25  Marcus D. Hanwell <marcus@cryos.org>

  * cmake/modules/AvoCPack.cmake, cmake/modules/AvoCPackOptions.cmake.in:
  Updates to the CPack build, more improvements on the way.

2009-02-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Don't update for renderPick()

2009-02-24  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/chargecolor.h,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/distancecolor.h: Add color by distance from atom 0
  (i.e., ignore atom index, just look at distances)

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/chargecolor.cpp, libavogadro/src/colors/chargecolor.h:
  Add color by charge: negative = red, positive = blue

2009-02-24  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui: Remove time limit and memory
  limit from GAMESS input generator. Not necessary.

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: More translation updates from
  Launchpad.

  * libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdialog.ui: String updates.

  * libavogadro/src/extensions/gaussianinputdialog.ui,
  libavogadro/src/extensions/qcheminputdialog.ui: UI consistency -- use "..."
  for showing a new dialog box.

  * avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h: Make sure
  to update when an engine is updated (e.g., enabled by an extension).

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Enable the force engine when
  displaying vibrations.

  * libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h: Update MOPAC dialog to show a
  progress dialog and allow cancelling jobs.

2009-02-24  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Use
  identifiers to check plugins -- won't change with translations.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Fix settings -- don't
  automatically save aliases and descriptions. Empty strings are handled
  correctly.

2009-02-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fi.ts, i18n/avogadro_fr.ts, i18n/avogadro_it.ts,
  i18n/avogadro_nl.ts, i18n/avogadro_pl.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_zh_CN.ts,
  i18n/avogadro_zh_TW.ts: Update translations after recent string cleanup.

  * libavogadro/src/extension.h,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/shaderextension.h,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/wiitrackextension.h: String cleanup for
  extensions.

  * libavogadro/src/engine.h, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h: Further cleanups of
  strings/names/descriptions with engines, being consistent with other plugins.

  * libavogadro/src/color.h, libavogadro/src/colors/elementcolor.h,
  libavogadro/src/colors/indexcolor.h, libavogadro/src/colors/residuecolor.h,
  libavogadro/src/colors/residuecolorsettings.ui: String update for color
  plugins.

  * libavogadro/src/engine.h, libavogadro/src/tool.h,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: String cleanup for tools -- similar
  to engines.

  * libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Cleanup of engine translatable strings. Macros only define names,
  identifiers, and descriptions once.

2009-02-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Split RibbonEngine into its original
  ribbon only and the experimental new CartoonEngine.

  * libavogadro/src/residue.cpp, libavogadro/src/residue.h: Add
  Residue::chainID / Residue::setChainID (note: this is not always the same as
  the chainNumber. Chains often get ids like 'A', 'B', ... but also ' ')

  * libavogadro/src/protein.cpp, libavogadro/src/protein.h: Protein: Use HELIX
  records from pdb file when available

2009-02-23  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/CMakeLists.txt, libavogadro/src/extensions/basisset.h,
  libavogadro/src/painter.h, libavogadro/src/periodictableview.cpp,
  libavogadro/src/periodictableview.h, libavogadro/src/primitive.h: Some more
  fixes and small changes.

  * cmake/modules/AvoCPack.cmake, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Several
  small fixes to classes. Made Python packaging on Windows optional.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/drawcommandtest.cpp,
  libavogadro/tests/hydrogenscommandtest.cpp,
  libavogadro/tests/moleculetest.cpp, libavogadro/tests/neighborlisttest.cpp:
  Small updates to some tests. Disabled hydrogens test for now - moc issues.

2009-02-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Improve helix rendering...

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: RibbonEngine: Improve helix
  rendering...

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: improve 4-turn helix rendering,
  currently the points are rendered as spheres. These points can be used to
  generator a nurbs or mesh...

2009-02-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/tests/drawcommandtest.cpp,
  libavogadro/tests/hydrogenscommandtest.cpp: update unit tests

  * libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/tests/hydrogenscommandtest.cpp: Fix HydrogensCommand (bug
  #2624046)

  * libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/hydrogenscommandtest.cpp: Add unit test for
  HydrogensCommand

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: continue working on drawing commands

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: Continue working on DrawCommands...

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: AddBondDrawCommand &
  ChangeBondOrderDrawCommand: Use AdjustHydrogens[Pre/Post]Command + unit tests

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: More unit testing and improvements for
  DrawCommands

2009-02-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: Unit tests for AddAtomDrawCommand,
  ChangeElementDrawCommand and DeleteAtomDrawCommand. All three pass, but
  DeleteAtom only because it copies the molecules. AddAtom and ChangeElement
  already use the Pre/Post Commands.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Molecule: Also
  (optionally) reuse bond ids when adding hydrogens.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/drawcommandtest.cpp:
  Add DrawCommandTest: unit testing for the Draw tool's QUndoCommands

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h:
  Add AdjustHydrogensPreCommand class, use this QUndoCommand before performing
  one of the real commands (ChangeElementDrawCommand, ...). Add
  AdjustHydrogensPostCommand class, use this QUndoCommand after performing one
  of the real commands (ChangeElementDrawCommand, ...).

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Molecule:
  (changes from DrawCommandTest) * bugfix in Molecule::operator=(...): call
  Atom::addBond * change addHydrogens(...) to optionally specify the hydrogen
  ids. This will be used by the AdjustHydrogens[Pre/Post]Command in the future.

  * libavogadro/src/python/atom.cpp, libavogadro/src/python/bond.cpp,
  libavogadro/src/python/main.cpp: Add some missing python
  functions/properties: * Atom::residue * Atom::residueId * Bond::beginAtom *
  Bond::endAtom Actualy export MoleculeList in main.cpp

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h: Implement Bond::midPos().

2009-02-20  Simon Ochsenreither <soc@desktop06.(none)>

  * libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/tools/python/template.py: Python 3 fixes (automated)

2009-02-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/AvoCPack.cmake, libavogadro/src/python/swig.cpp: Changes from
  win32 build...

2009-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/src/pluginmanager.cpp: First pass at using the
  avogadro binary location to locate plugins. Allows for multiple build
  directories and no environment variables, relocatable installs and all that
  good stuff. Feedback appreciated, does mean our wiki pages need updating.
  Also need to do this for scripts etc.

2009-02-18  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h: Use the new
  Extension::moleculeChanged() signal to handle reading new files.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/extension.h: Add new signal for extensions opening a molecule
  underneath a MainWindow.

2009-02-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/gaussianfchk.cpp: Changes to the GaussianFchk
  class, now with much more error checking. This should make the formatted
  checkpoint parsing much more resilient. Need to spend some more time with our
  parsing classes to improve resilience and fault detection.

2009-02-17  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h,
  libavogadro/src/extensions/mopacinputdialog.ui: Initial pass at a MOPAC
  generator, including local calculations.

  * libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h: Update density matrix import to
  handle columns (e.g, Q-Chem fchk files)

2009-02-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/gaussianfchk.cpp: Finally solved the GTO electron
  density bug! It was a single stray readline statement. The underlying
  mathematics was all correct. Spotted an issue with the S normalization which
  is now fixed too.

2009-02-17  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Update with latest Launchpad
  translations.

  * libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp: Set default filenames from
  molecule name and typical extension.

2009-02-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engines/orbitalengine.cpp: Fix bug with colors always
  appearing black. New gradient method was preferred over normal "set"
  function.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Added a real
  "Window" menu on Mac OS X.

2009-02-16  Geoff Hutchison <babel@geoffhutchison.net>

  * authors.txt, authors.xml, avogadro/AUTHORS, avogadro/COPYING,
  avogadro/NEWS, avogadro/README, gpltemplate: Remove unused files.

  * CMakeLists.txt, cmake/modules/AvoCTestConfig.cmake,
  cmake/modules/CTestConfig.cmake: Look for cmake files as "modules"

  * AvoCPack.cmake, CTestConfig.cmake, PythonDeps.cmake,
  cmake/modules/AvoCPack.cmake, cmake/modules/CTestConfig.cmake,
  cmake/modules/PythonDeps.cmake: Move cmake files into cmake directory (to
  clean up top-level directory). Adjust PythonDeps to handle Boost 1.38.

2009-02-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/moleculelist.cpp,
  libavogadro/src/python/moleculelist.h: Fix python module linking. Split
  MoleculeList into new compile unit. Ensure correct moc file is included
  (previously used any "molecule.moc"!)

2009-02-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/iso.h: Removed the retired iso code, superseded by
  new MeshGenerator class.

  * AvoCPack.cmake, CMakeLists.txt, avogadro/CMakeLists.txt,
  avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  libavogadro/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/extensions/CMakeLists.txt, libavogadro/src/primitive.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/tests/CMakeLists.txt: Clean
  ups to the build system, bumped the version number to 0.9.1 and a few small
  fixes.

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/mesh.cpp, libavogadro/src/primitive.cpp: Small improvements
  to initialisation.

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Finally tracked down that bug, I had
  not propagated through my improvements in the underlying engine code to this
  engine. Working much better now.

2009-02-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/qlist.cpp: Rename
  "long int" to simply "long" 

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt:
  Obey -DENABLE_PYTHON=FALSE for building python-free even when dependencies
  are present. 

2009-02-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/qlist.cpp: Rename
  "long int" to simply "long"

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/atom.cpp,
  libavogadro/src/atom.h, libavogadro/src/bond.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/selectextension.cpp, libavogadro/src/fragment.cpp,
  libavogadro/src/fragment.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/neighborlist.cpp,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h,
  libavogadro/src/tools/selectrotatetool.cpp: Several fixes to type names and a
  few clean ups.

2009-02-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt:
  Obey -DENABLE_PYTHON=FALSE for building python-free even when dependencies
  are present.

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui: Applied an adapted patch from
  Magnus Lundborg. Corrected some issues with render order and indentation.
  Adds transparency support to the ball and stick engine.

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h: The position function
  should take unsigned ints.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp: Now reading the SCF density
  matrix, added the code to calculate the electron density. There is a problem
  and so I need to go back and take another look at the equations. Made quite a
  few optimisations to the MO calculations and improved the data layout
  significantly.

  * libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Corrected incorrect calculation of
  the electron density for slaters.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Use guarded pointers to store the
  current mesh objects, fixes potential crashes if the mesh objects are
  removed.

2009-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/neighborlist.cpp, libavogadro/src/neighborlist.h:
  OrbitalExtension: use NeighborList class for ESP approximation...

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/neighborlist.h, libavogadro/src/pluginmanager.cpp: A few
  small fixes for issues pointed out by krazy2.

2009-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/python/example.py,
  libavogadro/src/pythonextension.cpp: Add message(const QString &) signal to
  PythonExtension

  * libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h: Add read/write
  Settings to PythonTool & PythonEngine

  * libavogadro/src/extensions/python/example.py,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonextension.h: Add
  dockWidget to PythonExtension

  * libavogadro/src/python/engine.cpp, libavogadro/src/python/main.cpp: minor
  python improvements

2009-02-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h,
  libavogadro/src/colors/residuecolorsettings.ui, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/surfaceengine.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/line.cpp, libavogadro/src/line.h, libavogadro/src/plugin.cpp,
  libavogadro/src/plugin.h, libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/python/plugin.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/manipulatetool.cpp:
  Update to add color settings (e.g., residue coloring). Required change of
  Plugin to inherit QObject, plus a variety of changes to assigning Color
  objects.

2009-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/sip.cpp, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythonextension.h: Add readSettings/writeSettings to
  pythonextension (TODO: Tool & Engine)

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/python/example.py: Python Extension example

  * libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/python/main.cpp, libavogadro/src/python/molecule.h,
  libavogadro/src/python/sip.cpp: more python...

2009-02-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/molecule.cpp, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/pythontool.cpp: More python stuff

  * libavogadro/src/python/molecule.cpp, libavogadro/src/python/molecule.h:
  Remove unneeded function

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/molecule.h, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/swig.cpp, libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/camera.py,
  libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/fragment.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/primitivelist.py,
  libavogadro/src/python/unittest/residue.py,
  libavogadro/src/python/unittest/tool.py,
  libavogadro/src/python/unittest/toolgroup.py,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythontool.cpp: Various python updates. All ownership issues
  should be solved now...

2009-02-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.h,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h, libavogadro/src/extension.h,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonterminal.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/vibrationextension.h, libavogadro/src/plugin.h,
  libavogadro/src/python/plugin.cpp, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonengine.h, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythonextension.h, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h, libavogadro/src/tool.h,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: Add unique, untranslated
  identifiers for plugins and factories. These will be used to ensure config
  files do not crash when changing languages.

2009-02-11  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Display a warning if no
  displacements exist (e.g. Gaussian output with OB-2.2.0)

2009-02-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/orbitalextension.cpp: Adapted orbital extension to
  use the slimmed down BasisSet class.

  * libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h: Added in a function to read in the
  SCF density matrix.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Big changes to the Gaussian type basis
  sets. Flattened out the data structure in order to be more efficient and
  flexible. Got rid of most structs and also removed old experimental code that
  is no longer used. Some of the variable names possibly need improvements and
  I still need to add the electron density calculation in.

2009-02-10  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h: Handle Q-Chem checkpoints with
  16-character fields. (Grrr.)

2009-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Removed a few more functions that
  are not used anymore.

2009-02-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonextension.h: Move
  PythonExtension to libavogadro

2009-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Added some extra hooks to
  colour by ESP estimated from partial charges. More mappings onto surfaces to
  come, tested on several test VdW surfaces.

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Removed most of the old code, this
  has been migrated to the orbital extension. This engine is now much simpler
  and should probably remain this way.

2009-02-07  Marcus D. Hanwell <marcus@cryos.org>

  * AvoCPack.cmake, CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/pluginsettings.cpp, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/pluginmanager.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: Move our Windows packaging to
  CPack. Various improvements and changes to the Windows build process,
  bringing it more into line with other architectures.

2009-02-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h: Some cleanups on the unit
  cell code, cannot use trunc as Windows does not have this function. Static
  cast to induce rounding seems to be an acceptable subsititute.

2009-02-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp: A variety of cleanups in
  the vibration extension, including UI layout fixes, calls for molecule/widget
  update, etc.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: New extension to begin
  animating vibrations. Right now, will add force vectors for viewing by the
  force engine. Data is read in through Q-Chem files currently and latest 2.2.x
  branch of Open Babel. More formats (and animations) to come.

  * libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h: Clean up code a bit to more modular
  calls, less casting pointers.

  * avogadro/src/aboutdialog.cpp, avogadro/src/aboutdialog.h,
  avogadro/src/addenginedialog.cpp, avogadro/src/addenginedialog.h,
  avogadro/src/application.cpp, avogadro/src/application.h,
  avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.h,
  avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h,
  avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/flattabwidget.cpp,
  avogadro/src/flattabwidget.h, avogadro/src/icontabwidget.cpp,
  avogadro/src/icontabwidget.h, avogadro/src/importdialog.cpp,
  avogadro/src/importdialog.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/pluginitemmodel.cpp, avogadro/src/pluginitemmodel.h,
  avogadro/src/pluginlistview.cpp, avogadro/src/pluginlistview.h,
  avogadro/src/pluginsettings.cpp, avogadro/src/pluginsettings.h,
  avogadro/src/primitivetreeview.cpp, avogadro/src/primitivetreeview.h,
  avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/labeldelegate.cpp,
  avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.cpp,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.h,
  avogadro/src/projectdelegates/selectiondelegate.cpp,
  avogadro/src/projectdelegates/selectiondelegate.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeitem.cpp,
  avogadro/src/projecttreeitem.h, avogadro/src/projecttreemodel.cpp,
  avogadro/src/projecttreemodel.h, avogadro/src/projecttreemodeldelegate.cpp,
  avogadro/src/projecttreemodeldelegate.h, avogadro/src/savedialog.cpp,
  avogadro/src/savedialog.h, avogadro/src/settingsdialog.cpp,
  avogadro/src/settingsdialog.h, libavogadro/src/atom.cpp,
  libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/boxcontrol.cpp, libavogadro/src/boxcontrol.h,
  libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/indexcolor.h, libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/cube.cpp,
  libavogadro/src/cube.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/elementtranslate.cpp,
  libavogadro/src/elementtranslate.h, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/iso.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/highlighter.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphdialog.h,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vdwsurface.h,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h,
  libavogadro/src/filetreeitem.cpp, libavogadro/src/filetreeitem.h,
  libavogadro/src/fragment.cpp, libavogadro/src/fragment.h,
  libavogadro/src/global.cpp, libavogadro/src/global.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/idlist.cpp, libavogadro/src/idlist.h,
  libavogadro/src/line.cpp, libavogadro/src/line.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/meshgenerator.cpp,
  libavogadro/src/meshgenerator.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/navigate.cpp,
  libavogadro/src/navigate.h, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/painterdevice.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/quaternion.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h,
  libavogadro/src/undosequence.cpp, libavogadro/src/undosequence.h,
  libavogadro/tests/moleculetest.cpp, libavogadro/tests/neighborlisttest.cpp:
  Fix homepage URL in headers and other URL strings.

2009-02-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginitemmodel.cpp, avogadro/src/pluginitemmodel.h,
  avogadro/src/pluginsettings.cpp: PluginSettings: detect if plugins need to be
  reloaded 

2009-02-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginitemmodel.cpp, avogadro/src/pluginitemmodel.h,
  avogadro/src/pluginsettings.cpp: PluginSettings: detect if plugins need to be
  reloaded

2009-02-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/forceengine.cpp, libavogadro/src/molecule.cpp:
  Brought back the force engine, including support for Atom::forceVector()
  which will be used as well by vibrations.

2009-02-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/protein.cpp,
  libavogadro/src/protein.h: Various updates to Protein class + basic rendering
  of 3 and 4 turn helixes in ribbon engine 

2009-02-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/include/avogadro/protein.h, libavogadro/src/molecule.cpp,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h: * Add Protein class
  to handle proteins specific molecule properties (2nd Structure) * Molecule:
  Fix chainNumbers 

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/protein.cpp,
  libavogadro/src/protein.h: Various updates to Protein class + basic rendering
  of 3 and 4 turn helixes in ribbon engine

2009-02-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Add "custom data" atom label,
  which will show custom data, when present. (Eventually should also add names
  of custom data to combo box.) Works perfectly with code requested by Q-Chem
  for NMR shifts.

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  libavogadro/src/atom.h, libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.h: Remove
  un-necessary #include <QAbstractItemModel> in primitive.h We should make a
  pass to remove un-needed #includes.

2009-02-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/include/avogadro/protein.h, libavogadro/src/molecule.cpp,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h: * Add Protein class
  to handle proteins specific molecule properties (2nd Structure) * Molecule:
  Fix chainNumbers

2009-02-02  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, PythonDeps.cmake, cmake/modules/FindAllPython.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/pluginmanager.cpp: Tidied up
  our build files a little more, ensured that Avogadro will build without
  Python.

2009-02-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h: HBondEngine: use new NeighborList
  class

2009-02-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/propextension.cpp, libavogadro/src/molecule.cpp:
  Fix some compiler warnings...

  * avogadro/src/mainwindow.cpp, avogadro/src/pluginitemmodel.cpp,
  avogadro/src/pluginitemmodel.h, avogadro/src/pluginlistview.cpp,
  avogadro/src/pluginlistview.h, avogadro/src/pluginsettings.cpp,
  avogadro/src/pluginsettings.h, avogadro/src/pluginsettings.ui,
  avogadro/src/settingsdialog.cpp,
  libavogadro/include/avogadro/pluginlistview.h,
  libavogadro/include/avogadro/pluginsettings.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h, libavogadro/src/pluginitemmodel.cpp,
  libavogadro/src/pluginitemmodel.h, libavogadro/src/pluginlistview.cpp,
  libavogadro/src/pluginlistview.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/pluginsettings.cpp,
  libavogadro/src/pluginsettings.h, libavogadro/src/pluginsettings.ui,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h: Move Plugin
  settings widget to avogadro.

  * libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h: Forgot
  pythonengine.*

  * libavogadro/include/avogadro/neighborlist.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h, libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/neighborlisttest.cpp: Add NeighborList class + unit tests
  (for this class). To Marcus: Feel free to change the
  libavogadro/tests/CMakeLists.txt file

  * libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/pythonsettingswidget.ui,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/pythontool.h,
  libavogadro/src/tools/CMakeLists.txt: Move PythonEngine to libavogadro

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeeditor.h,
  avogadro/src/projecttreeeditor.ui, avogadro/src/settingsdialog.cpp,
  avogadro/src/settingsdialog.h, libavogadro/include/avogadro/pluginsettings.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/plugindialog.cpp,
  libavogadro/src/plugindialog.h, libavogadro/src/plugindialog.ui,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/pluginsettings.cpp, libavogadro/src/pluginsettings.h,
  libavogadro/src/pluginsettings.ui: New configuration dialog

2009-01-31  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h,
  libavogadro/src/pythontool.cpp: Add toolTip support to the PythonTool &
  remove some debug msgs

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h: Continue moving PythonTool to libavogadro.
  Re-added the PythonToolFactory which allow us to use python tools just like
  any other C++ tools. In other words, we create a PythonToolFactory for each
  script and the ..Factory gets the name and description from running the
  script. You can now enable/disable python tools.  still TODO: * set the
  activate action's tooltip * icons??

2009-01-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/importdialog.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/plugin.cpp,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/manipulatetool.cpp: Fix compiler warnings

2009-01-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/python.png,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h,
  libavogadro/src/pythontool.qrc, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/python.png, libavogadro/src/tools/pythontool.cpp,
  libavogadro/src/tools/pythontool.h, libavogadro/src/tools/pythontool.qrc:
  Move PythonTool (1)

2009-01-28  Albert DeFusco <albert@defusco.msg.chem.iastate.edu>

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.ui: I like more precision in my
  input files. I also like yellow hydrogen bonds

2009-01-28  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, CTestConfig.cmake: Added some initial CDash support, see
  http://www.cdash.org/CDashPublic/index.php?project=Avogadro for our new
  CDash.

2009-01-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/glpainter.cpp: Fixes for Eigen cast warnings with
  Eigen-2.0rc1

2009-01-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt, cmake/modules/FindAllPython.cmake,
  cmake/modules/FindNumpy.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/sip.cpp,
  libavogadro/src/tools/CMakeLists.txt: Change the python dependency detection:
  All python dependencies are now in the cmake/modules/FindAllPython.cmake.
  Python support is only enabled when all dependencies (python interp+libs,
  boost python, sip, numpy) are found. Also, in the message saying X can't be
  found, I added the package names for debian/ubuntu. Perhaps we should do
  something similar for other distros/dependencies.

2009-01-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/python/eigen.cpp: replace WithAlignedOperatorNew with
  EIGEN_MAKE_ALIGNED_OPERATOR_NEW. This macro is available from version
  Eigen2-beta5 and up.

2009-01-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Draw tool refinements. Do not add/delete hydrogens when manually drawing
  bonds with a new H atom. Do not bond to hydrogen atoms when dragging unless H
  atoms are manually selected as the new element. 

2009-01-22  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Draw tool refinements. Do not add/delete hydrogens when manually drawing
  bonds with a new H atom. Do not bond to hydrogen atoms when dragging unless H
  atoms are manually selected as the new element.

  * avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.ui:
  Add support for color settings widgets when present. 

2009-01-21  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.ui:
  Add support for color settings widgets when present.

2009-01-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Listen for the Molecule::destroyed() signal to stop the AutoOpt Tool.
  (prevents crashes when closing avogadro while AutoOpt is running) 

2009-01-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Listen for the Molecule::destroyed() signal to stop the AutoOpt Tool.
  (prevents crashes when closing avogadro while AutoOpt is running)

2009-01-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Updated dipole engine which
  updates on-the-fly and handles recent changes. 

2009-01-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Updated dipole engine which
  updates on-the-fly and handles recent changes.

2009-01-12  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/python/eigen.cpp, libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/camera.py,
  libavogadro/src/python/unittest/eigen.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/glwidget.py: update python unit tests

2009-01-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.ui: Disabled parts of the dialog
  that need to be (re)implemented, removed obsolete parts. Fixed a bug with VdW
  surface generation.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Improved the metadata put
  into the meshes - orbital engines can infer the pairs and also draw cube
  extents again.

2009-01-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Implement
  translation of molecules. Solves PR#2497081.

2009-01-10  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added extra slots
  for atom and bond changes. Fixes bug 2497037.

2009-01-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/main.cpp, libavogadro/src/global.cpp: Add correct paths for
  translation files on windows.

2009-01-09  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.ui: Add short tooltip about
  clicking to insert a fragment. Should address PR#1971923.

2009-01-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Various updates to the
  Gaussian dialog.

  * libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Various improvements to the
  Q-Chem dialog.

  * libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/primitive.cpp: Removed Eigen Regression include where not
  needed, changed it to the new Eigen/LeastSquares in molecule.cpp.

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/drawtool.cpp:
  Ported to use the static ElementTranslator function rather than the global
  instance.

  * libavogadro/src/elementtranslate.cpp, libavogadro/src/elementtranslate.h:
  Changed to use a static member function rather than instantiating a global
  instance.

  * libavogadro/src/global.cpp, libavogadro/src/global.h: Some documentation
  updates and a little tidying up.

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp, libavogadro/src/global.cpp: Added some extra debug
  output when translation files cannot be found.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/namedselectionmodel.h,
  libavogadro/src/extensions/selectextension.cpp: Remove obsolete code (named
  selections moved to project tree)

  * .../src/projectdelegates/selectiondelegate.cpp,
  avogadro/src/projectdelegates/selectiondelegate.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreemodel.cpp: Add a
  ProjectDelegate for named selections.

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add a signal to
  the GLWidget to notify the project tree the named selections have changed
  (added, removed, renamed)

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile, libavogadro/src/atom.h, libavogadro/src/bond.h,
  libavogadro/src/colorbutton.h, libavogadro/src/fragment.h,
  libavogadro/src/mesh.h, libavogadro/src/molecule.h,
  libavogadro/src/pythoninterpreter.h, libavogadro/src/residue.h,
  libavogadro/src/textrenderer.h: Various updates to improve the API
  documentation.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/global.h, libavogadro/src/python/eigen.cpp: define
  EIGEN_WORK_AROUND_QT_BUG_CALLING_WRONG_OPERATOR_NEW_FIXED_IN_QT_4_5 in
  global.h and include it where needed (only python/eigen.cpp)

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Removed the duplicate button
  from the dialog, changed the menu entry name to surfaces and cleaned up a few
  compiler warnings.

  * libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h:
  Updated the API docs and removed an unused function.

2009-01-08  Geoff Hutchison <babel@geoffhutchison.net>

  * Doxyfile, Doxyfileext, doc/mainpage.dox, libavogadro/src/global.cpp:
  Doxygen changes. Move mainpage documentation out of global.cpp and into
  doc/mainpage.dox. Updated to output to doc/api and be a bit more consistent
  with Eigen and other projects.

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Few small fixes
  and updates. I think some of the new functions may need a little work but do
  seem to be working quite well.

2009-01-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projecttreeeditor.h, avogadro/src/projecttreemodel.h,
  avogadro/src/projecttreemodeldelegate.h, avogadro/src/savedialog.cpp: A
  variety of small krazy fixes.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h: remove obsolete files (Docking
  extension)

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h: * Add the properties extension again
  (including conformers)  * update force field extension to make use of the
  added conformers code.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Small bug fixes
  for conformers + Add energies/setEnergies

2009-01-07  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile, Doxyfileext, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt:
  Version changed to 0.9.0.

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/runkrazy.rb, scripts/runkrazy.rb: Removed
  the krazy subdirectory, will be autogenerated from now on. Also moved the
  script into our scripts directory.

2009-01-07  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp: Update extensions to add
  some menu separators

2009-01-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp: Initial porting of the
  animation tool to the new API.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Made the
  conformer support actually work now!

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Set the version to
  0.9_beta1 in preparation for the release.

2009-01-07  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreemodel.cpp: Find a
  few more un-translated strings.

  * avogadro/src/CMakeLists.txt, avogadro/src/mac/lang.sh: Cleanup of Mac
  .lproj (language directories) creation. Should improve translations.

2009-01-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: First attempt at
  adding conformer support, needs some testing.

2009-01-06  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, scripts/extract-messages.sh, scripts/extractrc.sh:
  Modified scripts and POT file to keep similar format for UI files as CPP and
  H

2009-01-05  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts: Updated
  en_GB de and fr TS files from Launchpad. All translations should now be using
  Launchpad.

2009-01-05  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version number
  for 0.9.0 beta.

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated
  translation strings.

  * avogadro/src/aboutdialog.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/povrayextension.cpp: Fix some un-translated (or
  confused) strings.

2009-01-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/bond.cpp, libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/glgraphicsview.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/periodictableview.cpp,
  libavogadro/src/plugindialog.cpp, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/textrenderer.cpp: Made a start on fixing issues pointed out
  by krazy2.

  * libavogadro/src/painterengine.cpp, libavogadro/src/painterengine.h: Removed
  orphaned source files.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added some
  functions to set and get the dipole moment of the molecule. Copying the
  dipole moment seems to cause segfaults here, so it is commented out for now.

2009-01-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated
  translations. Still need to work out a clean po -> ts solution.

2009-01-04  Carsten Niehaus <cniehaus@kde.org>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Pretty big update as I didn't run those tests for
  ages and Krazy2 improved a lot

2009-01-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Add new
  translations from Launchpad plus "update-translations" for new strings.

2009-01-01  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/macchempasteboard.cpp,
  avogadro/src/macchempasteboard.cpp.disabled,
  avogadro/src/macchempasteboard.h, avogadro/src/macchempasteboard.h.disabled:
  Disable Mac ChemPasteboard until we can fix it completely.

2008-12-31  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp: Finished the porting of the
  GAMESS input deck generator. Only performed cursory testing so far for quite
  a number of changes. Basic input deck generation seems to work at least.

2008-12-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/eigen.cpp,
  scripts/cmake-vs2005.bat: Some win32 specific changes

2008-12-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Reduction of includes that are not
  needed.

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h:
  Initial work to port the bondcentrictool to the new framework. This seems to
  mostly work, has some issues with atom updates that should not be too hard to
  sort out.

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Added a new function to
  return the bond between the atom and any other. Returns 0 if no bond between
  them exists.

2008-12-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/cube.h, libavogadro/src/fragment.h, libavogadro/src/global.h,
  libavogadro/src/mesh.cpp, libavogadro/src/mesh.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h: Added a little
  access control and friend classes. Id and index should only be set by the
  containing Molecule and are not part of our public API. They reflect internal
  state of the molecule.

  * CMakeLists.txt, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Updated the build system, now require
  CMake 2.6.0. Clean ups in several places.

  * libavogadro/src/python/atom.cpp, libavogadro/src/python/molecule.cpp:
  Ported to use the new API, new -> add and delete -> remove.

2008-12-29  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/atom.h, libavogadro/src/molecule.h: Documentation updates
  with previous syntax change.

  * avogadro/src/editcommands.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/atom.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/fragment.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/primitivelist.py,
  libavogadro/src/python/unittest/residue.py, libavogadro/src/pythonerror.cpp,
  libavogadro/src/pythonerror.h, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/tests/moleculetest.cpp: Change syntax of atoms and molecules. All
  references to "new" are now "add" and all references to "delete" are now
  "remove." So it's "addAtom" or "removeAtom" for consistency with Qt and the
  rest of our API.

2008-12-28  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/molecule.cpp: Lots of documentation updates,
  reorganised the functions and grouped in Doxygen tags. Some minor changes
  too, more are needed for const correctness.

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h: Added functions to
  retrieve bond positions, still need to implement the mid-point function.

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Documentation updates,
  added member function groupings and a destructor.

  * libavogadro/src/atom.cpp, libavogadro/src/bond.cpp, libavogadro/src/bond.h:
  Added some atom accessor functions to the Bond class. This should make using
  bonds easier. Fixed assignment order in Atom constructor.

  * libavogadro/src/atom.cpp, libavogadro/src/fragment.cpp,
  libavogadro/src/fragment.h, libavogadro/src/residue.cpp,
  libavogadro/src/residue.h: Made the classes aware of their parent. Added in
  calls in Residue to set and unset the Residue of its child atoms.

2008-12-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Added methods to set and
  get at the residue an atom belongs to.

2008-12-27  Geoffrey Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Fix
  glpainter and wireframe to bring back stipple for h-bond engine. (oops!)

2008-12-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  Environment variable redux - move from four environment variables to one.
  AVOGADRO_PLUGINS can be set to point to Avogadro plugins.

2008-12-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Fixed triangle windings for
  negative electron isosurfaces, changed default tab in the dialog.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/vdwsurface.cpp: Added the ability to generate VdW
  surfaces, and variants thereof. Still needs some work to tidy up the UI.

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Start of the simplification in the
  surface engine. Need to add back in coloured surfaces, currently draws
  surface meshes in the specified colour.

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui: Added Van der Waals surface tab
  and associated functions.

  * libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Added
  the option to reverse the winding of the generated mesh. This depends upon
  what you consider to be inside and outside of your isosurface.

  * libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vdwsurface.h: Added a VdWSurdface class that uses
  QtConcurrent to calculate a VdW cube. It may need further optimisation with
  binning etc.

  * libavogadro/src/engine.cpp, libavogadro/src/meshgenerator.cpp: Got rid of a
  few unused variables in function calls.

2008-12-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/highlighter.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h: Split python extension into 2
  extensions. One handles python extension scripts and the other one provied
  the terminal. Also add syntax highlighting to the terminal widget :P

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: PythonTerminalWidget: Allow
  python code indentation  

2008-12-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercelldialog.h,
  libavogadro/src/extensions/supercelldialog.ui: Remove supercell for now,
  until it can be finished for public use. 

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h, libavogadro/src/molecule.cpp:
  Add back unit cell extension. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, testfiles/ZnO.fract: Added back basic support for
  unit cells. (e.g., open testfiles/ZnO.fract) 

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt: Fix build
  error when ENABLE_PYTHON = false 

2008-12-23  Marcus D. Hanwell <marcus@cryos.org>

  * AUTHORS, INSTALL, authors.txt, authors.xml: Updated the author files, added
  a new authors.txt that can be used by Git to map SVN users to Git authors. 

  * libavogadro/src/engines/ringengine.cpp, libavogadro/src/glpainter.cpp:
  Noticed that the drawTriangle function was recalculating normals when it was
  given one. 

2008-12-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Some
  tidying up. Remove unnecessary GL calls. Still an issue with transparency in
  the ring engine. 

  * libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/selectextension.cpp: Ported the engines, and
  extension to use the new API introduced. Please let me know if you notice any
  new issues arising from all the changes. Hopefully the API changes can be
  kept to a minimum now. 

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Removed includes that
  should not be in the Engine header. Added a molecule member pointer that can
  be used to more efficiently take care of the lazy copying of lists. Separated
  atoms and bonds from general primitives. This allows for engines to
  specialise further, i.e. engines with no atoms/bonds can ignore these signals
  and avoid copying these pointer lists when custom primitives are to be
  rendered. Added new Engine slots for the new molecule signals. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Changed the
  transparent rendering. Enable GL_BLEND for the rendering cycle as everything
  in there currently enables/disables this. Also removed the depth mask stuff
  as this did not look good with any of the engines. Removed more calls to the
  PrimitiveList, there is no point in keeping two copies of this list and it
  will be phased out. Actually emit the moleculeChanged signal when the
  molecule is changed. Adding a new toggleSelected function which toggles the
  selection with no list. 

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added greater
  granularity to the Molecule. Separate atom and bond signals are emitted. All
  other primitives go in the old signals. Atoms and bonds are the most
  susceptible to change and in general the most numerous. 

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Some improvements to the behaviour
  of the selection tool. 

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Only draw eye candy when the view is
  moving. 

2008-12-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h: Improve
  python error reporting, all errors are now printed to the messages log... 

2008-12-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/basisset.cpp, libavogadro/src/glpainter.cpp:
  norm2() -> squaredNorm() due to deprecation in Eigen2. 

2008-12-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: MainWindow: Use the
  new Extension::actionsChanged() slot to reload an extension's actions when
  needed. 

  * libavogadro/src/extensions/python/deleteAll.py,
  libavogadro/src/extensions/python/example.py,
  libavogadro/src/extensions/python/test.py,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: PythonExtension: Make python
  extensions more like real extensions. Still needs some work but actions(),
  menuPath() & peroformAction are working... TODO: dockWidgets, work out
  example with QUndoCommand, ... 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: MainWindow: * Add
  slot to handle plugin reloading * replace strcasestr with equivalent QString
  functions * TODO: make smooth transitions work on win32 

2008-12-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: GLWidget:
  initialize m_navigateTool to 0 and check if it exists before trying to let it
  handle unaccepted events from other Tools. Add a toolsDestoryed() slot to set
  d->tool and d->activeTool to 0, connect the toolGroup::toolsDestroyed()
  signal to this slot in GLWidget::setToolGroup(...). 

  * libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h: ToolGroup: Add
  ToolGroup::removeAllTools() to clear the current list of tools + emit
  toolsDestroyed() when 1 or more tools are destroyed. 

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  PluginManager: Add a reload slot and reloadPlugins signal. The reload slot is
  called from the PluginDialog when accepted, PluginManager::reload() writes
  the settings, deletes the instances and emits reloadPlugins. Classes such as
  MainWindow and GLWidget connect to this signal to invalidate their current
  plugins and reload them.  Nore: MainWindow & GLWidget follow later, reloading
  plugins without restarting is only working for Tools & Extensions at the
  moment 

2008-12-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp:
  Further refinements to wireframe, including optimization and aromatic dashed
  bonds.   

2008-12-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/plugindialog.cpp, libavogadro/src/plugindialog.h:
  PluginDialog: Add a signal to inform the PluginManager when the plugins have
  changed. 

  * libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h:
  PythonScript: improve error handling 

  * libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h: pythonengine.*: Add win32 search
  paths + improve error handling 

2008-12-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/molecule.cpp: Added some code so that bond aromaticity
  can be exposed. 

2008-12-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/importdialog.cpp, avogadro/src/importdialog.h,
  avogadro/src/importdialog.ui, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h: New "import file" dialog to set specific Open
  Babel format and conversion options. In particular, turning off bond orders
  should be helpful with nanotubes / graphite or really large files. 

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: More
  wireframe refinements. Getting there. 

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp:
  Somewhat more refined multiple bonds for wireframe. Also made multi-bond
  wireframe the default to address bug report. Still need "aromatic" stipple. 

2008-12-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Finally got the new way of
  generating meshes working. It still has a few rough edges but on the whole is
  much improved. Adding color by another cube is now relatively simple. 

2008-12-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added new Mesh
  functions so that the Molecule can manage meshes properly too. 

  * libavogadro/src/cube.h, libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Working on adding
  the mesh generation to the extension and simplifying the orbital/surface
  engines. This will also ensure the molecule is cleared properly as engines
  should not be storing their own primitives to render. 

2008-12-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/engine.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/std_vector.cpp: some small syntax changes in the
  python module to make it compile with MSVC (not -> !) 

  * avogadro/src/projecttreeeditor.h, avogadro/src/projecttreemodel.h,
  avogadro/src/projecttreemodeldelegate.h: avogadro/src/*.h: Remove some more
  A_EXPORT 

  * avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectdelegates/residuedelegate.h:
  avogadro/src/projectdelegates/*.h: These classes are not in libavogadro
  anymore, remove A_EXPORT from their declaration. 

2008-12-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/python/engine.cpp: Engine flag overhaul. New flags: Layers
  (opaque, transparent, overlay) Primitives (atoms, bonds, etc.) Colors (none,
  indexed, plugins, etc.)  This should simplify the display settings windows,
  as well as new users. I've probably missed some engines, but I'll make
  another pass tomorrow. 

2008-12-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Tidied up the extension a
  little, fixed an initialisation issue. 

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: PQNs are actually integers, cache the
  effective PQNs in the loop - simplified slaterPoint. 

  * libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Spotted that the exponential factor
  could be cached outside of the loop in electron density calculations - nearly
  three times faster. I still want it to go faster though! 

2008-12-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: Fix PR#2396701 -- when clicking
  again on an atom, remove it from the list. This prevents NaN measurements and
  makes it efficient to check out multiple measurements in a large molecule. 

2008-12-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/slaterset.cpp: Increased the default step size to
  a more relaxed 0.18, reduced the default padding to 2.5 and added some logic
  to skip calculations where the factor is very small. 

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Added calculation of electron density
  to the MOPAC code, this should be quite simple to translate to the Gaussian
  type orbitals too. Fixed normalization of the MOs too. ESP calculation might
  be next... 

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Added the option to calculate
  all MOs. 

2008-12-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/avogadroformat.cpp, libavogadro/src/xml.cpp: Remove useless
  Avogadro format and XML code -- we can't get this to work with the current
  Open Babel 2.2 architecture. 

2008-12-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Added a renderPick to the ball and
  stick engine. Should be much quicker when picking in large scenes. 

  * libavogadro/src/navigate.cpp, libavogadro/src/tools/navigatetool.cpp: Fixed
  up the translation of the view by keyboard - much better now. 

  * libavogadro/src/navigate.cpp, libavogadro/src/navigate.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Added key press events for the navigate tool - now you can use the keyboard
  to modify the view. 

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/orbitalengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/painterdevice.h,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/glwidget.cpp: Pass
  the primitives list by reference in the primitives() return type. All engines
  just render the primitive list unless otherwise instructed by the user - only
  one copy of the list normally. Introduced a renderPick() function to the
  engines, this allows a specialised function for picking that can omit
  extraneous details. 

2008-12-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tool.cpp, libavogadro/src/tool.h: Added key press and
  release events to the tools - keyboard interaction! 

2008-12-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Added support for MOPAC AUX file
  parsing, and more generally Slater Type Orbitals. Features are still very
  new. I need to add in support for d-type orbitals and do further testing. 

2008-12-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/pythonengine.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/python.png,
  libavogadro/src/tools/python/template.py,
  libavogadro/src/tools/pythonsettingswidget.ui,
  libavogadro/src/tools/pythontool.cpp, libavogadro/src/tools/pythontool.h,
  libavogadro/src/tools/pythontool.qrc: Add Python Tool  

2008-12-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/pythonsettingswidget.ui,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/pythonscript.cpp: * libavogadro/src/pythoninterpreter.*: Make
  sure we don't call Py_Finalize() before all instances are destroyed. *
  libavogadro/src/engines/pythonengine.*: Allow python engines to have a
  settingsWidget, flags, transparencyDepth and changed() signal. *
  libavogadro/src/engines/python/wireframe.py: work out an example engine with
  a python settings widget.  

2008-12-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added the ability to save
  the dialog settings that make sense, added LANL2DZ and improved the routines
  to check if the new molecule coordinates should be used. 

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/tools/eyecandy.cpp: Give the user more control over the cube
  size to be calculated. Also reduced the size of the eye candy a little. 

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.h, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Make the navigate tool a super tool
  - one tool to rule them all (when they do not accept the mouse event). 

  * CMakeLists.txt, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt:
  Adjusted the build files a little. Qt 4.4.0 is required now as we are using
  QtConcurrent. Bumped the version in preparation for 0.9 release. 

2008-12-08  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/editcommands.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/atom.cpp, libavogadro/src/molecule.cpp: Fixed copy and
  pasting. 

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h, libavogadro/src/molecule.cpp:
  Fixes to the modality of the calculation, small fix to molecule and its
  setOBMol function. 

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h: Improved locking
  of the cube - too slow to make the class thread safe. Best solution is for
  users of it to lock/unlock. Orbitals now sees new cubes and updates the combo
  again. 

  * libavogadro/src/cube.h, libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/python/cube.cpp: Added a map form calculation - uses a lot
  less memory for large molecules. In my tests it is a little slower than whole
  cube but uses a lot less memory. On balance this is probably the best
  implementation for most people to use. 

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/savedialog.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added the coveted export to vector graphics
  option, provided by the GL2PS C library which is not built into Avogadro.
  Seems to work quite well and everyone loves vector graphics. 

  * avogadro/gl2ps/COPYING.GL2PS, avogadro/gl2ps/COPYING.LGPL,
  avogadro/gl2ps/TODO, avogadro/gl2ps/gl2ps.c, avogadro/gl2ps/gl2ps.h,
  avogadro/gl2ps/gl2ps.pdf, avogadro/gl2ps/gl2psTest.c,
  avogadro/gl2ps/gl2psTestSimple.c: Added a snapshot of GL2PS to build against.

2008-12-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/sip.cpp, libavogadro/src/python/unittest/suite.py: Add
  unit test for Camera  

  * libavogadro/src/python/TODO, libavogadro/src/python/bond.cpp,
  libavogadro/src/python/cube.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/qlist.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/std_vector.cpp,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/suite.py: update python bindings, including
  cube, fix bond & atom errors in unit tests, add std::vector<double>* to
  converter, unit test for GLWidget, simplify & document sip.cpp implementation
  a bit. Wrap GLHit and add QList<GLHit> to python converter.  

2008-12-07  Marcus D. Hanwell <marcus@cryos.org>

  * testfiles/benzene.fchk, testfiles/co.fchk: Added a couple of formatted
  checkpoint examples. 

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Quite a few optimisations. I
  got the mapped reduce feature working. I am still a little concerned about
  memory usage on really big molecules with lots of cores. It looks good on
  some of the molecules I have tested it on though. Scales quite linearly now
  with two cores. 

  * libavogadro/src/cube.cpp, libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Quite a few optimisations to the
  calculation. Memory grows out of control when calculating large molecules,
  this needs map reduce but have not been able to get that working... 

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/orbitalextension.cpp: Rewritten many of the
  calculation routines in an attempt to improve speed. Using QtConcurrent to
  actually calculate the cube on a shell by shell basis. Seems to be working
  quite well here. Still more tidying up/optimisation to do. 

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h,
  libavogadro/src/python/cube.cpp: Several modifications to the Cube class in
  order to make it more efficient and add flexibility. 

2008-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/sip.cpp: We now have signals/slots in python :-)  

2008-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/unittest/atom.py: Fix Atom::valence and update unit
  test  

  * libavogadro/src/CMakeLists.txt, libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/TODO, libavogadro/src/python/extension.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/qtlib.cpp,
  libavogadro/src/python/sip.cpp, libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/suite.py: More python classes & unit tests.
  Also add converters to allow us to return PyQt (SIP) wrapped objects and
  accept them as parameters.  

2008-12-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Added a
  clear() function. 

2008-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/meshgenerator.cpp: *
  libavogadro/src/engines/orbitalengine.cpp: Add extra check for
  m_settingsWidget in OrbitalEngine::updateOrbitalCombo *
  libavogadro/src/meshgenerator.cpp: Add extra check in ::initialize to make
  sure the Cube and Mesh pointer are valid  

2008-12-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.h, libavogadro/src/engines/orbitalengine.cpp: Fixed
  up the update engine a little and added a new entry into the Egine enum for
  surfaces. 

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h: Added minimum and maximum
  value functions to the Cube class, corrected some off by one errors in the
  Cube initialization functions. 

2008-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/engine.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/pluginmanager.cpp,
  libavogadro/src/python/primitivelist.cpp,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/pluginfactory.py,
  libavogadro/src/python/unittest/pluginmanager.py,
  libavogadro/src/python/unittest/suite.py: Added python unit tests for engine
  and updated the pluginmanager bindings  

2008-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  libavogadro/src/pluginmanager.*: Some additional functions to make plugin
  loading easier from python (or for 3rd party viewers which use libavogadro)  

2008-12-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Updated the orbital engine to use
  the new MeshGenerator class. It should be fixed to only render meshes,
  leaving generation to an exntension or tool. 

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h: Fixes for the Cube class
  to work with the new MeshGenerator class. 

  * libavogadro/include/avogadro/meshgenerator.h,
  libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Added a
  new MeshGenerator class. The basic code is derived from that found at
  http://local.wasp.uwa.edu.au/~pbourke/geometry/polygonise/ Specifically the
  marchingsource.cpp file authored by Cory Bloyd and placed in the public
  domain (thanks Cory). I then made it play nice with the new Avogadro classes
  and put it in its own thread. I have not actually added the duplicate vertex
  detection yet. This new class is able to generate meshes significantly faster
  that the previous code. 

2008-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/color.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/qtlib.cpp,
  libavogadro/src/python/tool.cpp, libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/suite.py,
  libavogadro/src/python/unittest/tool.py: Add python unit tests for Tool and
  Color  

  * libavogadro/src/python/TODO,
  libavogadro/src/python/unittest/pluginfactory.py,
  libavogadro/src/python/unittest/suite.py: Add python unit test for
  PluginFactory  

  * libavogadro/src/python/TODO, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/plugin.cpp,
  libavogadro/src/python/pluginmanager.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/pluginmanager.py,
  libavogadro/src/python/unittest/suite.py,
  libavogadro/src/python/unittest/toolgroup.py: Wrap PluginManager & ToolGroup
  classes and added unit tests for them  

  * libavogadro/src/plugin.h, libavogadro/src/toolgroup.cpp: *
  libavogadro/src/plugin.h: Remove ProjectPlugin from the Type enum. *
  libavogadro/src/toolgroup.cpp: Add index checking in
  ToolGroup::setActiveTool(int index).  

  * libavogadro/src/python/TODO, libavogadro/src/python/main.cpp,
  libavogadro/src/python/primitivelist.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/unittest/primitivelist.py,
  libavogadro/src/python/unittest/suite.py: Add python unit test for
  PrimitiveList  

  * libavogadro/src/python/TODO, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/mesh.cpp,
  libavogadro/src/python/std_vector.cpp,
  libavogadro/src/python/unittest/mesh.py,
  libavogadro/src/python/unittest/suite.py: *
  libavogadro/src/python/std_vector.cpp: Add std::vector<Vector3f>, needed for
  mesh * libavogadro/src/python/eigen.cpp: Add more typechecking, there was
  some pointer arithmatic going on with the wrong types  Python seems to use
  long and double here as default, but we also accept int and float. An array
  from python with doubles can now correctly be converted to a Vector3f.    

  * libavogadro/src/python/TODO, libavogadro/src/python/residue.cpp,
  libavogadro/src/python/unittest/residue.py,
  libavogadro/src/python/unittest/suite.py: Add python unit test for Residue  

  * libavogadro/src/cube.cpp, libavogadro/src/python/TODO,
  libavogadro/src/python/cube.cpp, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/std_vector.cpp,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/fragment.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/suite.py,
  libavogadro/src/python/unittest/template.py: *
  libavogadro/src/python/unittest/*: Add template & cube tests *
  libavogadro/src/python/*: Add std::vector wrapper, bug fix for eigen.cpp &
  cube.cpp * libavogadro/src/cube.cpp: Bugfix in setLimits(Molecule*, double,
  double), don't assume any atom will have coordinates < (0,0,0)  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/python/glwidget.cpp: Added a view option to turn quick
  rendering on and off, for those times when you want eye candy all of the
  time. 

2008-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/engines/bsdyengine.cpp: elementcolor.cpp: give atoms with
  atomicNumber 0 a drak grey color bsdyengine.cpp: give them a radius  Helps
  with interactive python scripting: molecule.newAtom() will show the atom when
  the bsdy engine using element coloring is enabled (=default)  

  * libavogadro/src/python/TODO, libavogadro/src/python/bond.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/primitive.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/suite.py: Python bindings unit tests for
  Atom, Bond & Molecule complete  

  * libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/src/python/atomTest.py: Replace import Numeric with import numpy 

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt: Removed the AVO_LINK_LIBS
  status message. Fixed up the Find LibXml2 call for those of us with case
  sensitive file systems. 

  * libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h: Fixed the rest of the shader
  calls that had not been ARBified. Added the ability to load shader programs. 

2008-12-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, cmake/modules/FindGLEW.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt:
  Updates to GLEW includes for those of us with non-standard paths.  

  * libavogadro/src/avogadroformat.cpp, libavogadro/src/xml.cpp: Draft attempts
  at an avogadro format.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/fileimportextension.cpp: Reorganize menus -- add
  an "Import" submenu on the File menu. (There should be a default to open
  files with strange extensions by specifying the Open Babel format.)  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/glwidget.cpp: Ported to use the ARB syntax, should work on
  older graphics cards. Still works the same here. 

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/mesh.cpp, libavogadro/src/mesh.h: The quest for greater
  stability continues, I think this is a reasonable solution for things like
  meshes. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Only use OpenGL
  2.0 functions when GLEW finds OpenGL 2.0 capabilities. 

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h: Implemented the bond
  length member function. I hope LaserJock is happy now. 

2008-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: Always call Molecule::update()
  when a user enters a command in the python terminal widget, makes the
  scripting terminal much more interactive...  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaders/phong.params,
  .../src/extensions/shaders/x-ray-cryos.frag,
  .../src/extensions/shaders/x-ray-cryos.params,
  .../src/extensions/shaders/x-ray-cryos.vert,
  libavogadro/src/extensions/shaders/x-ray.frag,
  libavogadro/src/extensions/shaders/x-ray.params,
  libavogadro/src/extensions/shaders/x-ray.vert, libavogadro/src/glwidget.cpp:
  Added a few new shaders along with their parameter files. Added the ability
  to load parameter files into shaders and got the x-ray shader working. 

2008-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * sip/README, sip/avogadro.sip, sip/camera.sip, sip/color.sip,
  sip/configure.py, sip/eigen.sip, sip/engine.sip, sip/glwidget.sip,
  sip/openbabel.sip, sip/painter.sip, sip/painterdevice.sip, sip/plugin.sip,
  sip/pluginmanager.sip, sip/primitive.sip, sip/primitivelist.sip, sip/test.py,
  sip/test.sdf, sip/test_Transform3d.py, sip/test_Vector3d.py, sip/tool.sip,
  sip/toolgroup.sip: Delete obsolete sip python bindings  

2008-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/eigen.py,
  libavogadro/src/python/unittest/suite.py: * libavogadro/src/python/eigen.cpp:
  add converters for all to/from Tranform3d objects. Add a class with get/set
  functions for all combinations of Vector3x/Tranform3d, used for unit testing.
   * libavogadro/src/python/unittest/*: Unit tests for python bindings.
  Currently atom, bond and the Eigen converters are covered.  To run test
  suite: $python libavogadro/src/python/unittest/suite.py  

  * avogadro/src/mainwindow.cpp, libavogadro/src/pluginitemmodel.cpp,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  pluginmanager.*: Add static method PluginManager::instance(), replaces the
  global instance pluginManager pluginitemmodel.cpp, mainwindow.cpp: update to
  use PluginManager::instance()  

2008-12-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/extensions/shaderextension.cpp: Made the shaders more
  flexible hopefully more robust. 

  * libavogadro/src/engines/surfaceengine.cpp, libavogadro/src/glpainter.cpp:
  Port to use squaredNorm() as norm2() is deprecated now. 

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h,
  libavogadro/src/extensions/shaders/clip.frag,
  libavogadro/src/extensions/shaders/clip.vert,
  libavogadro/src/extensions/shaders/gooch.frag,
  libavogadro/src/extensions/shaders/gooch.vert,
  libavogadro/src/extensions/shaders/light.frag,
  libavogadro/src/extensions/shaders/light.vert,
  libavogadro/src/extensions/shaders/marble.frag,
  libavogadro/src/extensions/shaders/marble.vert,
  .../src/extensions/shaders/per-pixel-lighting.frag,
  .../src/extensions/shaders/per-pixel-lighting.vert,
  libavogadro/src/extensions/shaders/per_pixel2.frag,
  libavogadro/src/extensions/shaders/per_pixel2.vert,
  .../src/extensions/shaders/phong-use-diffuse.frag,
  .../src/extensions/shaders/phong-use-diffuse.vert,
  libavogadro/src/extensions/shaders/phong.frag,
  libavogadro/src/extensions/shaders/phong.vert,
  libavogadro/src/extensions/shaders/plasma.frag,
  libavogadro/src/extensions/shaders/plasma.vert,
  libavogadro/src/extensions/shaders/vmd.frag,
  libavogadro/src/extensions/shaders/vmd.vert, libavogadro/src/glwidget.cpp:
  Added the ShaderExtension which allows you to assign a shader to an engine.
  Still not implemented shader loading from arbitrary files - will do it soon.
  It currently loads all shader pairs in share/libavogadro/shaders, probably
  not optimal but it allows people to check out shaders now while I finish up a
  few bits. 

  * avogadro/src/mainwindow.cpp, libavogadro/include/avogadro/glgraphicsview.h,
  libavogadro/src/glgraphicsview.cpp, libavogadro/src/glgraphicsview.h: Added
  experimental GLGraphicsView detachment, more a proof of concept right now,
  performance is quite poor, antialiasing is disabled and text does not render
  correctly. It does however draw widgets etc on top of the GLWidget. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added a new
  member function for the GLGraphicsView, added GLEW initialisation in order to
  check for shader support and hopefully did not break anything in the process.

2008-12-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, cmake/modules/FindGLEW.cmake,
  cmake/modules/FindNumpy.cmake, libavogadro/src/python/CMakeLists.txt: Minor
  Cmake magic to get everything compiling on Mac. (Silly Apple, stick to
  traditional paths more often!)  

2008-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/boost.h, libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/tests/CMakeLists.txt: * libavogadro/tests/CMakeLists.txt: remove
  ${EXECUTABLE_OUTPUT_PATH}, "make test" now works here... *
  libavogadro/src/engines/python/cubepoints.py: Another example engine, renders
  cubes as 10x10x10 points colored red/blue for -/+    

  * libavogadro/src/python/TODO, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/python/engine.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/mesh.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/painter.cpp,
  libavogadro/src/python/tool.cpp: Various updates to python bindings  

2008-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/python/color.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/plugin.cpp: * libavogadro/src/python/*: Wrap Plugin
  and Color classes. * libavogadro/src/engines/python/wireframe.py: Use Color
  class   

2008-12-02  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: Changes needed in order
  to compile libavogadro with GLEW, needs to be included before gl.h/QGLWidget.

  * CMakeLists.txt, cmake/modules/FindGLEW.cmake, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt: Build system updates. Some clean ups and also
  added an option for GLSL using the GLEW library. 

2008-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/python/engine.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/pythonsettingswidget.ui: Improve python engine and
  add a more realistic example: a wireframe engine  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/python/engine.py,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h: * libavigadro/engines/pythonengine.*:
  Initial attempt to create a python engine, still needs some work but it works
  \o/  * libavogadro/engines/python/engine.py: example engine (note: for now,
  the python engine uses the first script it finds...)  

  * libavogadro/include/avogadro/pythonscript.h,
  libavogadro/src/extensions/python/deleteAll.py,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h: *
  libavogadro/src/pythonscript.*: Moved here from pythonextension.* *
  src/extensions/pythonextension.*: remove PythonScript, now in libavogadro. *
  src/extensions/python/deleteAll.py: update this script to work with new API  

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/TODO,
  libavogadro/src/python/atom.cpp, libavogadro/src/python/atomTest.py,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/cube.cpp,
  libavogadro/src/python/fragment.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/painter.cpp, libavogadro/src/python/painterdevice.cpp,
  libavogadro/src/python/primitive.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/qstring.cpp, libavogadro/src/python/residue.cpp: *
  libavogadro/src/python/*: update boost python bindings (QString, QList<T>,
  QList<T*>, Painter, PainterDevice, ...)   

2008-12-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Fix minor bug with
  Mac and project tree editor.  

  * libavogadro/src/plugin.cpp, libavogadro/src/plugin.h: Add support for *all*
  plugins to have settings widgets (e.g., colors too)  

2008-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Added some very initial support for detached
  views. Still needs more work, cannot set engines etc right now. It does work
  in the basic sense though and can be amazingly useful for some work. I will
  hopefully smooth this out a little more very soon. 

  * libavogadro/src/molecule.cpp, libavogadro/tests/moleculetest.cpp: Updated
  with some new tests, noticed an initialisation bug in setAtomPos. There might
  be something in this unit testing thing... 

2008-11-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/atom.cpp,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/cube.cpp, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/fragment.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/primitive.cpp, libavogadro/src/python/residue.cpp:
  split boost python bindings into multiple files  

2008-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/tests/CMakeLists.txt, libavogadro/tests/moleculetest.cpp: Added
  some initial unit testing using QTestLib and CTest. Use make test for basic
  reporting, or run ctest -V in the build directory for more detailed output.
  Test coverage is currently terrible, but it gives a template and I will flesh
  it out. We need unit testing for core functionality. 

2008-11-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp,
  avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  avogadro/src/projecttreemodel.cpp, avogadro/src/projecttreemodel.h,
  libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h, libavogadro/src/glwidget.h,
  libavogadro/src/molecule.cpp, libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/wrapper.cpp, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/pythoninterpreter.h: * libavogadro/src/python: Compile the
  boost python bindings seperatly so they can also be used from outside
  avogadro.  * libavogadro/src/pythoninterpreter.*: remove the boost.h
  include...  * libavogadro/src/molecule.cpp: Don't segfault when you call
  atomPos before setPos.  * libavogadro/src/glwidget.h: remove undefined
  function toolManger (we have a toolGroup/setToolGroup.  *
  libavogadro/src/extensions/pythonextension.*: remove boost.h include...  *
  avogadro/src/projecttreemodel.*, avogadro/src/projectdelegates/*: some small
  improvements  * avogadro/src/mainwindow.cpp: Use QPixmap::grapWidget to
  export png images. (Should work on more platforms. If it causes problems on
  other platforms we can still use
  QGLFramebufferObject::hasOpenGLFramebufferObjects() to detect which method to
  use.)   

2008-11-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/indexcolor.h, libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h: Updated color plugins, including new
  "color by index" -- rainbow based on atom index.  

2008-11-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/bond.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp: Chased down the bonding bugs and
  hopefully optimized some of this code a little. Please test and report any
  issues I might have missed. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h, libavogadro/src/bond.cpp,
  libavogadro/src/bond.h, libavogadro/src/molecule.cpp: Some optimizations and
  tweaks to the atom, bond and molecule classes. Still some drawing bugs I am
  tracking down... 

2008-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/fileimportdialog.ui,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/fileimportextension.h: Added a new file import
  dialog, initially concentrating purely on xyz files and amber parameter
  files. Still pretty rough around the edges. 

  * libavogadro/src/atom.cpp, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/molecule.cpp: Some updates to the bond, atom and molecule
  classes. Hopefully improving speed a little. 

2008-11-25  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added a fog setting to the GLWidget. The numbers
  still need tweaking but it demonstrates the effect. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added partial
  charge calculation and caching. Also made a start on adding locking to the
  molecule class. I did not find any deadlocks but please report if you do.
  Still more locking needed, finer granularity may be necessary. 

2008-11-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/editcommands.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/tools/autoopttool.cpp: * libavogadro/src/molecule.*: Add
  Molecule::residue(index) and Molecule::residueById(id).  *
  avogadro/src/editcommands.cpp: Handle Bond and Residue primitives in
  ClearCommand and CutCommand.  *
  avogadro/src/projectdelegates/residuedelegate.cpp: Also add the residue
  itself to the primitives (for selection).  *
  libavogadro/src/tools/autoopttool.cpp: optimize the way we retreive
  coordinates from the OBMol object.   

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h: Add the force field
  extension again, conformers not handled at the moment and marked with FIXME. 

2008-11-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.ui: Few tweaks to tab order, added
  the fileName widget to the signals connected to the updateCommandLine slot. 

  * libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povrayextension.cpp: Several improvements to the
  POV-Ray extension, update the command line more frequently, use the supplied
  path and work from the directory specified. 

2008-11-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povrayextension.cpp: Set the working directory of
  the process, only use relative paths as POV-Ray can be paranoid. Should
  improve rendering success on systems configured in quite restrictive ways. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h, libavogadro/src/cube.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/painter.h,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Main change is having the
  molecule manage the atom's coordinates. This should open up the possibility
  of quickly changing the coordinate set and redrawing. The main practical
  difference is Vector3d being a pointer rather than a reference. Everything
  else is pretty much porting to the new API. Small fix to the molecule
  constructor to assign a default file name. 

2008-11-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp: * small bug fix for
  ResidueDelegate * remove obsolete connect() call from mainwindow.cpp  

  * avogadro/src/projectdelegates/moleculedelegate.cpp,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreemodel.cpp: * Add
  ResidueDelegate  

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/labeldelegate.cpp,
  avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.cpp,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectplugin.cpp, avogadro/src/projectplugin.h,
  avogadro/src/projectplugins/atomitems.cpp,
  avogadro/src/projectplugins/atomitems.h,
  avogadro/src/projectplugins/bonditems.cpp,
  avogadro/src/projectplugins/bonditems.h,
  avogadro/src/projectplugins/labelitems.cpp,
  avogadro/src/projectplugins/labelitems.h,
  avogadro/src/projectplugins/moleculeitems.cpp,
  avogadro/src/projectplugins/moleculeitems.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeeditor.h,
  avogadro/src/projecttreeitem.cpp, avogadro/src/projecttreeitem.h,
  avogadro/src/projecttreemodel.cpp, avogadro/src/projecttreemodel.h,
  avogadro/src/projecttreemodeldelegate.cpp,
  avogadro/src/projecttreemodeldelegate.h: * Some renaming in the Project Tree
  area:  There is now the ProjectTreeModel which delegates its work to various
  ProjectTreeModelDelegate objects.  * Dynamic initialization of the model: 
  \o/  Using QAbstractItemModel::hasChildren(), canFecthMore() and fetchMore()
  it is possible to delay the initialization (and connecting of singals) until
  the user actually expands the item.  * Still need to update some
  documentation and add a ResidueDelegate, ...   

2008-11-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/CMakeLists.txt, avogadro/src/back.png, avogadro/src/down.png,
  avogadro/src/forward.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/minus.png, avogadro/src/plus.png,
  avogadro/src/projectplugin.cpp, avogadro/src/projectplugin.h,
  avogadro/src/projectplugins/atomitems.cpp,
  avogadro/src/projectplugins/atomitems.h,
  avogadro/src/projectplugins/bonditems.cpp,
  avogadro/src/projectplugins/bonditems.h,
  avogadro/src/projectplugins/labelitems.cpp,
  avogadro/src/projectplugins/labelitems.h,
  avogadro/src/projectplugins/moleculeitems.cpp,
  avogadro/src/projectplugins/moleculeitems.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeeditor.h,
  avogadro/src/projecttreeeditor.qrc, avogadro/src/projecttreeeditor.ui,
  avogadro/src/projecttreeitem.cpp, avogadro/src/projecttreeitem.h,
  avogadro/src/projecttreemodel.cpp, avogadro/src/projecttreemodel.h,
  avogadro/src/up.png, libavogadro/include/avogadro/projectplugin.h,
  libavogadro/include/avogadro/projecttreeeditor.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/cube.cpp, libavogadro/src/projectplugin.cpp,
  libavogadro/src/projectplugin.h,
  libavogadro/src/projectplugins/CMakeLists.txt,
  libavogadro/src/projectplugins/selectionitem.cpp,
  libavogadro/src/projectplugins/selectionitem.h,
  libavogadro/src/projectplugins/smartsitems.cpp,
  libavogadro/src/projectplugins/smartsitems.h,
  libavogadro/src/projectplugins/smartsitems.ui,
  libavogadro/src/projecttreeeditor.cpp, libavogadro/src/projecttreeeditor.h,
  libavogadro/src/projecttreeeditor.ui: * move Project Tree stuff from
  libavogadro to avogadro * implement a QAbstractItemModel for the tree * lots
  of bug fixes   

2008-11-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/extensions/povpainter.cpp: Fixed
  up the POV-Ray drawColorMesh function - looks very nice. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/molecule.cpp,
  libavogadro/src/painter.h: Ported the surface engine to the new API, added
  multiple color support to the GLPainter. added partial charge importing to
  Atom and a few minor cleanups. 

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp: Commented out the new ProjectTree stuff for now
  - it was causing build failures. Also Avogadro should be able to build
  independently of LibAvogadro. Depending on the ui header generation in
  libavogadro from avogadro should not be done as it will not necessarily
  exist. 

2008-11-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h: Port
  patch from Carsten with const iterators.  

2008-11-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/projecttreeeditor.cpp, libavogadro/src/projecttreeeditor.h:
  update the project tree widget without needing a restart  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/include/avogadro/projectplugin.h,
  libavogadro/include/avogadro/projecttreeeditor.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/molecule.cpp,
  libavogadro/src/plugin.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/projectplugin.cpp,
  libavogadro/src/projectplugin.h,
  libavogadro/src/projectplugins/CMakeLists.txt,
  libavogadro/src/projectplugins/selectionitem.cpp,
  libavogadro/src/projectplugins/selectionitem.h,
  libavogadro/src/projectplugins/smartsitems.cpp,
  libavogadro/src/projectplugins/smartsitems.h,
  libavogadro/src/projectplugins/smartsitems.ui,
  libavogadro/src/projecttreeeditor.cpp, libavogadro/src/projecttreeeditor.h,
  libavogadro/src/projecttreeeditor.ui: * libavogadro/src/projectplugin.*: A
  new plugin type to create a user configurable tree view with various items
  (User Selections, Chains/Residues, smarts, ...)  *
  libavogadro/src/pluginmanager.*: load the new ProjectPlugins.  *
  libavogadro/src/molecule.cpp: Add a check in ::OBMol() to make sure the both
  bond atoms exist before adding the bond. This was causing a problem when
  functions, invoked by the Molecule::primitive*() signals, called it.  *
  libavogadro/src/projectplugins/smartsitems.*: A ProjectPlugin for smarts
  patterns. This is the only plugin working at the moment, still some
  performance issues too.  * libavogadro/src/projectplugins/selectionitem.*:
  still need to update this, not build right now...  *
  libavogadro/src/projecttreeeditor.*: The tree editor. Still need to add the
  arrow images...  * libavogadro/src/plugin.h: Add the new type to the Type
  enum.  * avogadro/src/mainwindow.*: Use the Project Tree View system. The old
  Project dock is replaced, the editor is available through Settings > Project
  Tree Editor.  The code still has some rough edges, but it works well enough
  to illustrate what it could become....  

2008-11-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h: Added the polygon engine back in. I
  think valency needs implementing properly but this works for now... Next is
  adding multiple colour support into the Mesh class. 

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/extensions/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/residue.cpp,
  libavogadro/src/residue.h: Improved residue support, added back in the
  GLWidget and ported the ribbon engine. 

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/selectextension.cpp: Ported the select extension.
  Seems to work quite well but had to comment out some bits in the
  namedselectionmodel class. Tim - I think that might need a little TLC. 

2008-11-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/fragment.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h: First attempt at
  fleshing out the Residue class. It probably still needs to bring more data
  across from the OBMol. Also fleshed out the setOBMol function a little, needs
  adding to OBMol in Molecule to save the Residues too. 

2008-11-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Made the orbital extension
  much cleverer. It now uses the molecules file name, determines if it can
  process it and then imports it. Also unhidden the fields where the cube size
  can be set. 

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h: Added the setFileName call to
  the MainWindow class. Ported POVRayExtension to take advantage of the
  fileName parameter. 

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added fileName as
  a property of the molecule. Gives extensions etc access to this information
  if set. Also added various objects to the destructor and removed some
  debugging. Added more documentation for the new API. 

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povraydialog.ui,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h: Added lots more options to the
  POV-Ray dialog, it now saves its settings (as can all extensions now). Should
  be more robust. 

2008-11-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h: OK, I spotted the silly mistake. A
  bool is not a double! I think this update also makes it simpler for users to
  change the aspect ratio themselves. 

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povrayextension.cpp: Some updates to respect the
  requested image dimensions. The aspect ratio is still not getting through and
  so many images come out distorted. Any ideas? 

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/savedialog.cpp,
  libavogadro/include/avogadro/atom.h, libavogadro/include/avogadro/bond.h,
  libavogadro/include/avogadro/boxcontrol.h,
  libavogadro/include/avogadro/cube.h, libavogadro/include/avogadro/fragment.h,
  libavogadro/include/avogadro/line.h, libavogadro/include/avogadro/mesh.h,
  libavogadro/include/avogadro/molecule.h,
  libavogadro/include/avogadro/point.h, libavogadro/include/avogadro/residue.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/atom.cpp,
  libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/boost.h, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/boxcontrol.h, libavogadro/src/camera.cpp,
  libavogadro/src/color.h, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp, libavogadro/src/cube.cpp,
  libavogadro/src/cube.h, libavogadro/src/engine.cpp,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/hbondengine.cpp, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/iso.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povraydialog.ui,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/fragment.cpp, libavogadro/src/fragment.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/line.cpp, libavogadro/src/line.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/painter.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitivelist.cpp,
  libavogadro/src/primitivelist.h, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: MERGE the primitive branch with
  trunk. There are still quite a few extensions not ported, some engines and
  tools too. I would appreciate testing, comments and help with porting. There
  are some big changes to the API, some disabled functions and likely some new
  bugs introduced. 

2008-09-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/colors/CMakeLists.txt, sip/README,
  sip/avogadro.sip, sip/color.sip, sip/configure.py, sip/eigen.sip,
  sip/engine.sip, sip/glwidget.sip, sip/openbabel.sip, sip/plugin.sip,
  sip/pluginmanager.sip, sip/primitive.sip, sip/test.py, sip/test.sdf,
  sip/test_Transform3d.py, sip/test_Vector3d.py, sip/toolgroup.sip: *
  libavogadro/src/colors/CMakeLists.txt: remove elementcolor, this is
  statically linked into libavogadro.  * sip/*: Update SIP python bindings.   

2008-09-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: *
  libavogadro/src/engines/surfaceengine.cpp: Don't try to compute and render a
  surface when there are no atoms. This was also causing a crash when starting
  avogadro with the surface engine enabled on one of my computers here.   

2008-08-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp, libavogadro/src/cylinder.cpp,
  libavogadro/src/glpainter.cpp: - make color store its channels as an array.
  Otherwise, there's no guarantee that they're adjacent in memory so usage of
  glColor4fv is dangerous.  - make use of the 'v' GL functions like glVertex3dv
  instead of glVertex3d everywhere in GLPainter.  - some cosmetic fixes in
  Cylinder.   

  * CMakeLists.txt, INSTALL, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, cmake/modules/FindEigen.cmake,
  cmake/modules/FindEigen2.cmake,
  cmake/modules/FindPackageHandleStandardArgs.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/camera.cpp,
  libavogadro/src/camera.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/iso.h, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/painterengine.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/sphere.h, libavogadro/src/textrenderer.h,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/manipulatetool.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h, scripts/cmake-vs2005.bat,
  sip/camera.sip, sip/eigen.sip: * Port to Eigen2 * Some misc simplifications
  and optimizations * CMakeLists: use CMAKE_BUILD_TYPE is the same way as KDE
  does   

2008-08-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Fixed
  compilation errors introduced with the new setQuickRenderEnabled and
  isQuickRenderEnabled. Is the Enabled part needed? 

2008-08-14  Naomi Fox <naomi.fox@gmail.com>

  * libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphdialog.h,
  libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h: * animationextension.* :
  added functionality to read xyz trajectory file as defined here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html  *
  linmorphextension.* : added functionality to write xyz trajectory file.  *
  linmorphdialog.ui: removed save-pov-snapshots button and replaced with
  save-xyz-trajectory button.  * animationdialog.ui : added *.xyz extension for
  open file option.   

2008-08-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h:
  Removed "stable" attribute from the glwidget.  There was a reason we had this
  but I can't remember anymore.  Updated the ChangeLog 

2008-08-14  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp: Revert the settingsWindow from
  being instantiated as a child of MainWindow - caused issues here. 

2008-08-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.h,
  avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/plugindialog.cpp, libavogadro/src/pluginitemmodel.cpp,
  libavogadro/src/pluginitemmodel.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h: Rehauled the PluginManager to be much easier to
  use.  By default all Factories are loaded and retrieved through the
  PluginManager.  In addition, instances of Colors, Tools, and Extensions can
  be retrieved from the manager by creating an instance and using the
  appropriate function.  This fixed a bug where every MainWindow was sharing
  the same set of Plugins.  Added an option in the settings to select which
  direction the tabs on the tabbed widget should go {top, bottom, left, right}.
   Fixed up a few other things to utilize the new pluginmanager architecture.
  There was some refactoring done. 

2008-08-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/boost.h,
  libavogadro/src/pluginmanager.cpp: Fixed a bug in the animated "center"
  command.  Added some extra functions to the Python module.  Added a *.so
  filter to the plugin manager for when loading plugins on linux. 

2008-08-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui: Added
  settings to disabled smooth transitions on the GLwidget.  This is really the
  animation of certain movements.  Right now only "center view" is animated.
  These additions animate the camera movement and don't work so well with the
  surface engine. 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: "Center" command is
  now more fluid.  This is the first step into having more fluid movement. 
  While this is "eyecandy" some people might find it more intuitive and nice
  when using the program.  Soon to have an option this is just my testing code.

2008-08-09  Naomi Fox <naomi.fox@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h: * Fixed a bug in
  libavogadro/src/extensions/CMakeLists.txt where a needed source
  (linmorphdialog) was absent from the linmorph sources.  * Added a progress
  dialog to trajectory video maker.  * Added trajectory video making capability
  to the animation extension.   

2008-08-08  Naomi Fox <naomi.fox@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphdialog.h,
  libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h, testfiles/tyr-33-conf1.pdb,
  testfiles/tyr-33-conf2.pdb: * Took functionality of making a video of a
  trajectory from linmorph and placed into a separate class, TrajVideoMaker,
  with static functions. This way it can be reused with other trajectories.  *
  Fixed a bug in linmorph so now the number of frames and the number of
  conformations match.   

2008-08-06  Naomi Fox <naomi.fox@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt: Merged revisions
  1520-1542,1544-1549 via svnmerge from
  https://avogadro.svn.sourceforge.net/svnroot/avogadro/branches/animate 
  ........ r1523 | naomifox | 2008-06-17 12:28:56 -0400 (Tue, 17 Jun 2008) | 11
  lines  LinMorph - first take. To run, open up testfiles/tyr-33-conf1.pdb,
  then under extensions --> animate mol, load file testfiles/tyr-33-conf2.pdb
  and press play.  These two conformations were taken from:
  http://molmovdb.org/cgi-bin/morph-classic.cgi?ID=035639-9827  I took out all
  extensions from CMakeLists.txt other than the linmorph extension. ........
  r1526 | naomifox | 2008-06-24 13:35:55 -0400 (Tue, 24 Jun 2008) | 3 lines 
  linmorphextension now inherits from extension.  not animatemolextension.
  ........ r1527 | naomifox | 2008-06-24 13:37:37 -0400 (Tue, 24 Jun 2008) | 6
  lines  linmorph now has its own dialog window and does not use
  animatemolextension's dialog (which will be removed).  added a button for
  saving a trajectory as a file. ........ r1528 | naomifox | 2008-06-24
  13:42:18 -0400 (Tue, 24 Jun 2008) | 3 lines  Initialized merge tracking via
  "svnmerge" with revisions "1-1518" from
  https://avogadro.svn.sourceforge.net/svnroot/avogadro/trunk ........ r1529 |
  naomifox | 2008-06-25 10:32:21 -0400 (Wed, 25 Jun 2008) | 3 lines  Ran
  svn-merge with branch. ........ r1531 | naomifox | 2008-07-01 10:09:05 -0400
  (Tue, 01 Jul 2008) | 7 lines  linmorph has feature to save a series of .pov
  snapshots that can later be compiled into a movie.  also fixed the "player"
  so that numframes is adjusted correctly. ........ r1532 | naomifox |
  2008-07-01 10:25:56 -0400 (Tue, 01 Jul 2008) | 3 lines  Neatened up.  Added
  headers for files. ........ r1533 | naomifox | 2008-07-01 10:40:18 -0400
  (Tue, 01 Jul 2008) | 5 lines  Fixed the order of initialization of member
  variables in the constructor to be the same ordering as that in the class
  declaration so we don't get compiler warnings.  ........ r1534 | naomifox |
  2008-07-01 11:02:40 -0400 (Tue, 01 Jul 2008) | 9 lines  (1) removed any
  reference to animatemol (was going to be an abstract class for animations,
  but decided it was oo-overkill).  (2) copied animation.qrc to linmorph.qrc. 
  this is the file for those buttons (originally from Tim V).  (3) updated
  linmorphdialog.ui to use linmorph.qrc, not animatemol.qrc ........ r1544 |
  naomifox | 2008-07-23 11:06:02 -0400 (Wed, 23 Jul 2008) | 5 lines  1. did
  svnmerge.py merge with the trunk 2. fixed linmorphextension and
  applyforceextension factories so that they now inhert from plugin factory and
  use the correct macros. ........ r1545 | naomifox | 2008-07-28 16:24:22 -0400
  (Mon, 28 Jul 2008) | 3 lines  Added ability to make a video of linmorph using
  povray and mencoder. ........  

2008-07-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/addenginedialog.cpp, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/engineitemmodel.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/include/avogadro/plugin.h,
  libavogadro/include/avogadro/pluginlistview.h,
  libavogadro/include/avogadro/pluginmanager.h, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/colorplugin.cpp,
  libavogadro/src/colorplugin.h, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/extension.cpp,
  libavogadro/src/extension.h, libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/unitcellextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/plugindialog.ui, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h: Remove ColorPlugin cause it really doesn't need to be
  there.  Also eliminated some un-needed functions in the engine class. 
  Everything should rock now.  I wish i could tell you more. 

2008-07-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/addenginedialog.cpp,
  avogadro/src/addenginedialog.h, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/enginecolorswidget.ui, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.h, libavogadro/src/colorplugin.cpp,
  libavogadro/src/colorplugin.h, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/elementcolor.cpp,
  libavogadro/src/elementcolor.h, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/overlaysettingswidget.ui,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h, libavogadro/src/extension.cpp,
  libavogadro/src/extension.h, libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/namedselectionmodel.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/unitcellextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/plugin.cpp,
  libavogadro/src/plugin.h, libavogadro/src/plugindialog.cpp,
  libavogadro/src/plugindialog.ui, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/residuecolor.cpp,
  libavogadro/src/residuecolor.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: * avogadro/src/addenginedialog.*:
  Use new PluginFactory class. * avogadro/src/enginecolorswidget.*: Use new
  ColorPlugin class. * avogadro/src/main.cpp: Load the plugins here... *
  avogadro/src/mainwindow.cpp: Remove call to PluginManager::loadExtensions().
  * libavogadro/src/CMakeLists.txt: Statically link ElementColor in
  libavogadro. * libavogadro/src/color.h: Move settingsWidget() to ColorPlugin.
  * libavogadro/src/elementcolor.*: Moved to colors/. *
  libavogadro/src/engine.*: Use new Plugin base class. *
  libavogadro/src/engines/CMakeLists.txt: Add overlay engine. *
  libavogadro/src/engines/*engine.h: Use new PluginFactory class. *
  libavogadro/src/extension.*: Use new Plugin base class. *
  libavogadro/src/extensions/*extension.h: Use new PluginFactory class. *
  libavogadro/src/glwidget.*: Use new PluginFactory class. *
  libavogadro/src/plugindialog.*: Use the PluginFactory's descriptions. Added
  Colors to the combo box. * libavogadro/src/pluginmanager.*: Load all plugins
  in the same generic function, PluginFactory::type() is used to determine the
  plugin type. * libavogadro/src/residuecolor.*: Moved to colors/. *
  libavogadro/src/tool.*: Use new Plugin base class. *
  libavogadro/src/toolgroup.cpp: Remove call to PluginManager::loadTools(). *
  libavogadro/src/tools/*tool.h: Use new PluginFactory class. *
  libavogadro/src/colorplugin.*: Add new ColorPlugin class for Color plugins. *
  libavogadro/src/colors/: New directory for color plugins. ElementColor and
  ResidueColor can now be found here. *
  libavogadro/src/engines/overlayengine.*,
  libavogadro/src/engines/overlaysettingswidget.ui: Replaces overlay extension.
  There is an initial delay when creating the QPainter on the QGLWidget... :( *
  libavogadro/src/plugin.*: New Plugin base class.  

2008-07-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h: * libavogadro/src/pluginmanager.*: Added
  support for extensions.  * avogadro/src/mainwindow.cpp: Use PluginManager for
  extensions.  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/overlayextension.cpp,
  libavogadro/src/extensions/overlayextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/plugindialog.cpp,
  libavogadro/src/plugindialog.h, libavogadro/src/plugindialog.ui,
  libavogadro/src/pluginitemmodel.cpp, libavogadro/src/pluginitemmodel.h,
  libavogadro/src/pluginlistview.cpp, libavogadro/src/pluginlistview.h,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/toolgroup.cpp: Plugin Manager: -------------- *
  libavogadro/src/pluginmanager.*: The PluginManager class. This class is now a
  central class to handle the loading of plugins.  *
  libavogadro/src/pluginitemmodel.*: The PluginItemModel class.  *
  libavogadro/src/pluginlistview.*: The PluginListView class.  *
  libavogadro/src/plugindialog.*: The PluginManager dialog.  *
  libavogadro/src/glwidget.*: Use PluginManager.  *
  libavogadro/src/toolgroup.cpp: Use PluginManager.  *
  avogadro/src/mainwindow.ui, avogadro/src/mainwindow.cpp: Use the
  PluginManager. Added the menu entry "Settings > Plugin Manager".  TODO: -
  Avogadro needs to be restarted at the moment in order for the changes to take
  effect. - Not yet used for extensions. - Better descriptions, download
  updates, ...  Compiling problems? - run cmake again to include the new *.h,
  *.cpp and *.ui files... - if mainwindow.cpp can't find
  <avogadro/pluginmanager.h>, copy the file to /usr/(local/)include/avogadro  

2008-07-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/painter.h, libavogadro/src/painterdevice.h,
  sip/README, sip/avogadro.sip, sip/camera.sip, sip/color.sip,
  sip/configure.py, sip/eigen.sip, sip/engine.sip, sip/glwidget.sip,
  sip/openbabel.sip, sip/painter.sip, sip/painterdevice.sip, sip/primitive.sip,
  sip/primitivelist.sip, sip/test.py, sip/tool.sip, sip/toolgroup.sip: * sip/*:
  Initial attempt to make SIP python bindings.  *
  libavogadro/src/painter(device).h: export Painter and PainterDevice. See
  sip/README for more info (revert if this is wrong)   

2008-07-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/enginecolorswidget.h, avogadro/src/enginecolorswidget.ui,
  avogadro/src/mainwindow.cpp, libavogadro/src/engine.cpp: *
  avogadro/src/enginecolorswidget.*: Widget for setting an engine's color map. 
  * avogadro/src/mainwindow.cpp: Add the color widget to engine settings
  window.  * libavogadro/src/engine.cpp: emit changed() when
  Engine::setColorMap() is called.  

2008-07-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp: Use some of the newer
  OBGridData API - requires OpenBabel trunk/OpenBabel 2.2.0 release. 

2008-06-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/color.cpp, libavogadro/src/povpainter.cpp,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h:
  port a fix by Laurent Montel fixing 2 memleaks, in PrimitiveItemModel and in
  POVPainter.  See: http://websvn.kde.org/?view=rev&revision=822121  By the
  way, this made me re-read the Color class. Why do we have all these virtual
  methods? Is there any reason why we might want to subclass Color? Or is it
  not-performance-critical? Also there now are many members to this class. That
  might be fine but one just needs to keep that in mind, don't allocate a whole
  array of objects of Color class, and don't create a new Color object too
  frequently (i.e. every few drawn triangles! i hope e.g. the Surface engine is
  not doing that).   

2008-06-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Added some initial dipole
  engine settings. Klunky.  

2008-06-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/boost.h: * libavogadro/src/boost.h: Add
  extract_swig_wrapped_ptr to convert SWIG object (from openbabel) to be
  converted to boost::python/C++ objects. Still very limited, but you can now
  do: >>> atom = obcore.OBAtom() >>> atom.SetAtomicNum(6) >>>
  Avogadro.molecule.AddAtom(atom)   

2008-06-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Added a new QChem input deck
  generator. The input file generated is still not correct but VLANs and the
  fact that it compiles mean it is better to add it now.  

2008-06-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Added bond length label.  

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp: Remove Mac
  pasteboard converter -- currently prevents drag-and-drop.  

  * libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/extensions/unitcellextension.cpp: Update to unit cell support
  -- update molecule to reflect changes in unit cell and translate properly to
  show super cell planes.  

2008-06-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp: When
  opening a 2D file, ask to do a quick conversion to 3D. (scale bonds, wedge ->
  Z+1, hash -> Z-1, UFF 100 steps, should we add hydrogens?)   

2008-06-11  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp: Fixed initialisation of the
  QVarLengthArray.  

2008-06-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercelldialog.h,
  libavogadro/src/extensions/supercelldialog.ui: Initial "super cell builder."
  For now, simply rotate the camera to expose a partiacular Miller plane of the
  crystal.  

2008-06-09  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added a compact form of
  the z-matrix as an option.  

2008-06-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/namedselectionmodel.h: forgot files :(  

  * ChangeLog, libavogadro/src/boost.h: * libavogadro/src/glwidget.*: Functions
  for named selections.  * libavogadro/src/extensions/selectextension.*,
  libavogadro/src/extension/namedselectionmodel.*: Use them. At the moment the
  model is a simple list. I needed this functionality for specifying
  interaction groups in the force field setup dialog. This would be expanded in
  the future (tree view).  * libavogadro/src/boost.h: adjust
  OBMol::AddHydrogens() for added pH paramter.   

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: * libavogadro/src/glwidget.*: Functions for named
  selections.  * libavogadro/src/extensions/selectextension.*,
  libavogadro/src/extension/namedselectionmodel.*: Use them. At the moment the
  model is a simple list. I needed this functionality for specifying
  interaction groups in the force field setup dialog. This would be expanded in
  the future (tree view).   

2008-06-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/overlayextension.cpp,
  libavogadro/src/extensions/overlayextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: * libavogadro/src/glwidget.*: Add resized()
  signal.  * libavogadro/src/extensions/overlayextension.*: 2D overlay
  extension for displaying ESP gradient, 2D representations, ???   

2008-06-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * scripts/avogadro.nsi, scripts/cmake-vs2005.bat,
  scripts/installer/Changelog.txt, scripts/installer/avogadro.ico,
  scripts/installer/dist/gpl.txt,
  scripts/installer/installer_languages/english.nsh,
  scripts/installer/installer_languages/german.nsh,
  scripts/installer/setup.nsi: New win32 installer. 

2008-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bumped
  version number of trunk to 0.8.2 now that trunk is open again.  

2008-06-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts: Translation updates from
  Launchpad.  

2008-06-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/tools/selectrotatetool.cpp: *
  libavogadro/src/tools/selectrotatetool.cpp: When selecting residues, also
  select the bonds.  * libavogadro/src/extensions/hydrogenextension.*: Added
  "Add Hydrogens for pH...".   

2008-06-06  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Added calls to
  tr for i18n, thanks to Louis Ricard in bug 1986689.  

  * ChangeLog, libavogadro/src/primitive.cpp: Tweaked the calling order for the
  signals.  

2008-06-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Fixed copyright lines to
  give credit to Michael Banck for his contribution.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Finally added the z-matrix
  support from Michael Banck in bug 1954332.  

  * ChangeLog, libavogadro/src/extensions/gamessinputdialog.ui: Reduced the
  vertical size of the GAMESS dialog, fixes bug 1982113.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Added more verbosity to engine
  loading in order to diagnose engine loading issues.  

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp: Fixed issue with the
  atom IDs not getting trimmed and so the ribbon not being displayed.  

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Actually draw the extents of the
  cube if requested to.  

2008-06-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/gaussianinputdialog.ui: Remove "Deck Generator"
  from dialog title. Let's stick to "Gaussian Input" or something like this.
  "Input Deck" sounds like we're using punch cards...  

  * avogadro/src/CMakeLists.txt, scripts/extract-messages.sh: Minor Mac
  localization improvements.  

2008-06-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: *
  libavogadro/src/engines/surfaceengine.cpp: Scale numBoxes with quality.   

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Added a quick render and render
  transparent function.  

  * ChangeLog, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: Added a quick render function to fix
  rendering when quick draw is used.  

2008-06-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: *
  libavogadro/src/engines/surfaceengine.cpp: Instead of iterating over all
  atoms for each grid point, iterate over all atoms once and only update grid
  points around the atom. This is 100-200x times faster...   

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/addenginedialog.cpp: Fixes bug 1984080 - the added
  engine was somewhat random before.  

2008-06-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-pt.ts, i18n/avogadro_pt.ts: Fix name of Portuguese
  translation.  

  * ChangeLog, avogadro/src/CMakeLists.txt, i18n/avogadro-pt.ts,
  i18n/avogadro.pot, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fr.ts,
  libavogadro/src/extensions/animationdialog.ui, scripts/extract-messages.sh: *
  i18n/*, scripts/extract-messages.sh: Added additional resources for .pot and
  .po file generation to integrate with Rosetta/Launchpad. Includes pt and es
  initial translations.  * avogadro/src/CMakeLists.txt: Use a file glob for ts
  files to build into qm files.   

2008-06-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindLinguist.cmake, i18n/avogadro.pot, i18n/avogadro_de.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts,
  libavogadro/src/extensions/selectextension.cpp, scripts/extract-messages.sh,
  scripts/extractrc.sh: Minor i18n improvements and scripts for generating
  po/pot files.  

2008-06-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engine.h, libavogadro/src/extension.h,
  libavogadro/src/tool.h: Bumped our plugin version to 1.1 - should help with
  bugs 1973909 and 1982102 - warning a make clean is needed.  

2008-06-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h: *
  libavogadro/src/engines/dipoleengine.*: New dipole moment engine -- needs
  more work, but displays dipole moments from Gaussian, GAMESS and Q-Chem
  output  with recent OB-trunk.   

2008-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp: Fixed bug 1968565 -
  orbitals are now cleared correctly along with everything else.  

2008-05-30  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Implemented showing and
  hiding of the preview text - defaults to shown.  

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h: Fixed up the template
  extension so that it would actually compile, added an example minimal entry
  in the CMake file too (commented out).  

2008-05-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp: emit
  enableEngineSettingsButton(false) when you delete an engine. Otherwise when
  you pressed "Settings...", it would segfault. 

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/toolgroup.cpp: * libavogadro/src/glwidget.cpp,
  libavogadro/src/toolgroup.cpp, avogadro/src/mainwindow.cpp: In windows, use
  QCoreApplication::applicationDirPath() to find the plugins. (fixes #1977338) 

  * ChangeLog, libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h: *
  libavogadro/src/extensions/constraintsdialog.ui: Disable unimplemented
  Save/Load buttons.  * libavogadro/src/extensions/forcefieldextension.*: Only
  create new dialogs when needed. (in performAction, not in constructor)  *
  libavogadro/src/extensions/constraintsdialog.cpp: Small GUI changes (min/max
  values, singleStep, ...)  * libavogadro/src/extensions/propmodel.cpp: Angle
  and Torsion properties are not editable, don't set writable flag.  *
  libavogadro/src/extensions/propextension.*: Only create dialogs (views) and
  models when needed. Call QObject::deleteLater() on both the model and the
  view in PropertiesView::hideEvent().  * libavogadro/src/tools/autoopttool.*:
  Exit, wait, and delete the thread in the destructor. Display the energy while
  running. Added conjugate gradients again.   

2008-05-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/insertfragmentdialog.cpp: *
  libavogadro/src/tools/insertfragmentdialog.cpp: workaround for bug #1977172.
  Create a new OBConversion object each time you insert a fragment from the
  library.   

2008-05-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h: *
  libavogadro/src/tools/directorytreemodel.*: Invalidate persistent indexes.
  See this blogpost for details: last code block at the bottom
  http://der-dakon.net/blog/KDE/persistent-crash.html (This fixes the crashes I
  was having with the "Reset List" button.)   

2008-05-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/unitcellparamdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: *
  libavogadro/src/glwidget.*: Add method to clear unit cell data.  *
  libavogadro/src/extensions/unitcell*: Improved unit cell dialog. Added
  "Apply" button to change parameters. Automatically changes number of cells to
  display via signals/slots. Button to delete unit cells. New button to "fill"
  unit cells with symmetry-defined atoms via the space group.   

  * libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Workaround for Qt/Mac cursor
  problems.  

2008-05-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/propmodel.cpp: *
  libavogadro/src/extensions/propmodel.cpp: Get energy for all conformers and
  only use OBMol::GetEnergy() if no ConformerData is available. (fixes
  #1976199)   

2008-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp: Fixed PR 1973714 - removed the file
  ending from the file name passed to the save dialog. Also placed the
  macchempasteboard.h in a Mac ifdef to fix compilation on other OSes.  

2008-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: *
  libavogadro/src/tools/drawtool.cpp: Do not try to change the bond order for
  X-H bonds when adjust hydrogens is on. Not sure if we should ever have double
  bonds to hydrogens...   

2008-05-27  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/macchempasteboard.cpp,
  avogadro/src/macchempasteboard.h, avogadro/src/mainwindow.cpp: *
  avogadro/src/macchempasteboard.*: Add mime converter to supply MIME types for
  Mac chemical clipboard/pasteboard types (i.e. ChemDraw).  *
  avogadro/src/mainwindow.cpp: Add support for ChemDraw. Doesn't parse -- need
  more debugging.   

2008-05-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, Doxyfile, avogadro/src/mainwindow.h, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/elementcolor.cpp,
  libavogadro/src/elementcolor.h, libavogadro/src/elementtranslate.h,
  libavogadro/src/engine.h, libavogadro/src/extension.h,
  libavogadro/src/global.cpp, libavogadro/src/global.h,
  libavogadro/src/glwidget.h, libavogadro/src/idlist.h,
  libavogadro/src/navigate.h, libavogadro/src/painter.h,
  libavogadro/src/primitive.h, libavogadro/src/residuecolor.h,
  libavogadro/src/textrenderer.h, libavogadro/src/toolgroup.h: * Doxyfile,
  avogadro/src/mainwindow.h, libavogadro/src/*: Update doxygen documentation.  

  * ChangeLog, avogadro/src/CMakeLists.txt,
  avogadro/src/mac/locversion.plist.in: * avogadro/src/CMakeLists.txt,
  avogaro/src/mac/locversion.plist.in: Add additional Mac i18n support, solving
  PR#1972467.   

2008-05-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * CMakeLists.txt, cmake/modules/TestIfWeNeedFPermissive.cmake: patch from
  Simon: improve and make use of TestIfWeNeedFPermissive.cmake This solves
  issues with gcc >= 4.3.1 being stricter than current boost code. In fact the
  present test is slightly stricter in that 4.3.0 also needs -fpermissive. GCC
  4.2 doesn't require it.   

2008-05-25  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Update for Krazy 

2008-05-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog: Bump our dependencies on CMake and Qt.  

2008-05-22  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/python/deleteAll.py: Fixed the
  deleteAll script to use the new DeleteAtom function signature.  

  * ChangeLog, libavogadro/src/extensions/pythonextension.cpp: Search the
  system path for Python plugins too.  

2008-05-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/insertfragmentdialog.cpp: *
  libavogadro/src/tools/insertfragmentdialog.cpp: Fix insert smiles. Also
  disable the driectoryTreeView and smilesLineEdit while in insert mode. This
  makes it impossible to change the smiles and forget to press Stop/Start.   

2008-05-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add help URLs to the website.  

  * libavogadro/src/elementtranslate.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/drawtool.cpp:
  Change extern elementTranslate to ensure there's only one copy.  

2008-05-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/hydrogensextension.cpp: Fixed PR
  1947734, now the number of hydrogrens most people would expect are added.... 

2008-05-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt, ChangeLog, avogadro/src/main.cpp,
  libavogadro/src/cylinder.cpp, libavogadro/src/elementtranslate.cpp,
  libavogadro/src/engines/iso.cpp, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/drawtool.cpp: * CMakeLists.txt: Change "C:\Program
  Files\avogadro" into "C:\\Program Files\\avogadro".  * avogadro/src/main.cpp:
  Windows build had problems with printVersion/printHelp. Quick fix with cout &
  #ifdef WIN32.  * libavogadro/src/cylinder.cpp: Make sure M_PI isdefined.  *
  libavogadro/src/elementtranslate.cpp: Global instance should be extern.  *
  libavogadro/src/engines/iso.cpp: MSVC doesn't have __attribute__
  ((aligned(16)). Quick fix with #ifdef WIN32 and without the data alignment. 
  * libavogadro/src/engines/labelengine.cpp: Local instance should not be
  extern.  * libavogadro/src/engines/polygonengine.cpp: Change
  static_cast<const Atom*> into static_cast<Atom*>.  *
  libavogadro/src/periodictableview.cpp: Local instance should not be extern. 
  * libavogadro/src/tools/aligntool.cpp: Change static_cast<const Atom*> into
  static_cast<Atom*>.  * libavogadro/src/tools/bondcentrictool.cpp: This file
  defined its own isnan() function which resulted in a conflict with
  OpenBabel::IsNan(). Now uses OpenBabel::IsNan().  *
  libavogadro/src/tools/drawtool.cpp:  Local instance should not be extern.  *
  scripts/avogadro.nsi: update installer generating script.   

2008-05-19  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Fixed the bug where zoom would
  corrupt the camera matrix in the draw tool. Made the molecule check in the
  navigate tool a little safer.  

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Made the manipulate tool a lot faster
  by only saving undo points on mouse up and mouse down.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Added back in target_link_libraries as
  they are needed on the Mac at least.  

  * CMakeLists.txt, ChangeLog, avogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Various changes to the build system.
  Added -DQT_NO_DEBUG to our release mode. Changed all plugins to be built as
  modules.  

2008-05-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt: Add
  the OpenBabel library directory to the linker path.  

  * CMakeLists.txt, ChangeLog: Respect the users CXXFLAGS.  

2008-05-17  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: Add some caching in the tool so
  measurements are only echoed once.  

  * ChangeLog, avogadro/src/mainwindow.ui: Tweaks to the UI.  

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Propagate new grids through
  to the combo and some UI cleanup.  

2008-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/iso.cpp: *
  libavogadro/src/iengines/iso.cpp: Surfaces are now centered around atom
  again. The - 0.5 * m_stepSize correction is only needed for
  vMarchCube1(float,float,float). This is a bug in OBFloatGrid?   

  * ChangeLog, libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: *
  libavogadro/src/tools/drawtool.*: Use new OBForceField::SetIgnoreAtom() to
  make sure the new atom doesn't push away other fragment you want to connect
  with. Also fix the atom when you hit an atom that already exists. This makes
  drawing rings with AutoOpt enabled really easy.  *
  libavogadro/src/autoopttool.*: Use new OBForceField::SetFixAtom()  *
  libavogadro/src/extensions/animationdialog.ui: Make the dialog more compact.
  Removed the group boxes.   

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.ui: Hide more advanced options for
  now, cleanups.  

2008-05-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/drawtool.cpp:
  Minor interface cleanups.  

2008-05-16  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Krazy  

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h:
  Added options to align everything or just the current molecule.  

2008-05-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version for 0.8
  release.  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/tools/autorotatetool.cpp: *
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/propextension.cpp, avogadro/src/mainwindow.ui,
  avogadro/src/mainwindow.cpp: More interface cleanup -- any menu item or
  button which brings up a dialog should have "..." at the end. (KDE, Windows,
  and Mac UI guidelines.)   

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: More layout improvements.  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Layout improvements in the
  tool set up dialog.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added the ability to edit
  the input deck, revert etc.  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Added some extra signals on
  mouse release to ensure molecule is updated.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.ui: Fixed the tab
  ordering of the dialog.  

  * ChangeLog, libavogadro/src/periodictableview.cpp: Some changes to improve
  layout in Linux (and hopefully Windows).  

  * ChangeLog, cmake/modules/FindOpenBabel2.cmake: Hopefully a new and improved
  FindOpenBabel2 using the new PkgConfig functions.  

  * CMakeLists.txt, ChangeLog: Set the CMake policy for CMake 2.6.  

2008-05-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: * avogadro/mainwindow.h, avogadro/mainwindow.cpp:
  Changed engine configuration to a new button which brings up an extra
  "settings" window with tabs. Add signal/slot for enabling the Engine Settings
  window -- only enables button for engines with settings.   

  * avogadro/src/enginelistview.cpp, avogadro/src/primitivetreeview.cpp: *
  src/enginelistview.cpp, primitivetreeview.cpp: Add setUniformItemSizes(true)
  -- supposedly improves performance.   

  * avogadro/src/enginesetupwidget.cpp, avogadro/src/enginesetupwidget.h,
  avogadro/src/enginesetupwidget.ui: Removed deprecated code.  

2008-05-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/elementcombobox.cpp.disabled, avogadro/src/elementcombobox.h:
  Remove deprecated code.  

2008-05-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  libavogadro/include/avogadro/idlist.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h, libavogadro/src/idlist.cpp,
  libavogadro/src/idlist.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h: Added the IDList class which holds an organized
  list of IDs like PrimitiveList except that you cannot iterate through them
  all since IDs are specific to the type they belong.  Moved id to be a
  property of all primitives.  Fixed the Hydrogens commands and the
  editcommands to use IDs instead of pointers which should alleviate much of
  the crashing.  See PR#1964661  

2008-05-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.cpp: Made some
  changes to the surface engine and the GLWidget to improve locking. Seems to
  have prevented crashes in the surface engine here. More locking is needed.  

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Added Control
  modifier to the tool to fix PR 1962903 - toggle selected primitives.  

  * ChangeLog, libavogadro/src/color.h: Cast GLFloats to ints to suppress
  warning.  

  * ChangeLog, libavogadro/src/CMakeLists.txt: Only add the Boost_INCLUDE_DIR
  if boost is found - fixes a CMake error with CMake 2.6.  

2008-05-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Added unique identifiers for each atom that is created and this helps us with
  adding and deleting atoms with our drawing tool.  

2008-05-14  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/pythonextension.cpp: Fixed typo.  

2008-05-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animation.qrc,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/icons/amarok_back.png,
  libavogadro/src/extensions/icons/amarok_next.png,
  libavogadro/src/extensions/icons/amarok_pause.png,
  libavogadro/src/extensions/icons/amarok_play.png,
  libavogadro/src/extensions/icons/amarok_stop.png, testfiles/spc216.pdb,
  testfiles/spc216.xtc: * libavogadro/src/extensions/animation*.*: Basic
  animation extension.  * testfiles/spc216.*: Added pdb topology and xtc
  trajectory to test animation.   

2008-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog: Allow ENABLE_PYTHON variable to allow disabling
  of Python.  

2008-05-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Fix
  PR#1839866 with graphical bugs and multiple bond wireframe view.  

  * libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: Fixed PR#1959763.  

2008-05-13  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Krazy  

2008-05-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: Some Linux fixes for the
  insert fragment paths.  

2008-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Fixed uninitialised
  variables.  

2008-05-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/primitiveitemmodel.cpp: A few minor "const" fixes for
  foreach() keyword.  

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfacesettingswidget.ui: Disable the "Custom Color"
  widget when using ESP coloring.  

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/insertfragmentdialog.ui: Update some translation
  strings.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Fix a potential file corruption
  problem if save file fails. Instead, save to a new name, then rename the
  file.  * avogadro/src/mainwindow.cpp: Implement save to a new file, then a
  rename. (If others have ways to improve this, please let me know.)   

2008-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp: Fixed the code to fail properly
  when the file to be opened does not exist.  

2008-05-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Geoff fixed many many more issues. <10 left! 

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp: *
  libavogadro/src/extensions/propmodel.cpp
  libavogadro/src/extensions/propextension.h
  libavogadro/src/extensions/propextension.cpp: Updates to fix some
  translations and to allow resizing the window without showing large amounts
  of empty space.   

  * Doxyfile, Doxyfileext: Update for 0.8 version number.  

  * avogadro/src/addenginedialog.h, avogadro/src/application.h,
  avogadro/src/editcommands.h, avogadro/src/elementcombobox.h,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.h,
  avogadro/src/enginesetupwidget.h, avogadro/src/flattabwidget.h,
  avogadro/src/mainwindow.h, avogadro/src/primitivetreeview.h,
  avogadro/src/savedialog.h, avogadro/src/settingsdialog.h,
  libavogadro/src/boost.h, libavogadro/src/camera.h, libavogadro/src/color.h,
  libavogadro/src/colorbutton.h, libavogadro/src/cylinder.h,
  libavogadro/src/elementcolor.h, libavogadro/src/elementtranslate.h,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/extension.h, libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h,
  libavogadro/src/filetreeitem.h, libavogadro/src/global.h,
  libavogadro/src/glpainter.h, libavogadro/src/glwidget.h,
  libavogadro/src/navigate.h, libavogadro/src/painter.h,
  libavogadro/src/painterdevice.h, libavogadro/src/painterengine.h,
  libavogadro/src/periodictableview.h, libavogadro/src/povpainter.h,
  libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.h, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/residuecolor.h, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.h, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/quaternion.h, libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/skeletontree.h, libavogadro/src/undosequence.h: More
  Krazy fixes.  

2008-05-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Update Krazy after Geoffs many fixes 

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/flowlayout.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/painterengine.cpp, libavogadro/src/painterengine.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/skeletontree.cpp,
  libavogadro/src/tools/skeletontree.h: * Many files: Fix a pile of Krazy
  warnings.   

2008-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed uninitialised undoStack
  pointer.  

2008-05-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/aligntool.cpp: Fixed for case where the
  molecule was already alined to the chosen axis.  

2008-05-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, ChangeLog, libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: * CMakeLists.txt: Install our
  fragments. Destination may need tuning on Linux and Windows.  *
  libavogadro/src/tools/insertfragmentdialog.cpp: Update to include default
  fragment paths as much as possible. This will need tuning on Linux and
  Windows. Does Cmake set a -D define for an installation path, e.g. /usr vs
  /usr/local?  * libavogadro/src/tools/directorytreemodel.cpp: Ignore hidden
  files.   

  * fragments/coordination/3-trigonal-planar.cml,
  fragments/coordination/3-trigonal-pyramidal.cml,
  fragments/coordination/4-planar.cml,
  fragments/coordination/4-tetrahedral.cml,
  fragments/coordination/5-square-pyramidal.cml,
  fragments/coordination/5-trigonal-bipyramidal.cml,
  fragments/coordination/6-octahedral.cml: Add coordination fragments for metal
  centers  

2008-05-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/forcefieldextension.cpp: *
  libavogadro/src/extensions/forcefieldextension.cpp: Added a
  QMessageBox::information() box to display the energy when the user clicks
  "Calculate Energy". (#1947745)   

  * ChangeLog, libavogadro/src/extensions/forcefieldextension.cpp: *
  libavogadro/src/extensions/forcefieldextension.cpp: Move call to SetLogFile
  (fixes #1960307)   

2008-05-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * fragments/cyclic alkanes/adamantane.cml, fragments/cyclic
  alkanes/cyclobutane.cml, fragments/cyclic alkanes/cycloheptane.cml,
  fragments/cyclic alkanes/cyclohexane.cml, fragments/cyclic
  alkanes/cyclopentane.cml, fragments/cyclic alkanes/cyclopropane.cml: New
  alkane rings.  

2008-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * fragments/alcohols/ethanol.cml, fragments/alcohols/methanol.cml,
  fragments/alcohols/propan-1-ol.cml, fragments/alcohols/propan-2-ol.cml,
  fragments/aldehydes/acetaldehyde.cml, fragments/aldehydes/formaldehyde.cml,
  fragments/alkanes/2-methylpropane.cml, fragments/alkanes/ethane.cml,
  fragments/alkanes/methane.cml, fragments/alkanes/propane.cml,
  fragments/alkenes/but-1-ene.cml, fragments/alkenes/ethene.cml,
  fragments/alkynes/acetylene.cml, fragments/alkynes/propyne.cml,
  fragments/amides/N_N-dimethylacetamide.cml,
  fragments/amides/N_N-dimethylformamide.cml, fragments/amides/acetamide.cml,
  fragments/amides/ethyl_carbamate.cml, fragments/amides/oxamide.cml,
  fragments/amines/ammonia.cml, fragments/amines/azepane.cml,
  fragments/amines/ethylamine.cml, fragments/amines/methylamine.cml,
  fragments/amino_acids/D-alanine.cml,
  fragments/amino_acids/D-allo-threonine.cml,
  fragments/amino_acids/D-arginine.cml, fragments/amino_acids/D-asparagine.cml,
  fragments/amino_acids/D-aspartic_acid.cml,
  fragments/amino_acids/D-cysteine.cml,
  fragments/amino_acids/D-glutamic_acid.cml,
  fragments/amino_acids/D-glutamine.cml, fragments/amino_acids/D-histidine.cml,
  fragments/amino_acids/D-isoleucine.cml, fragments/amino_acids/D-leucine.cml,
  fragments/amino_acids/D-lysine.cml, fragments/amino_acids/D-methionine.cml,
  fragments/amino_acids/D-phenylalanine.cml,
  fragments/amino_acids/D-proline.cml, fragments/amino_acids/D-serine.cml,
  fragments/amino_acids/D-threonine.cml,
  fragments/amino_acids/D-tryptophan.cml, fragments/amino_acids/D-tyrosine.cml,
  fragments/amino_acids/D-valine.cml,
  fragments/amino_acids/L-4-nitrophenylalanine.cml,
  fragments/amino_acids/L-alanine.cml,
  fragments/amino_acids/L-allo-isoleucine.cml,
  fragments/amino_acids/L-arginine.cml, fragments/amino_acids/L-asparagine.cml,
  fragments/amino_acids/L-aspartic_acid.cml,
  fragments/amino_acids/L-cysteine.cml,
  fragments/amino_acids/L-glutamic_acid.cml,
  fragments/amino_acids/L-glutamine.cml, fragments/amino_acids/L-histidine.cml,
  fragments/amino_acids/L-isoleucine.cml, fragments/amino_acids/L-leucine.cml,
  fragments/amino_acids/L-lysine.cml, fragments/amino_acids/L-methionine.cml,
  fragments/amino_acids/L-phenylalanine.cml,
  fragments/amino_acids/L-proline.cml, fragments/amino_acids/L-serine.cml,
  fragments/amino_acids/L-threonine.cml,
  fragments/amino_acids/L-tryptophan.cml, fragments/amino_acids/L-tyrosine.cml,
  fragments/amino_acids/L-valine.cml, fragments/amino_acids/glycine.cml,
  fragments/aromatics/1H-indene.cml, fragments/aromatics/aniline.cml,
  fragments/aromatics/anisole.cml, fragments/aromatics/anthracene.cml,
  fragments/aromatics/benzaldehyde.cml, fragments/aromatics/benzene.cml,
  fragments/aromatics/benzoic_acid.cml,
  fragments/aromatics/benzoyl_chloride.cml, fragments/aromatics/caffeine.cml,
  fragments/aromatics/naphthalene.cml, fragments/aromatics/nitrobenzene.cml,
  fragments/aromatics/phenol.cml, fragments/aromatics/toluene.cml,
  fragments/buckminsterfullerene.cml, fragments/carbamides/urea.cml,
  fragments/carbohydrates/d-allose.cml, fragments/carbohydrates/d-altrose.cml,
  fragments/carbohydrates/d-arabinose.cml,
  fragments/carbohydrates/d-erythrose.cml,
  fragments/carbohydrates/d-erythrulose.cml,
  fragments/carbohydrates/d-fructose.cml,
  fragments/carbohydrates/d-galactose.cml,
  fragments/carbohydrates/d-glucose.cml,
  fragments/carbohydrates/d-glyceraldehyde.cml,
  fragments/carbohydrates/d-gulose.cml, fragments/carbohydrates/d-idose.cml,
  fragments/carbohydrates/d-lyxose.cml, fragments/carbohydrates/d-mannose.cml,
  fragments/carbohydrates/d-psicose.cml, fragments/carbohydrates/d-ribose.cml,
  fragments/carbohydrates/d-ribulose.cml,
  fragments/carbohydrates/d-sorbose.cml,
  fragments/carbohydrates/d-tagatose.cml, fragments/carbohydrates/d-talose.cml,
  fragments/carbohydrates/d-threose.cml, fragments/carbohydrates/d-xylose.cml,
  fragments/carbohydrates/d-xylulose.cml,
  fragments/carbohydrates/dihydroxyacetone.cml,
  .../carboxylic_acids/2_2-dichloroacetic_acid.cml,
  .../2_2_2-trichloroacetic_acid.cml, .../2_2_2-trifluoroacetic_acid.cml,
  fragments/carboxylic_acids/D-lactic_acid.cml,
  fragments/carboxylic_acids/D-malic_acid.cml,
  fragments/carboxylic_acids/D-tartaric_acid.cml,
  fragments/carboxylic_acids/L-ascorbic_acid.cml,
  fragments/carboxylic_acids/L-lactic_acid.cml,
  fragments/carboxylic_acids/L-malic_acid.cml,
  fragments/carboxylic_acids/L-tartaric_acid.cml,
  fragments/carboxylic_acids/acetic_acid.cml,
  fragments/carboxylic_acids/butanoic_acid.cml,
  fragments/carboxylic_acids/citric_acid.cml,
  fragments/carboxylic_acids/formic_acid.cml,
  fragments/carboxylic_acids/isobutyric_acid.cml,
  fragments/carboxylic_acids/oxalic_acid.cml,
  fragments/carboxylic_acids/propanoic_acid.cml, fragments/cyclic
  alkanes/cubane.cml, fragments/cyclic alkanes/norbornane.cml,
  fragments/ethers/di-tert-butylether.cml, fragments/ethers/dibutylether.cml,
  fragments/ethers/diethylether.cml, fragments/ethers/diisopropylether.cml,
  fragments/ethers/dimethylether.cml, fragments/ethers/dipropylether.cml,
  fragments/ethers/ethylmethylether.cml, fragments/ethers/tetrahydrofuran.cml,
  fragments/fatty acids/decanoic_acid.cml, fragments/fatty
  acids/hexanoic_acid.cml, fragments/fatty acids/lauric_acid.cml,
  fragments/fatty acids/linoleic_acid.cml, fragments/fatty
  acids/octanoic_acid.cml, fragments/fatty acids/oleic_acid.cml,
  fragments/fatty acids/palmitic_acid.cml, fragments/fatty
  acids/stearic_acid.cml, fragments/heteroaromatics/1H-indole.cml,
  fragments/heteroaromatics/1H-pyrazole.cml,
  fragments/heteroaromatics/1H-pyrrole.cml,
  fragments/heteroaromatics/1_2-oxazole.cml,
  fragments/heteroaromatics/1_2-thiazole.cml,
  fragments/heteroaromatics/1_3-oxazole.cml,
  fragments/heteroaromatics/1_3-thiazole.cml,
  fragments/heteroaromatics/benzofuran.cml,
  fragments/heteroaromatics/benzothiophene.cml,
  fragments/heteroaromatics/furan.cml, fragments/heteroaromatics/pyridine.cml,
  fragments/heteroaromatics/thiophene.cml, fragments/ketones/acetone.cml,
  fragments/ketones/butanone.cml, fragments/macrocycles/porphin.cml,
  fragments/nucleobases/adenine.cml, fragments/nucleobases/cytosine.cml,
  fragments/nucleobases/guanine.cml, fragments/nucleobases/thymine.cml,
  fragments/nucleobases/uracil.cml, fragments/steroids/cholesterol.cml,
  fragments/steroids/estradiol.cml, fragments/steroids/testosterone.cml,
  fragments/sulfoxides/dimethyl_sulfoxide.cml,
  fragments/thiols/ethanethiol.cml, fragments/thiols/methanethiol.cml,
  fragments/thiols/pentane-1-thiol.cml, fragments/water.cml: Added new fragment
  library based on chem-file Blue Obelisk repository. These are selected files,
  and I haven't added the CMakeLists.txt to install them. Suggestions welcome. 

2008-05-07  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt: Optionally use CMake 2.6 and the
  much improved FindBoost to check for and use Boost Python on more than just
  Linux - works great on the Mac.  

2008-05-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefielddialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h: *
  libavogadro/src/extensions/forcefielddialog.*: Removed gradients option. Now
  handled OBForceField::HasAnalyticalGradients()  *
  libavogadro/src/extensions/conformersearchdialog.*: Same.  *
  libavogadro/src/extensions/forcefieldextension.*: Same.  *
  libavogadro/src/extensions/constraintsdialog.*: Update for static
  constraints. We now only need to set it once.  *
  libavogadro/src/tools/autoopttool.*: Replaced convergence spin box by steps
  per update spin box.   

2008-05-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Set the navigate tool as the
  active tool after loading a file.  

2008-05-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Added saving of the current
  element to the draw tool.  

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp: Add checks in for whether
  the force field was initialised correctly.  

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: More updates to the orbital engine
  to improve rendering consistency.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Fixed another
  crasher - when no basis set has been loaded.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Corrected the
  MO title in the cube title.  

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Added some settings persistence,
  improved the quickRender a little too.  

2008-05-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: More guarded pointers to prevent
  crashing caused by dangling pointers.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Only switch to quickRender on
  mouse move, not press.  

  * ChangeLog, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.h: Used guarded pointers (QPointer) to make
  the align tool much harder to crash.  

2008-05-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Adding some extra detail on
  the cube parameters along with the ability to modify this. Also added a
  little extra debug output while support if improved.  

2008-05-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added several new options
  and modifications based upon discussion in bug 1954113. Editing of the text
  edit box still needs to be added.  

2008-04-30  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Update the display after axes or
  debug rendering is turned on or off.  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Updated
  with new view menu actions for axes and debug information.  

2008-04-29  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp: *
  avogadro/src/mainwindow.cpp: Fix up Mac/Windows save dialogs. Also disable
  save/revert menu actions until the document is modified.  *
  avogadro/src/savedialog.cpp: Remove incorrect #ifdef for setting filters on
  Mac. Now done in mainwindow.cpp. Use static QFileDialog on Windows (and Mac).
    

  * libavogadro/src/tools/align.png, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.qrc: New icon for the align tool.  

2008-04-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Several
  fixes suggested by Michael Banck in bugs 1954108, 1954101 and 1954099.  

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Only recalculate the
  isosurface when editing is finished, minimum spinner value of zero.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Tracked the bug of the disappearing
  molecule - it was never set for extensions after the first window.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Return if the
  file name is empty.  

2008-04-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Also
  connected molecule signals to the dialog.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Made the
  reset button work.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Update the
  preview when setMolecule is called. Also added some logic to disable basis
  sets with certain theories.  

  * ChangeLog, libavogadro/src/extensions/basisset.cpp: Actually call the doD
  and doD5 functions - this really helps when trying to use d-type orbitals to
  generate cubes...  

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added a new Gaussian input
  deck generator. Still quite basic with a few bugs but is already generating
  valid input decks.  

2008-04-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp,
  avogadro/src/savedialog.h: Cleaned up Mac-specific save dialog (we can use
  the Qt static methods). Make sure to save the selected filter on all
  platforms -- we should remember what the user picked and make it the default
  next time.  

2008-04-27  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Found a few more cases where
  foreach loops needing fixing.  

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/toolgroup.cpp:
  Made changes to foreach loops as suggested by Albert Astals Cid, prevent
  unnecessary creation of temporary objects.  

2008-04-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: *
  avogadro/src/mainwindow.*: Add drag-and-drop support. Files dragged onto a
  window will be loaded.   

  * libavogadro/src/moleculetreeview.cpp.disabled,
  libavogadro/src/moleculetreeview.h.disabled,
  libavogadro/src/primitiveitemmodel.cpp: *
  libavogadro/src/primitiveitemmodel.cpp: Added in layout change signals. Will
  hopefully prevent crashing.   

2008-04-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/orbitalextension.cpp: Ported to use std::vector to
  store everything. Changed the way normalisation is handled. Added d-type
  orbitals - this has not been verified yet.  

2008-04-24  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/basisset.cpp: Added destructor bits. 

2008-04-23  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Sorted out the
  units in the cube calculation initialisation...  

2008-04-22  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Also added a
  call to processEvents() to maintain interactivity.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Work out the
  dimensions of the cube from the molecule, also clear the molecule.  

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Added a new orbital extension.
  This extension uses the new BasisSet class along with GaussianFchk to load a
  formatted checkpoint file and calculate MOs. Support for more programs and
  more features soon.  

2008-04-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/savedialog.cpp, avogadro/src/savedialog.h,
  libavogadro/src/tools/navigatetool.cpp: * fix bug: when using navigatetool on
  empty molecule, the camera got corrupted. * fix file comment in savedialog.* 
   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/savedialog.cpp, avogadro/src/savedialog.h,
  libavogadro/src/povpainter.cpp: * make the SaveDialog generic enough to be
  useful for more than just saving molecules. * move it to separate
  savedialog.* files * use it in "export graphics" and "export POV-Ray". * fix
  crash when doing "export POV-Ray" on empty molecule   

2008-04-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: Fixed reloading of python
  script issue.  

2008-04-20  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Add SaveDialog
  class inheriting QFileDialog, currently in mainwindow.* but feel free to move
  to separate files. This class sets a default filename suffix based on the
  currently selected filter. Having our own class allows us to act on the
  filterSelected signal, which is necessary for a consistent behavior.  Closes
  avogadro-Bugs-1945955   

2008-04-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/include/avogadro/filetreeitem.h,
  libavogadro/include/avogadro/treeitem.h, libavogadro/src/filetreeitem.cpp,
  libavogadro/src/filetreeitem.h, libavogadro/src/treeitem.cpp,
  libavogadro/src/treeitem.h: Step two: FileTreeItem not TreeItem  

  * libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h, libavogadro/src/treeitem.cpp,
  libavogadro/src/treeitem.h: Step one of renaming TreeItem to FileTreeItem  

  * libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/insertfragmentdialog.ui: Fixed crashes with fragment
  window -- need to emit layoutChanged signals. Now also checks for duplicate
  directories and allows the directory list to be cleared.  

2008-04-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating Krazy2 checks  

2008-04-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: Add support for
  always giving a transparent background. We can make this a configuration
  option (e.g., amount of transparency), but it's currently great for exporting
  graphics.  

  * ChangeLog, libavogadro/include/avogadro/treeitem.h,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/insertfragmentdialog.ui, libavogadro/src/treeitem.cpp,
  libavogadro/src/treeitem.h: * libavogadro/src/treeitem.*: New class for
  handling filenames in model/view context, particularly a tree browser.  *
  libavogadro/src/tools/directorytreemodel.*: New class for handling directory
  trees with multiple paths. (Basic Qt class QDirModel gives too much file info
  and doesn't handle multiple top-level directories.)  *
  libavogadro/src/tools/insertfragmentdialog.*: New class to combine the SMILES
  generation and reading in fragment files. Still needs a bit of polish.  *
  libavogadro/src/tools/drawtool.*: Use above.  *
  libavogadro/src/tools/drawcommand.*: Change InsertSMILES class to
  InsertFragment (now that we have a general fragment browser).   

  * ChangeLog, libavogadro/src/navigate.cpp, libavogadro/src/navigate.h: *
  libavogadro/src/navigate.*: Add general rotate(x, y, z) method (for
  scripting).   

2008-04-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Use the shift key rather than alt key
  as the second modifier.  

2008-04-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/config.h.in, avogadro/src/mainwindow.cpp,
  libavogadro/src/config.h.in, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/toolgroup.cpp: Added
  INSTALL_LIBDIR define in order to more reliably load plugins. Adapted the
  loading scheme for tools, engines and extensions to use INSTALL_LIBDIR.  

2008-04-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui: Removed the axes and debug display options
  from the global config - to be relocated to the view menu. Also (hopefully)
  improved the display quality feedback.  

  * ChangeLog, libavogadro/include/avogadro/navigate.h,
  libavogadro/src/navigate.cpp, libavogadro/src/navigate.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Moved the navigate functions from
  the tools directory into the library. They should be exposed as part of our
  API and would be useful in scripting.  

  * ChangeLog, libavogadro/src/tools/CMakeLists.txt: Removed the duplicate
  definition of bondcentrictool.  

  * CMakeLists.txt, libavogadro/src/global.h: Disabled the visibility flags
  again (for now) while I work on getting it working in OpenBabel - still
  having issues with the formats and visibility.  

2008-04-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfacesettingswidget.ui: *
  libavogadro/src/engines/surfaceengine.*,
  libavogadro/src/engines/surfacesettingswidget.ui: Clipping now works for any
  specified plane.   

2008-04-12  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/src/global.h: Only do the GCC visibility stuff
  when we have a supported compiler.  

2008-04-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating the Krazy files  

2008-04-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: *
  libavogadro/src/engines/surfaceengine.*,
  libavogadro/src/engines/surfacesettingswidget.ui: Added clipping plane. This
  feature could later be moved to glwidget to clip any engine... This would
  probably require engines to have a clipped and solid property (like they
  currently have radius)   

2008-04-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp, libavogadro/src/glwidget.cpp:
  Parts of the patch from Benoit Jacob - fix handling of quality change.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed bug where display lists were
  not being invalidated when the display quality was adjusted.  

  * ChangeLog, libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp: Fixed some compiler warnings.  

2008-04-09  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/camera.h, libavogadro/src/textrenderer.h,
  libavogadro/src/tools/drawtool.cpp: Fixed a few compiler warnings.  

2008-04-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/boost.h, libavogadro/src/extensions/pythonextension.cpp:
  Add some preliminary auto-complete features for the Python terminal and
  several new Open Babel features in the scripting support.  

2008-04-08  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/CMakeLists.txt: Removed duplicate call to
  automoc.  

2008-04-07  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog: Only set the linker flag on Linux systems.  

  * CMakeLists.txt, ChangeLog,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h: Disabled the visibility
  flags for now as the seem to break forcefield support.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Added a warning dialog when no
  engines and/or tools were loaded.  

  * ChangeLog, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/glwidget.cpp:
  Statically linked the ball and stick engine to libavogadro. This guarantees
  the minimal ability to display a molecule.  

  * CMakeLists.txt, ChangeLog: Added the pedantic compiler flag to spot many
  issues with C++ code such as those picked up by KDE developers. Also
  introduce symbol hiding if a recent GCC is installed. We need to explicitly
  export all symbols on Linux/Apple systems.  

  * ChangeLog, cmake/modules/FindBoostPython.cmake,
  cmake/modules/MacroEnsureVersion.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt: Added extra cmake modules from KDE
  4.1 (trunk) to improve Boost Python detection and check versions. Improved
  the Boost Python detection and linked to the dynamic Python library.  

  * ChangeLog, avogadro/src/application.h, avogadro/src/enginelistview.h,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/enginesetupwidget.h,
  avogadro/src/mainwindow.h, libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/surfaceengine.h, libavogadro/src/extension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/tools/autoopttool.h: Fixed errors pointed out by the pedantic
  compiler flag - mainly extra ;s and ,s.  

  * ChangeLog, libavogadro/src/pythoninterpreter.h: Ensure the Python
  interpreter exports its symbols.  

2008-04-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/tool.h: Changes made by Pino Toscano in KDE upstream.  

  * ChangeLog, libavogadro/src/periodictableview.h: Only export the
  PeriodicTableView class.  

  * ChangeLog, libavogadro/src/tools/navigatetool.cpp: Remember to account for
  the situation where no molecule is loaded.  

  * ChangeLog, libavogadro/src/global.h: Added visibility attributes to the
  A_EXPORT definitions so that our symbols are correctly exported when the
  default visibility is changed to hidden (as in KDE 4.1 trunk).  

2008-04-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/aligntool.qrc: Added new align tool. Currently it just
  aligns the selected atom to the origin, if there are two selected atoms they
  will be aligned along the chosen axis.  

2008-04-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h:
  Added new axes engine to display the x, y, z axes in the scene. More options
  soon.  

2008-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gamessinputdialog.cpp: Correct bug
  where nd was also being used to set np in the basic tab.  

2008-03-31  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt: Updated CMake
  files to properly link with Python and Boost.  Thanks to Jens Thomas for
  reporting and helping me debug.  

2008-03-24  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating to latest Krazy  

2008-03-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/boost.h,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/python/deleteAll.py,
  libavogadro/src/extensions/python/test.py,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h:
  Python scripts are now available.  This means you can write a python script
  (including PyQt) and it will function along with the data loaded already.  We
  have not yet exposed all parts of the API but this should give us the basis
  of where to go.  To utilize this new stuff.  Place scripts in
  $HOME/.avogadro/scripts  Avogadro should automatically detect them on loadup.
   Also, if you modify a script while the application is running it will reload
  that script before executing it again.  See the example scripts provided. 
  They are installed to $PREFIX/libavogadro/scripts but they are not
  automatically enabled.  Until we get a "script manager" then we will keep it
  like this.  -- Donald  

  * libavogadro/src/boost.h, libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminalwidget.ui: Python Extension input
  line now remembers your command history.  

  * CMakeLists.txt, avogadro/src/mainwindow.cpp,
  libavogadro/include/avogadro/boost.h,
  libavogadro/include/avogadro/pythoninterpreter.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/boost.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminalwidget.ui,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h:
  Added initial python support.  Python Extension includes an interactive
  interpreter.  

  * libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h: Added a set of extension
  template files.  

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h: Finalize moving extensions to
  the library and make a few patches.  See the updated ChangeLog for more
  details.  There is now an Extension::setMolecule function (which is a signal)
  that Extensions can reimplement and keep better tabs on the underlying data
  model.  

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h: Move extensions to
  libavogadro  

2008-03-22  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/runkrazy.rb: Reran Krazy.  

  * krazy/avogadro-src-extensions.html, krazy/libavogadro-src-extensions.html:
  new directory (src/extensions moved)  

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating the Krazy files  

2008-03-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/CMakeLists.txt,
  avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/conformersearchdialog.h,
  avogadro/src/extensions/conformersearchdialog.ui,
  avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/dockingextension.cpp,
  avogadro/src/extensions/dockingextension.h,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdata.h,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/gamessinputdialog.ui,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/liganddialog.cpp,
  avogadro/src/extensions/liganddialog.h,
  avogadro/src/extensions/liganddialog.ui,
  avogadro/src/extensions/pocketdialog.cpp,
  avogadro/src/extensions/pocketdialog.h,
  avogadro/src/extensions/pocketdialog.ui,
  avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h,
  avogadro/src/extensions/selectextension.cpp,
  avogadro/src/extensions/selectextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/extensions/unitcellparamdialog.ui,
  avogadro/src/extensions/wiitrackextension.cpp,
  avogadro/src/extensions/wiitrackextension.h, avogadro/src/mainwindow.cpp,
  libavogadro/include/avogadro/extension.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  .../src/extensions/conformersearchdialog.ui,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/constraintsdialog.ui,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefielddialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  .../src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessefpmatchdialog.ui,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/liganddialog.ui,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/pocketdialog.ui,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/unitcellparamdialog.ui,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h, libavogadro/src/tool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Moved extensions to libavogadro. 
  Added Extension::setMolecule as a signal.  Updated previous engines to take
  advantage of this new ::setMolecule function. Gives more view on when the
  underlying data model changes.  

2008-03-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, testfiles/ch3cl.cube.gz, testfiles/multicubes.cube.gz: *
  testfiles/ch3cl.cube.gz: Deleted incorrect test file.  *
  testfiles/multicube.cubes.gz: Added new multi-cube test file supplied by
  Louis Ricard.   

2008-03-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h: POV-Ray export: the aspect-ratio input dialog
  belongs to avogadro not libavogadro. In lib, just make the POVPainterDevice
  constructor take an aspectRatio argument.   

2008-03-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Modified the
  selection behaviour to be more consistent with other applications. Just the
  selected primitives are selected when clicking primitives or drawing
  selection boxes. Pressing shift causes them to be added to the existing
  selection.  

2008-03-15  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating Krazy. I fixed many issues and updated
  to the latest release of Krazy2  

  * avogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/engines/iso.cpp, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/clickmeasuretool.cpp: Many Krazy fixes  

2008-03-14  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: new run of Krazy  

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Update Krazy  

2008-03-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/wiitrackextension.cpp,
  avogadro/src/extensions/wiitrackextension.h: *
  avogadro/src/extensions/wiitrackextension.*: Wiimote head tracking extension.
   * avogadro/src/extensions/CMakeLists.txt: Do not compile Wiimote head
  tracking extension as default   

2008-03-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h: - pov-ray: fix lighting (add 2nd light, emulate
  lights at infinity even though pov-ray is too stupid to understand that
  notion, fix light position when cam moves, fix material properties) -
  #include "config.h" as suggested by Donald   

2008-03-11  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/povpainter.cpp: - fix bug #1911509 : missing bg color in
  povray export - #include<config.h> gave me headaches because another config.h
  file was getting included! I fixed that in glwidget.cpp which was enough for
  me, but potentially all the other #include<config.h> could give that problem.
  Not sure what the standard practice is. We have many include paths defined
  including OB's so it's not surprising that #include<config.h> can fail!   

2008-03-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/colorbutton.h,
  libavogadro/src/periodictableview.h: * libavogadro/src/colorbutton.h: Added
  A_EXPORT.  * libavogadro/src/periodictableview.h: Added A_EXPORT.   

2008-03-11  Jordan Mantha <jordan.mantha@gmail.com>

  * ChangeLog, doc/CMakeLists.txt: * fixed up doc CMakeLists.txt so that it
  detects docbook.{pdf,html} * added some install rule bits, but left them
  commented out for now as it's still a bit buggy  

2008-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/povpainter.cpp: *
  libavogadro/src/povpainter.cpp: Add } to camera {. Fixes #1911507   

2008-03-10  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/aboutdialog.cpp, avogadro/src/engineprimitiveswidget.h,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/dockingextension.h,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/propmodel.h: Krazy fixes  

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating KRAZY files.  

2008-03-10  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp, libavogadro/CMakeLists.txt,
  libavogadro/src/config.h.in, libavogadro/src/global.cpp,
  libavogadro/src/global.h, libavogadro/src/glwidget.cpp: With Marcus advising
  we updated the threading makeCurrent/doneCurrents in the GLWidget once again.
   It's getting better all the time.  

2008-03-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, i18n/avogadro_de.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts, libavogadro/src/CMakeLists.txt,
  libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/textrenderer.cpp: -update french translation -CMakeLists: now
  do cmake -DRELEASE_MODE=ON to enable "release mode": defines NDEBUG, and adds
  -O3 flag if using gcc. -textrenderer: change gamma factor from 0.5 to 0.75
  for more moderate effect -painters: pass vectors by const reference, not by
  value. Even if the implementation needs to make a copy, this should not
  influence the API. Hope I didn't introduce bugs. -painterengine.cpp: minor
  readibility improvement. Hope I got it right. -camera: fix warning with gcc
  4.3.   

2008-03-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version numbers.
  I'm not sure what the next release will be, but for now trunk is 0.6.9.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/sticksettingswidget.ui: Add settings for sticks,
  fixes PR#1909099.  

2008-03-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: *
  libavogadro/src/engines/orbital*.*: Add support for multiple orbitals/cubes. 
  * testfiles/ch3cl.cube.gz: Example file for multiple cubes.   

2008-03-09  Jordan Mantha <jordan.mantha@gmail.com>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui: Added support for nitrogens
  in backbone for ribbon engine rendering  

2008-03-09  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp: Patch from Jordan Mantha
  <jordan.mantha@gmail.com> fixes ribbon rendering - go right to the end of the
  protein backbone. Thanks for the patch Jordan.  

2008-03-08  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Reverted - locks up a lot...  

  * ChangeLog, libavogadro/src/glwidget.cpp: Added some read and write locks in
  the GLWidget. It should help but it may need to be finer grained... Should
  help to reduce race conditions in threads.  

  * ChangeLog, avogadro/src/main.cpp: Looks like some drivers have bad
  XInitThreads() functions, only enable for threaded GL builds.  

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Just return form the render function
  if the VdW thread is running, should fix the crashes observed.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Removed the doneCurrent() calls in
  the non-threaded GL code paths. These calls were breaking hits calls among
  other things.  

2008-03-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp, libavogadro/src/glwidget.cpp: Stepped through the
  rendering pipeline and makeCurrent / doneCurrent should now be in the correct
  spots.  

2008-03-07  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/main.cpp: Added extra GL initialisation debug
  output.  

2008-03-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp:
  Check that a window isn't moved off-screen on Mac or Windows (since we
  remember window positions on those platforms). PR#1903437. (saveFile) Add
  .cml extension to a filename if none is provided. PR#1817621.   

2008-03-06  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/eyecandy.cpp: Make the eye candy opaque.
  Still looks great in my opinion. This does get rid of potentially expensive
  blending operations in the quick render pipeline.  

  * ChangeLog, libavogadro/src/engine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: The engines now emit changed when their status is
  changed. Updated the GLWidget logic for invalidating its display lists and
  also added a new slot to do this.  

2008-03-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefieldextension.cpp: Change default force field
  to MMFF94, 500 iterations, steepest descent. (Good options, since typical
  structure is far from the minima.)  

2008-03-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h: *
  libavogadro/src/engines/forceengine.*: Render forces on atoms. Uses
  OBConformerData, needs latest OB SVN to work.   

2008-03-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Stop invalidating the cache on
  mouse release. I think we have all of the events that should invalidate the
  display cache covered now.  

2008-03-05  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/propextension.h, krazy/runkrazy.rb,
  libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/elementcolor.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/residuecolor.cpp, libavogadro/src/tool.cpp: Adding many fixes
  for Krazy issues  

2008-03-05  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * Doxyfile, Doxyfileext: Update documentation version numbers.  

2008-03-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp: Just draw GL_LINES.  

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Change cursor types
  depending upon the action being performed - better visual cues.  

2008-03-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Added a second light source to the
  GLWidget - improved surfaces.  

2008-03-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * doc/figures/screenshot1.png, doc/index.docbook, doc/pdf/index.pdf: A much
  improved handbook. This version shows how to do links and picutures  

  * doc/generate_handbook.sh, doc/handbook.html, doc/pdf/index.pdf: Now
  ./generate_handbook.sh is generating PDF in the 'pdf' subdir and HTML in the
  'html' subdir. As the html is generated in multiple files I will only add the
  PDF in SVN.  

2008-03-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp: Draw multiple bonds in
  the quick render function - no more flicking bonds.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Add back in some makeCurrent calls
  that really were necessary outside of the threaded GL #ifdefs. This fixes
  PR#1906403.  

2008-03-02  Carsten Niehaus <carsten.niehaus@gmail.com>

  * CMakeLists.txt, doc/CMakeLists.txt, doc/index.docbook: First version of the
  new handbook  

2008-03-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Added a renderQuick function to this
  engine. Selected atoms/bonds rendered as opaque objects using the selection
  colour. Multiple bonds are not displayed. No transparency used.  

  * ChangeLog, libavogadro/src/engine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/sphereengine.h, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp: API cleanup - remove the second unused argument
  from the quickRender function. Ported everything to use the new quickRender
  function.  

2008-02-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Correct a bug in the setSelected
  function which was causing it to toggle the selection rather than set it as
  the calling functions were expecting. Reverted the fix in mainwindow.cpp as
  setSelected now works as expected. The select molecule function in the select
  rotate tool also works as expected now.  

2008-02-29  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version numbers
  to 0.6  

  * avogadro/src/mainwindow.cpp, libavogadro/src/tools/selectrotatetool.cpp:
  Fix selection bugs: select all doesn't toggle (weird bug). Selecting molecule
  will now also select all connected bonds.  

2008-02-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Run as a single thread  

2008-02-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/extensions/forcefieldextension.cpp: Disable the
  constraints menu item for now.  

  * ChangeLog, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Fixed the integer based
  eval function to actually use the m_iso value set. Defaulted the orbital
  engine to not use interpolation but added a check box that will force
  interpolation if desired.  

  * ChangeLog, libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp: Added a new marching cubes
  function that does not use interpolation. This should significantly reduce
  the resources needed to calculated many surfaces. Ported surface engine to
  use the non-interpolated functions - should never interpolate values we
  calculate at the resolution we choose. The orbital engine should optionally
  use interpolation but I need to hunt down a bug in the non-interpolated
  functions that is affecting the orbital cubes.  

2008-02-29  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating the krazy files  

2008-02-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: Update the surface
  engine to use the new features of the GridData class - requires fresh
  OpenBabel SVN...  

2008-02-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Provide more visual cues by changing
  the mouse cursor.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed up some of the makeCurrent
  and doneCurrent calls - this seems to improve things a little here. My ATI
  driver still hates Avogadro though...  

2008-02-26  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Make VDWSurface a thread  

2008-02-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: Removed the set step size
  and associated functions.  

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Removed the set step size
  spinner and functions.  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Adapted the
  IsoGen class to use the global quality level to set the step size.  

  * libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added new virtual function - quality() so that
  IsoGen can use it.  

2008-02-21  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h, libavogadro/src/painterdevice.h:
  Tweaked include files a little so that IsoGen doesn't include the whole of
  GLWidget. Fixed others.  

2008-02-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Small bug fixes  

2008-02-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: readSettings and writeSettings for
  SphereEngine  

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: readSettings and writeSettings for
  BSDYEngine  

  * libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringengine.h: readSettings and writeSettings for
  RingEngine  

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h: readSettings and writeSettings for
  HBondEngine  

  * libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: readSettings and writeSettings for
  WireEngine  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: readSettings and writeSettings for
  BondCentric tool.  

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  readSettings and writeSettings for AutoOpt tool.  

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Various
  bug fixes for draw tool (undo/redo) while adjust hydrogens is on. AutoOpt:
  drawText with some information when running  

2008-02-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Label Engine now saves settings.  

  * avogadro/src/mainwindow.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Updated Tools to read/write settings.  The
  tools will need to be updated to take advantage of this but the mechanism is
  there.  Please see drawtool.cpp/h for an example of how to implement this
  functionality.  

2008-02-19  Carsten Niehaus <carsten.niehaus@gmail.com>

  * testfiles/2-aminoethanol.cml, testfiles/2-thioethanol.cml,
  testfiles/2_2_2-trifluoroethanol.cml, testfiles/but-2-yne-1_4-diol.cml,
  testfiles/butane.cml, testfiles/ethane-1_2-diol.cml, testfiles/ethane.cml,
  testfiles/ethanol.cml, testfiles/methane.cml, testfiles/methanol.cml,
  testfiles/propan-1-ol.cml, testfiles/propan-2-ol.cml, testfiles/propane.cml,
  testfiles/thiophene.cml: sync  

2008-02-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h: Fixed auto-change of tools.  Tools are loaded
  during main window initialization.  Still delays showing the widget until
  later.  Removed some debugging code from the engine class and removed a
  function for setting primitives from a QList<Primitve *> which we don't need
  since PrimitiveList has a default constructor for QList<Primitive *>  

2008-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Added renderTransparent and
  renderQuick functions to ensure proper rendering of the surfaces. Also
  modified tbe criteria for surface invalidation and cleaned up other parts of
  the code.  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Several
  changes made to make the IsoGen class more general. It now gets the minimum
  and maximum points of the cube directly from the grid and then uses the step
  size more intelligently.  

2008-02-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Insert Smiles is now undo-able  

2008-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Tweaked the surface engine to use
  the standard functions to invalidate the surface. Still needs more tweaking I
  think.  

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Used Geoff's new colour
  widget in the configuration dialog. Added support for drawing both the
  positive and negative iso surfaces as well as ensuring the surfaces are only
  recalculated if the molecule was modified.  

2008-02-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/addenginedialog.cpp,
  avogadro/src/addenginedialog.h: * avogadro/src/addenginedialog.*: Set the
  default "name" when adding an engine to the engine type. (This saves some
  typing.)   

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp: Auto-addition of hydrogens. Should work
  cleanly. Try it out and report bugs. (There are probably still some corner
  cases.)   

2008-02-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  More progress to auto-add hydrogens. (Currently defaults to off -- still some
  weird bugs with interactive drawing.)   

2008-02-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalsettingswidget.ui: Modified the default value
  for the iso surface - still needs a little more work to show the orbitals
  correctly but the big stuff is now working.  

2008-02-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Fix PR#1849616
  with "flash of reorganizing tools".  

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: * libavogadro/src/tools/drawtool.*,
  libavogadro/src/tools/drawcommand.*: Indentation and comment cleanup in draw
  tool. Added initial support for adjusting hydrogens while drawing. Still
  needs interactive drawing changes for hydrogens, but changing elements,
  delete, etc. work.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Mac fixes --
  unified toolbar and saving window position.  

2008-02-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Add "Change Bond Order" to drawtool. Make
  this feature and "Change Element" undo-able.  

2008-02-16  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h, avogadro/src/mainwindow.cpp:
  DockWidget and Toolbar state are now saved in the settings.  

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui: Cleaned up the
  openFile and loadFile functions.  loadFile is now private. MainWindow now
  handles all opening of files.  Please check the updated main.cpp to see how
  this works.  This solves a problem where if you specified a file more than
  once on the command line you would get multiple windows with the same file. 
  Also, this makes opening files look nicer, one window pops up at a time.
  Unfortunatly this means we have to push events through.  MainWindow::show()
  simply does a ::setVisible and draws the preliminary outline of the window
  but doesn't do a "Polish" which means that the window looks like it's stuck
  loading.  I made loadFile private because I believe that openFile will
  eventually call loadFile but it also handles checking that the file is not
  already loaded in another window.  The other change I made is that I stopped
  read/write of settings for the window position.  In linux the window
  positioning should really be handled by the window manager.  The other reason
  is that because of our settings being saved we weren't getting any benefit. 
  If this needs to be implemented in mac (which I think mac can do it's own
  smart window placement) then we can add it back in for mac only.   Dimensions
  are still saved.  

2008-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Moved VDWSurface to IsoGen thread to
  make surface engine more interactive  

2008-02-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/skeletontree.cpp: *
  libavogadro/src/tools/skeletontree.cpp: Fix bug with bond-centric manipulate
  tool. Translations and rotations were not telling atoms that they were
  updated. Fixes PR#1854343.   

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: *
  libavogadro/src/colorbutton.*: New widget to show the current color and bring
  up a color picker when clicked.  *
  libavogadro/src/engines/surfacesettingswidget.ui: Use it.  *
  libavogadro/src/engines/surfaceengine.*: Ditto.   

2008-02-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/engineprimitiveswidget.cpp, avogadro/src/enginesetupwidget.cpp,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/engine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/manipulatetool.cpp: PrimitiveList now acts exactly as a
  QList<Primitive *> and with benefits.  This means you should always pass
  around a PrimitiveList and not a QList<Primitive *>.  I have updated all the
  function calls etc.  

  * avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h,
  avogadro/src/engineprimitiveswidget.ui,
  avogadro/src/extensions/selectextension.cpp,
  libavogadro/include/avogadro/periodictableview.h, libavogadro/src/glwidget.h,
  libavogadro/src/periodictableview.h: Added a button to set the engine
  primitives to the current selection.  

  * avogadro/src/avogadro.qrc, avogadro/src/engineprimitiveswidget.ui,
  avogadro/src/icons/copy.png, avogadro/src/icons/cut.png,
  avogadro/src/icons/paste.png, avogadro/src/icons/rebuild.png,
  avogadro/src/icons/selecttable.png, avogadro/src/icons/tab_new.png,
  avogadro/src/icons/tab_remove.png, avogadro/src/mainwindow.ui: Added some new
  icons, updated the mainwindow and added a new button for setting engine
  primitives to the selection.  

2008-02-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Fixed the orbitals engine
  to the point that it now compiles. Still not showing any actual molecular
  orbitals yet though...  

2008-02-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Added initial (broken compile)
  orbital engine for Marcus.  

2008-02-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Added m_surfaceValid boolean to hold
  the state (valid or not) of the surface. For large molecules, the
  VDWSurface() function should also be in a thread. Do we create a seperate
  thread for this?  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Make IsoGen run as a real thread  

2008-02-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfaceengine2.cpp,
  libavogadro/src/engines/surfaceengine2.h,
  libavogadro/src/engines/surfacesettingswidget.ui: Added settings widget for
  the surface engine  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Make sure the surface center is the
  same as the molecule center. Added espColor function to handle ESP surface
  coloring. The cut-off energy is still too rough, it should be more smouth... 

2008-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: I couldn't resist playing and so now
  we have a semi-transparent surface engine rendering in red right now using
  triangles... It is looking pretty good already. It still needs more work in
  order to get the colours right and make it more useful. The algorithm seems
  to be working quite well with small molecules at the very least.  

2008-02-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp:
  Removed lots of qDebug statements. Thanks lots to Tim for spotting the bug!  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: It compiles, but completely fails to
  find any triangles! Obviously more work is required and I can't spot where it
  is failing. Comparing it to the work done in surfaceengine2.* may help but I
  think it is close...  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: It
  compiles! Still need to verify it is doing useful things though...  

2008-02-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine2.cpp,
  libavogadro/src/engines/surfaceengine2.h: Surface engine, able to draw the
  dots of the surface. Still needs some work...  

2008-02-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Tweaked
  formatting to fit with ours, removed some application specific elements and
  tried to get it working in the Avogadro framework. More work still required
  as there are several application specific elements remaining before this
  class is self contained and able to generate isofurfaces.  

2008-02-05  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp: The "duplicate" button on the engine
  list now works properly.  It required adding a Engine::clone function that is
  purely virutal (there is no way around this).  Did some minor testing but
  seemed to work fine.   

2008-02-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Engine *clone const; instead of XXXEngine *clone const;  

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Added ::clone() functions  

2008-02-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: Added support for measuring the
  dihedral angle. Also made the tool update dynamically as the molecule is
  changed, optimised the label placement and ported it to use the OpenBabel
  functions to find the angles concerned.  

2008-02-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp: Fix a bug where the
  angle between bonds was miscalculated. Thanks to Albert DeFusco for reporting
  the bug and providing a test case.  

2008-01-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonizer.cpp,
  libavogadro/src/engines/polygonizer.h: Remove old polygonizer code (since
  we'll use the iso.cpp code instead.)  

2008-01-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessinputdata.cpp: Fixed bug with GAMESS dialog
  remaining present even after the main application window had closed.  Also
  fixed a problem with the generated GAMESS input file being incorrect.   

2008-01-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Importing
  iso.h and iso.cpp from the Zhu3D project (3.4.0). These can be adapted and
  used to provide surface support in Avogadro. These files are not yet modified
  for use in Avogadro and so are not currently compiled/linked to. They are
  thread safe and I think this algorithm is the best choice. I will make
  modifications to these files in the near future.  

2008-01-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h: Use OpenBabel::OBRotorKeys  

2007-12-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h: * libavogadro/src/tools/autoopt.[h,cpp]:
  Use new HasAnalyticalGradients() method from Open Babel SVN trunk.   

2007-12-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/camera.cpp, libavogadro/src/camera.h: Added a
  copy constructor.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed the race condition in the
  render quick code.  

2007-12-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: New function to
  render unit cell axes for crystal cells. Needs a config option to turn on and
  off display.  

2007-12-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  AutoOpt: removed conjugated gradients, added molecular dynamics  

2007-12-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Add in more bond granularity
  -- more steps, and a thin bond at the smallest size. Suggested by Andrew
  Dalke.  

  * ChangeLog, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: * libavogadro/src/tools/*.cpp:
  Add Navigate::zoom() to wheel operations for all tools.   

2007-12-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp: * libavogadro/src/color.[h, cpp]: New
  method setToSelectionColor to allow overloading and customization of the
  selection color in render engines.  * libavogadro/src/engines/*.cpp: Use it. 
   

2007-12-16  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: fix mousewheel action which hadn't got
  updated in the last round; and by the way make it much faster by always
  assuming that no atom is clicked (instead of performing an expensive gl
  selection) and instead using the m_referencePoint which is already quite
  precisely what the user sees. Also, fine-tune a constant in the
  m_referencePoint computation.   

2007-12-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Draw cylinders between backbone
  points when using quickRender.  

  * ChangeLog, libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringengine.h: Added support for colouring rings based
  upon the number of ring members.  

2007-12-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h: *
  libavogadro/src/tools/autoopttool.[h,cpp] Add support for OBPluginList to
  dynamically get list of force field types.  *
  avogadro/src/extensions/forcefieldextension*: As above.   

  * avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: Added OBPluginList support to
  add force fields to the menu. Now auto-discovers any force fields added to
  Open Babel.  

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Fix
  incomplete implementation of line stipple to be used for hydrogen-bonding.
  Now shows nice dashed lines for the hbond engine.  

2007-12-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/hbondsettingswidget.ui: Added HBond engine  

2007-12-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: the updating of
  the quicklist now occurs on mouseRelease, not on mousePress. The rational is
  that we want a very low latency on mousePress. With this change, on
  mousePress, we already have a quick-list ready for use. This further reduces
  latency when handling very large molecules. This prompted some deeped changes
  in GLWidget/GLWidgetPrivate, I hope they are OK, for instance pd is now in
  GLWidgetPrivate, I hope I got it right, as I didn't see any reason not to
  have it here (though it has to be constructed in GLWidget::constructor(), not
  in GLWidgetPrivate, because we need the this pointer of the GLWidget).   

  * libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: fix this bug: [ avogadro-Bugs-1849990
  ] movement shoud be relative to visible part of the molecule When no atom is
  clicked, the navigatetool is now moving relatively to a weighted barycenter
  of the atoms, where atoms have a higher weight when they are central in the
  view and a lower weight when they are outside the frustum. A decreasing
  exponential formula is used to compute the weights. This may sound intensive,
  but is only done once on mousePress, and turns out (according to some
  qDebugs) to be almost negligible and not the cause for the short lag occuring
  on mousePress with big molecules (tested with a mol with 7000 atoms). The
  complexity is linear.   

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/tools/navigatetool.h: fix the issue that I reported on the
  mailing list, about computeClickedAtom(). Will write an explanation on the
  list about that.   

2007-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/dockingextension.cpp,
  avogadro/src/extensions/selectextension.cpp: Spelling fixes with action
  names.  

2007-12-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Added angles and torsions to PropertiesModel, added Numerical/Analytical
  gradients option to AutoOpt  

2007-12-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Disabled drawing of labels when moving
  the view, i.e. in quickRender().  

2007-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: *
  libavogadro/src/glwidget.cpp (renderCrystal): Clean up main render() function
  with additional function to handle translations of crystal cells via display
  lists. Much cleaner code and should be faster on larger crystals.   

2007-12-13  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts, libavogadro/src/textrenderer.cpp: - improve text
  rendering: -- apply a gamma (0.5) correction to the rawbitmap to get rid of
  dim legs in "n" and "m" letters; this also makes all the text look a bit
  bolder, I hope you like it and agree it's more suitable for outlining --
  fine-tune the 7x7 outlining brush - improve french translation   

  * avogadro/src/extensions/dockingextension.cpp, i18n/avogadro_fr.ts: - update
  french translation, make it more complete (I used google/online chemistry
  dictionaries/wikipedia for some chemistry terms) - fix typos in
  dockingextension.cpp   

2007-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/icons/Aspirin.png,
  avogadro/src/icons/AvoDocument.png, avogadro/src/mac/AvogadroDocument.icns,
  avogadro/src/mac/MacOSXBundleInfo.plist.in: Updated Mac OS document icons.  

2007-12-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h: Removed the debug engine - moved to
  the GLWidget now.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added debug
  information to the GLWidget along with config options etc.  

2007-12-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: * libavogadro/src/glwidget.cpp: Add in
  display lists for renderQuick. Wraps all engines into one list for maximum
  speed.  * libavogadro/src/engines/wireengine.[h,cpp]: Skip display lists, as
  glWidget now handles this for us.   

2007-12-12  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engine.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp: Added more logic to implement renderQuick in
  the engines, GLPainter and the GLWidget. The renderQuick function.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Don't use dynamic scaling to
  render the axes - cylinders were reduced to lines before.  

  * ChangeLog, libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h:
  Added a dynamic scaling variable to the clas and a setter. This turns dynamic
  scaling on (default) and off.  

  * avogadro/src/CMakeLists.txt, i18n/avogadro_en_GB.ts,
  libavogadro/src/CMakeLists.txt: Added a British English translation (you know
  - the original one that uses all the extra letters).  

2007-12-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propmodel.cpp: *
  avogadro/src/extensions/propmodel.cpp,
  avogadro/src/extensions/propextension.cpp: Minor fixes to get compilation
  working again.   

2007-12-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/dockingextension.cpp,
  avogadro/src/extensions/liganddialog.cpp,
  avogadro/src/extensions/liganddialog.ui,
  avogadro/src/extensions/pocketdialog.cpp,
  avogadro/src/extensions/pocketdialog.ui,
  libavogadro/src/tools/autoopttool.cpp: *
  libavogadro/src/tools/autoopttool.[h,cpp]: Added "Ignored atoms are movable"
  and "Fixed atoms are movable". Small changes to ::redo() and ::undo(), undo
  still seems to work. I had to change it to makje sure the passed molecule
  pointer would not point to a molecule that would be deleted. This caused the
  constraints in the model to be lossed. (note: OB does not support angle and
  torsion constraints yet, ignoring atoms only works for MMFF94 at the moment.)
   * avogadro/src/extentions/constraintsmodel.[h,cpp]: now connects to
  primitiveRemoved signal from a Molecule to delete invalid constraints as you
  remove atoms.  * avogadro/src/extentions/constraintsdialog.[h,cpp]: You can
  now only add valid constraints.  *
  avogadro/src/extentions/forcefieldextension.cpp: Added "Ignore selected
  atoms" and "Fix selected atoms" + changes to make sure constraints are
  consistent for both the forcefield extension and the AutoOpt tool. Undo
  doesn't work for conformersearch yet, I'll probably fix this by moving the
  ConformerSearchDialog to the ForceFieldCommand itself.  *
  avogadro/src/extentions/liganddialog.[ui,h,cpp]: Dialog to create a ligand.
  (dockingextension)  * avogadro/src/extentions/pocketdialog.[ui,h,cpp]: Dialog
  to create a pocket. (dockingextension)  *
  avogadro/src/extentions/dockingextension.[h,cpp]: Avogadro class to handle
  docking.  * avogadro/src/extensions/propmodel.cpp: Small  change to the way
  rows are added and deleted.   

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/dockingextension.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/liganddialog.h,
  avogadro/src/extensions/pocketdialog.h,
  avogadro/src/extensions/propmodel.cpp, libavogadro/src/tools/autoopttool.h:
  see ChangeLog...  

2007-12-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: Initial wireframe optimization.  

2007-12-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Ported
  the renderAxesOverlay function to use the new renderCone function.  

  * ChangeLog, libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added a drawCone function to draw 3D cones that
  can be used for arrows etc.  

  * libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added new drawCone function to the painters.  

2007-12-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/selectextension.cpp,
  avogadro/src/extensions/selectextension.h: Added select by element, residue
  and solvent  

2007-12-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/include/avogadro/periodictableview.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: Moved the PeriodicTableGV from the
  tools directory to the library directory. Also renamed it to
  PeriodicTableView and added an include file in the includes directory. Some
  small enhancements to the layout too.  

2007-12-09  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, cmake/modules/FindOpenBabel2.cmake: Updated
  the CMake script to use OPENBABEL2_VERSION_MET keyword and fixed a bug I was
  having with a slow GLWidget when first starting up.  PR#1847479   

2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: setting the number of
  conformers to be generated is now connected  

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/conformersearchdialog.h,
  avogadro/src/extensions/conformersearchdialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp: Added Conformer Search dialog  

2007-12-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/glpainter.h,
  libavogadro/include/avogadro/sphere.h,
  libavogadro/include/avogadro/textrenderer.h: re-add four mini-headers that
  somehow were missing, making the compilation fail.   

2007-12-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/engines/labelengine.cpp: Use new element
  translation feature.  

  * ChangeLog, libavogadro/include/avogadro/elementtranslate.h,
  libavogadro/src/elementtranslate.cpp, libavogadro/src/elementtranslate.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/periodictablegv.cpp: *
  libavogadro/src/elementtranslate.[h,cpp]: New class to handle
  translation/i18n of element names.  * libavogadro/src/tools/drawtool.cpp: Use
  the new translation feature. Also add in custom elements (from Periodic Table
  widget) into an ordered list.  * libavogadro/src/tools/periodictablegv.cpp:
  Use the new translation feature.   

2007-12-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: Added a double click event to the
  periodic table - choose the element and close.  

2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h:
  Added PropertiesModel and PropertiesView to handle the represenwtation of
  properties in QTableViews  

2007-12-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt,
  scripts/distclean.sh: * scripts/distclean.sh: An enhanced "distclean" script
  for preparing source releases.  * avogadro/CMakeLists.txt,
  libavogadro/CMakeLists.txt: Bumped version number to 0.3.0b2.   

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: *
  libavogadro/src/tools/drawtool.cpp: Enhanced custom element support. Picking
  elements from the table will add a new entry and select it. Picking elements
  form the table *already* in the list will simply select that element again.  

2007-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h:
  Improved atom, bond cartesian editor + added conformer table, selecting an
  item in the table will also select the item in the 3D widget, or change the
  conformer.  

2007-12-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: More tweaking of the ElementDetail
  painting.  

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/periodictabledialog.ui,
  libavogadro/src/tools/periodictablegv.cpp: Removed the old perdiodic table
  dialog as it has now been replaced. Few tweaks to build files and stuff.  

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: After much work I think my super
  QGraphicsView based periodic table is ready for the world to see. It still
  has some rough edges that will need taking care of but it is already very
  functional and I think in many ways surpasses what we already have in place.
  Feel free to make suggestions or buy me beer ;-)  

2007-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h:
  Added Conformer dialog, still needs selection handling  

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h,
  libavogadro/src/tools/autoopttool.cpp: Added editable atom and bond
  properties tables + cartesian coordinates editor  

2007-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h: Added emitData()  

  * ChangeLog, avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  You can now fix the position for an atom :D more constraints comming soon... 

2007-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog, Doxyfile, Doxyfileext, INSTALL,
  avogadro/Doxyfile, avogadro/README, avogadro/src/CMakeLists.txt,
  avogadro/src/addenginedialog.cpp, avogadro/src/addenginedialog.h,
  avogadro/src/application.cpp, avogadro/src/editcommands.cpp,
  avogadro/src/editcommands.h, avogadro/src/elementcombobox.h,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.cpp,
  avogadro/src/enginelistview.h, avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/selectextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/flattabwidget.cpp, avogadro/src/flattabwidget.h,
  avogadro/src/flowlayout.cpp, avogadro/src/icontabwidget.cpp,
  avogadro/src/icontabwidget.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/primitivetreeview.cpp, avogadro/src/primitivetreeview.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  cmake/modules/COPYING-CMAKE-SCRIPTS, cmake/modules/FindAvogadro.cmake,
  cmake/modules/FindLinguist.cmake, gpltemplate,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/elementcolor.cpp,
  libavogadro/src/elementcolor.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/polygonizer.cpp,
  libavogadro/src/engines/polygonizer.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/global.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/glpicker.cpp.disabled,
  libavogadro/src/glpicker.h.disabled, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp.disabled,
  libavogadro/src/moleculetreeview.h.disabled, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/residuecolor.cpp,
  libavogadro/src/residuecolor.h, libavogadro/src/sphere.cpp,
  libavogadro/src/sphere.h, libavogadro/src/textrenderer.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/quaternion.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/undosequence.cpp,
  libavogadro/src/undosequence.h: Removed trailing white space as discussed on
  the mailing list.  

2007-12-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/application.h, avogadro/src/editcommands.h,
  avogadro/src/elementcombobox.h, avogadro/src/engineitemmodel.cpp,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.h,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/extension.h,
  avogadro/src/extensions/forcefieldextension.h, avogadro/src/mainwindow.cpp,
  libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/elementcolor.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/global.cpp, libavogadro/src/global.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/painterengine.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/primitiveitemmodel.h, libavogadro/src/primitivelist.cpp,
  libavogadro/src/primitivelist.h, libavogadro/src/residuecolor.cpp,
  libavogadro/src/sphere.h, libavogadro/src/textrenderer.cpp,
  libavogadro/src/textrenderer.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/undosequence.cpp: *
  libavogadro/*, avogadro/*: Update headers using script based on
  fixkdeincludes. Removes a *huge* pile of un-needed #include statments in both
  *.h and *.cpp files. Should improve compilation time.   

2007-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/forcefieldextension.cpp: Small fix to fix compilation
  - include the .moc file.  

2007-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: Added constraints dialog  

2007-12-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/tools/bondcentrictool.h: use const& QString and explicit
  ctors if possible 

2007-12-03  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: updated the Krazy files. 

2007-12-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.cpp.disabled,
  libavogadro/src/moleculetreeview.h,
  libavogadro/src/moleculetreeview.h.disabled: Disabled moleculetreeview --
  unused, deprecated. Use primitiveitemmodel.cpp and others.  

2007-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp: Added IsSetupNeeded to
  AutoOpt to increase performance  

2007-12-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h: More
  documentation improvements. Also moved some empty function implementations in
  POVPainter to the header to make it clearer that they do not do anything.  

  * ChangeLog, libavogadro/src/glpainter.h: Improvements to the GLPainter
  documentation.  

  * ChangeLog, libavogadro/src/glwidget.h: Updated the documentation of the
  GLWidget and GLHits classes.  

2007-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: Added progress bar to
  Systematic Rotor Search  

2007-12-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/debugengine.cpp: Small fix to use the
  painter.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Moved the axes
  engine into the GLWidget where it belongs. Added a global configuration
  option for it.  

2007-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engine.h: Fixed up the documentation a little. 

  * ChangeLog, libavogadro/src/color.h: Fixed up the documentation a little. 

  * ChangeLog, libavogadro/src/camera.h: Fixed up the documentation a little. 

  * ChangeLog, avogadro/src/mainwindow.h: Fix the API documentation title. 

2007-11-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp: *
  libavogadro/src/tools/autoopttool.cpp: Remove "OBPatched" ifdefs. These are
  now all supported in OB-2.2.   

2007-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringsettingswidget.ui: Made the ring engine default
  to being opaque... 

2007-11-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/elementcolor.cpp, libavogadro/src/elementcolor.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/painterdevice.h,
  libavogadro/src/povpainter.h: Initial color map support, including default
  base class (i.e., color by element)  

2007-11-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: smiles to 3D added to DrawTool  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Added widgets for OBBuilder class, see
  Changelog for details  

  * ChangeLog, avogadro/src/extensions/forcefieldextension.cpp: Corrected
  important typo: MMF94 -> MMFF94 (ffID)  

2007-11-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui: Removed the opacity slider
  for now. Also added in a new display type - lines. Renders cylinders between
  points and spheres at each point. 

  * ChangeLog, libavogadro/src/engines/wireengine.cpp: Optimised the bond
  drawing, only use multiLines when the bond order is greater than one.  

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h: Added my name
  to the copyright headers.  

2007-11-27  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Changed unified
  toolbar (on Mac) to use Designer flag.  

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h: Fix a few names to be more
  readable. (Should also improve translation?)  

  * Doxyfile, Doxyfileext: Update for 0.3.0b2 version number.  

2007-11-27  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/addenginedialog.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp: engine.h:  New macros AVOGADRO_ENGINE and
  AVOGADRO_ENGINE_FACTORY can help people with their engine headers so they
  don't have to include redundant functions.  These are things we can generate
  automatically at the moment.  Updated all the engines.  Properly fixed the
  addenginedialog.cpp hack.   

2007-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.h: Added new
  drawTriangle function that takes a normal as the fourth argument. Calculate a
  normal and use it for the whole ring - improved lighting with no artifacts in
  each ring, still issues around turning points. 

  * ChangeLog, libavogadro/src/engines/ringengine.cpp: Add back in
  optimisations for the ring engine. 

2007-11-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/addenginedialog.cpp, avogadro/src/addenginedialog.ui,
  avogadro/src/settingsdialog.ui: User Interface fixes.  

2007-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.cpp: Fixed the case of the back transformed
  axis functions and ported the existing code. 

2007-11-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h,
  avogadro/src/engineprimitiveswidget.ui, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui: Separated the Engine
  Configuration dialog into two separate dialogs.  The titles need some
  changing and/or they need to become icons.  This is what we should actually
  do.  Unfortunatly I believe this is deeply embeded in the MainWindow widget
  and far be it for me to want to dig into it.   

2007-11-25  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/extensions/gamessinputdata.cpp,
  krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/runkrazy.rb, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h: * Updated the krazy results and fix two of the
  issues  

2007-11-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/selectextension.cpp,
  avogadro/src/extensions/selectextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h, avogadro/src/mainwindow.cpp: *
  avogadro/src/extensions/selectextension.cpp: Renamed extension for SMARTS
  selection. Added support for new options, such as invert selection. (More to
  come later, e.g., atom selection by name, residue by name, etc.)   

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Some test code for surfaces.  

2007-11-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h, libavogadro/src/glpainter.cpp: More
  tweaks to the drawTriangle function. Added a new polygon engine. Render
  certain structures as polygons. 

2007-11-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/glpainter.cpp: * libavogadro/src/glpainter.cpp:
  Refinement of multiple bonds in wireframe view.   

  * ChangeLog, libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h,
  libavogadro/src/engines/wiresettingswidget.ui, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: * libavogadro/src/painter.h,
  libavogadro/src/glpainter.h, libavogadro/src/povpainter.h,
  libavogadro/src/glpainter.cpp: Add drawMultiLine method for wireframe
  multiple bonds.  * libavogadro/src/engines/wireengine.h,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wiresettingswidget.ui: Add multiple bond indications
  for wireframe render engine. (Still needs some refinement, particularly
  triple bonds.)   

2007-11-17  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/engines/ringsettingswidget.ui,
  libavogadro/src/engines/spheresettingswidget.ui: Added spacers to the engine
  configuration dialogs. 

2007-11-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui: Revised menu structure, adding "Build" and
  "Select" menus. Changed extensions to build menu paths by catenation of
  strings. This facilitates translation.  

2007-11-17  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui: Added check box to show higher
  order bonds or not. 

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/glpainter.cpp: Added a new OpenGL material that should work
  better with the ring engine. 

2007-11-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/engines/wiresettingswidget.ui: Added new settings for the
  wireframe engine -- turn off the dots for atoms. Provides a really nice view
  for proteins.  

  * testfiles/Fe.sdf, testfiles/icsd_83086.cif, testfiles/icsd_83086.res,
  testfiles/tpy-Ru.sdf: Added a few test files for a polygon engine.  

2007-11-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version number
  for 2007-11-14 snapshot.  

2007-11-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.h: Fixed a small bug in
  the drawTriangle function. 

2007-11-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/untitled01.gpr, testfiles/benzene-homo.cube.gz,
  testfiles/ch3cl-density.cub.gz, testfiles/ch3cl-esp.cub.gz,
  testfiles/untitled01.gpr: Added some test files, including cube/surface
  tests.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonizer.cpp,
  libavogadro/src/engines/polygonizer.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: First pass at a surface engine,
  using OB-2.2 SVN trunk. Definitely needs some work, but it does compile and
  show some surfaces.  

2007-11-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringengine.h: Correct file headers.  

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/ringsettingswidget.ui: Added opactiy slider,
  transparency now working.  

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h:
  Added new ring engine, renders ring structures. Transparency is not working
  yet.  

2007-11-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Updated the ribbon engine so that we
  now have multiple chain colours! 

2007-11-12  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp: And the glpainter...  

  * libavogadro/src/glpainter.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/painter.h, libavogadro/src/painterdevice.h: Exposed the
  loaded Molecule to the PainterDevice. Added the drawTriangle function.  

2007-11-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts, libavogadro/src/glwidget.cpp:
  Missing tr() in glwidget to set the default engine.  This will be obsolete
  soon as we can save settings.  Fixed some translations.    

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: reverted some of Benoits original
  french translations that somehow got lost in the transfer 

  * avogadro/src/aboutdialog.cpp, avogadro/src/engineitemmodel.cpp,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/flattabwidget.cpp, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/sphere.cpp,
  libavogadro/src/textrenderer.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/quaternion.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/skeletontree.cpp: Big i18n fix.  Class implementations
  (.cpp) need to be surrounded by namespace Avogadro {} if the class is defined
  in that namespace.  Causes inconsistencies between linguist and lupdate   

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp, libavogadro/src/tool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: tool.h: the Tool class now has a
  signal for emitting messages.  main.cpp: fixed some translation loading
  issues. (MORE TO COME).  mainwindow.cpp: tools that emit messages now get
  sent to the message box.  clickmeasuretool.*: now emit distances and angles. 
  fixes PR #1807092   

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts, libavogadro/src/glpainter.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Updated translation files.  libavogadro/src/tools/eyecandy.*: Added some
  functions to allow specifying your own parameters for eyecandy.  Can still
  pass a pointer to an atom and have the parameters specified for you.  Added
  eyecandy for zooming.  libavogadro/src/tools/manipulatetool.*: Added eyecandy
  to manipulate tool. This resolves PR #1823559. 
  libavogadro/src/tools/navigatetool.cpp: Optimized some code that was repeated
  in all if/else statements.  libavogadro/src/glpainter.cpp: Removed unused
  variable.   

2007-11-10  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp
  (copy, exportGraphics): Embed MDL molfile and SMILES data in exported
  graphics. Should allow PNG files to be read back in via Open Babel 2.2.   

2007-11-06  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp: More tuning has really improved
  the render speed - thanks to Thomas Margraf for providing an example which
  inspired what I did here. 

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/glpainter.cpp: Added ability to set the ribbon radius, also
  tried to add transparency but that is not working for me here. Added some
  extra calculations to the drawSpline function so the tube should not be
  flattened and has a defined radius. 

2007-11-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/glpainter.cpp: Now filled with NURBS goodness. Still needs
  quite a bit of tuning and testing but visually improved. 

2007-11-05  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: General force field extension,
  allowing UFF and MMFF94. We still need to use OBPlugin to get a list of the
  active forcefields, rather than a hard-coded list.  

2007-11-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/navigatetool.cpp: Improvements in the eye-candy: - move
  the zoom-eyecandy from navigatetool.cpp to eyecandy.cpp, and let it honor the
  MINIMUM_APPARENT_SIZE constant - don't draw anything for the
  zoom-to-molecule-center as I can't think of any useful visual cue in that
  case. zoom-to-atom remains a sphere, but with minimum size scaled by a factor
  of 0.3 - reduce the value of the MINIMUM_APPARENT_SIZE constant. - introduce
  m_color member in Eyecandy to centralize the color.  This should close Bug
  #1825419   

2007-11-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Reimplemented the setPrimitives
  function due to changes in molecule loading. 

  * ChangeLog, libavogadro/src/glwidget.cpp: Updated the setMolecule function
  to call setPrimitives for each engine at the end of molecule loading, should
  make our molecule loading more efficient. 

  * ChangeLog, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Also added partial charge
  labelling for atoms, feature request 1824337.  

  * ChangeLog, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Updated the label engineto
  label atoms by residue name and number and bonds by their order. Feature
  request 1820686 and 1824338.  

2007-10-31  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Improvements to the ribbon code so
  that it caches the chain and updates it if the molecule is changed. 

2007-10-31  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h: ToolGroup now
  supports changing tool by name. When changing groups, the buttons should now
  enable/disable properly.  

2007-10-29  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi, scripts/avogadro.nsi: Moved avogadro.nsi script to the
  scripts directory. 

  * avogadro.nsi, scripts/cmake-vs2005.bat: Added cmake bat file for easier
  generation in Windows Updated Windows installer Script 

2007-10-27  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: updated translations 

2007-10-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp: Improve the ribbon
  engine to render multiple chains correctly and not crash when there is no
  chain. 

2007-10-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/1CRN.pdb, testfiles/1CRN.pdb: moved test file to the 'testfiles'
  directory 

2007-10-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/unitcellextension.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/CMakeLists.txt, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Updates to translate more
  strings. Also fix version numbers of libavo and avo.  

2007-10-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ribbonengine.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added what I have for the ribbon drawing so
  far. I have added a function to draw a cubic spline through a set of control
  points. The ribbon engine uses this with the CA atoms to draw secondary
  structure. This is still far from perfect and I am working on it. Feedback is
  welcome.  

2007-10-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added stretch to layout, improves
  look.  

  * libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added labels for tool options,
  and translation support.  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autoopttool.ui, libavogadro/src/tools/drawtool.cpp:
  Updated auto-optimization tool. Removed Designer interface (using code makes
  it look better on Mac) and eliminated less-used options.  

2007-10-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp: Updated to use
  renderOpaque() and to draw cylinders between the CA atoms. The next step is
  to draw a smoothed curve between the points but the current code picks out
  the CA atoms of a molecule and connects the dots... Still disabled.  

2007-10-13  Carsten Niehaus <carsten.niehaus@gmail.com>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: regenerate after my fixuifiles
  script 

  * avogadro/src/enginesetupwidget.ui,
  libavogadro/src/engines/bsdysettingswidget.ui,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/engines/spheresettingswidget.ui: Using KDEs "fixuifiles" so
  that the "Form" string no longer appears in the .ts-files!  find . -name *.ui
  | xargs ~/svn/kdesdk/scripts/fixuifiles  

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: * Updating the .ts-files after my
  string-changes. Also adding some * translation for testing  

  * avogadro/src/extensions/smartsextension.cpp, avogadro/src/mainwindow.cpp: *
  Fixing a couple of i18n issues  

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp: adding a couple of comments for
  translators 

2007-10-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  scripts/release_translations.sh, scripts/update_ts_files.sh: No longer need
  the translation scripts.  To update translations do 'make
  update-translations' 

  * cmake/modules/FindLinguist.cmake, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  libavogadro/include/avogadro/library.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/tools/bondcentrictool.cpp: Update French Translations and
  cleaned some bad uses of tr() 

  * avogadro/src/aboutdialog.cpp, avogadro/src/main.cpp,
  libavogadro/CMakeLists.txt, libavogadro/src/global.cpp,
  libavogadro/src/global.h: Added translation information and put the library
  functions (for version / svnrevision) in a file and put a function for the
  Library that does a ::createTranslator() 

2007-10-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, avogadro/CMakeLists.txt, avogadro/i18n/CMakeLists.txt,
  avogadro/i18n/avogadro_de.ts, avogadro/i18n/avogadro_fr.ts,
  avogadro/src/CMakeLists.txt, avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/gamessextension.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  libavogadro/CMakeLists.txt, libavogadro/i18n/CMakeLists.txt,
  libavogadro/i18n/libavogadro_de.ts, libavogadro/i18n/libavogadro_fr.ts,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/drawtool.cpp: Updated Translation Stuff (common
  directory) and fixed up the CMakeLists to auto-generate the translation files
  (.qm) 

  * avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: Attempt to fix the non-hiding
  geometric optimization dialog.  It works much better.  It's something to do
  with the way signals are getting passed to the thread and dialog. 

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/glwidget.cpp: made a branch for
  the splash screen and disabled it.  for normal loading there is hardly any
  load time so the splash screen doesn't really do anything.  in the future
  this may be worth loading up depending on how costly plugin loading is (or
  startup time for that matter). 

  * avogadro/src/application.cpp,
  avogadro/src/extensions/ghemicalextension.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added delayed initialization so that
  the mainwindow constructor creates all the objects but doesn't do any loading
  of plugins until the GUI is already up and running.  Once I did this, I
  realized it might be cool to have a splash screen because we do load a
  relatively large ammount of plugins and stuff.  Anyways, this is the result.
  We can revert it if it's too gaudy (too much). 

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: Fix for PR
  #1805401  We weren't properly setting background color.  Needed a call to
  qglClearColor before calling the renderGL function. 

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Only ever copy to the
  clipboard.  In Linux we don't currently copy to the selection buffer. 
  However, this should change in the future.  Fixed a bug where trying to undo
  the copy / cut commands was trying to restore the clipboard contents but this
  ends up causing crashes because the data gets deleted.   

2007-10-05  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.cpp: Fixed a bug that caused avo to
  crash when you switched to our tool, did nothing then switched to another
  tool.  Also threaded the Geometry Optimisation in the AutoOpt tool  

2007-10-05  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added some documentation and fixed a
  few cases during dihedral manipulation where mishapen or small rectangles
  were drawn.  

2007-10-04  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added the ability to draw obtuse
  angle-sectors (defaults to acute)  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Improved the math for calculating
  the rotation of bond angles and dihedral angles.  Interaction should be a lot
  smoother in the case where the bond being modified is almost perpindicular to
  the screen.  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Initial implementation of dihedral
  angle manipulation.  Still a little buggy and a few special cases that it
  doesn't work on but the basic concept is there.  

2007-10-04  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  The current status of AutoOpt tool, has #define that can be uncommented if
  you have a patched version of OpenBabel  

2007-10-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.ui,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Cleanups for Mac mouse buttons. Fixes
  PR#1720875.  

2007-10-03  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Fixed a bug with undo in the bond
  centric tool. Added the ability to view the dihedral/torsional angles of a
  given atom in relation to the selected bond by clicking on it.  This is in
  preparation for dihedral angle editing.  

2007-10-02  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Some documentation and improved undo
  functionality.  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added a new procedure that checks if
  two atoms are bonded together in preparation for Dihedral angle manipulation.
   

2007-10-02  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Removed toolgroup signal hack  

2007-10-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/selectrotatetool.cpp: Re-added selectrotatetool to the
  CMakeLists.txt and fixed a selection bug. 

2007-10-02  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Changed it back as the thread was not working properly in linux  

2007-10-01  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Added a thread class to the autoopt tool for running the optimizer in  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autoopttool.png, libavogadro/src/tools/autoopttool.qrc,
  libavogadro/src/tools/autoopttool.ui: My research project for my Honors, an
  interactive Automatic Optimisation tool  

2007-09-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi, libavogadro/src/global.h, libavogadro/src/povpainter.h,
  libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/tools/bondcentrictool.cpp: Windows compile fixes.  Needed
  exports to library functions. 

2007-09-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/gamessextension.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/periodictabledialog.cpp: Mac interface fixes, including
  for PR#1723768 -- quit now prompts for save and closes each window.  

2007-09-19  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/CMakeLists.txt, avogadro/i18n/CMakeLists.txt,
  libavogadro/i18n/CMakeLists.txt: Hey, now the .qm files even install in the
  correct directory ($PREFIX/i18n/)  

2007-09-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/i18n/avogadro_de.ts, avogadro/i18n/avogadro_fr.ts,
  libavogadro/i18n/libavogadro_de.ts, libavogadro/i18n/libavogadro_fr.ts: I
  hope this was correct. I ran lupdate on the files and started a basic
  translation. 

2007-09-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/avogadro.pro, avogadro/i18n/avogadro_de.ts,
  avogadro/i18n/avogadro_fr.ts, avogadro/src/elementcombobox.cpp.disabled,
  avogadro/src/main.cpp, libavogadro/i18n/libavogadro_de.ts,
  libavogadro/i18n/libavogadro_fr.ts, testfiles/acid_chlorides.smi,
  testfiles/amines.smi: Added french and german (de?) translations to avogadro.
   To add a new translation, find out the code (fr) and then do  touch
  libavogadro/i18n/libavogadro_(code).ts touch avogadro/i18n/avogadro_(code).ts
   I know i know.  It's somewhat a pain to think of libavogadro and avogadro as
  separate but I reallly prefer them this way so we save having to split up
  translations later.  Please start doing some translations and i'll figure out
  how the hell to incorporate them.   

2007-09-17  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/CMakeLists.txt, avogadro/src/elementcombobox.cpp,
  avogadro/src/elementcombobox.cpp.disabled, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glpicker.cpp, libavogadro/src/glpicker.cpp.disabled,
  libavogadro/src/glpicker.h, libavogadro/src/glpicker.h.disabled: Make use of
  GLOB in CMakeLists whenever applicable, e.g.: FILE(GLOB libavogadro_SRCS
  "*.cpp") I browsed our CMakeLists to see which files should be excluded, and
  found glpicker.* and elementcombobox.cpp. So I appended ".disabled" to their
  filenames, so that they don't get globbed.   

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: make the translation-eyecandy share the
  same infrastructure as the rotation-eyecandy, which uniformizes looks, and
  move all that in a separate eyecandy.{h,cpp} file.   

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: tweaking and cleanup in the rotation
  eyecandy   

  * libavogadro/src/cylinder.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Big improvements in the eyecandy in
  navigatetool: -- move rotation-eyecandy code to a separate class (now we
  should go on and do the same for translation-eyecandy) -- now also do
  eyecandy for mol-based movement (not only atom-based movement) -- improve how
  sizes are computed, so that the eyecandy is visible from far away in big
  molecules -- take away redundant code between front-face and back-face
  drawing, using glCullFace() -- fix bugs in comments where front-face and
  back-face were mixed up -- fix rendering bug caused by that mixing up   

2007-09-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/textrenderer.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Fixed PR#1796030  Also some other
  minor bug fixes introduced when allowing GL Names of 0. 

2007-09-16  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Fix for PR#1788659 
  Open file and save file dialogs now remember last directory.   

  * libavogadro/CMakeLists.txt, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp: Updated GLPainter and GLWidget so that
  when doing pushName / popName / setName, 0 is an acceptable value for a name.
   ie. no longer offset bonds.  drawtool.cpp: as per PR#1717871 the draw tool
  now deletes bonds  glwidget.cpp: added define to enable threaded OpenGL
  widget.  Disabled by default so we can get a release out.  It's some bug
  caused by XCB on my system. If you want to compile with a thread-enabled
  GLWidget do 'cmake -DENABLE_THREADED_GL ..' that should do it.  patch for
  PR#1760151    

2007-09-06  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html, krazy/runkrazy.rb: I am
  now using Krazy2. Updated the html files 

2007-09-06  Benoit Jacob <jacob.benoit.1@gmail.com>

  * CMakeLists.txt, avogadro/src/main.cpp, cmake/svn.h.cmake: fix the svn
  revision thingy -- don't install svn.h, instead store it in the CMake
  builddir, and add that dir to the list include dirs. make avogadro output it
  (example of usage. feel free to remove)   

  * CMakeLists.txt, cmake/svn.h.cmake: Let CMake produce a special header file
  definining a string SVN_REVISION_STRING. The header is installed at
  $CMAKE_INSTALL_PREFIX/include/avogadro/svn.h This allows applications using
  libavogadro to be aware of which revision they are using.   

2007-08-28  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.h, libavogadro/src/tools/navigate.cpp: remove two
  useless includes, add a copyright line for myself   

2007-08-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdata.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Updated GLWidget to include the ::current()
  function which returns the current GLWidget.  This isn't the best solution
  but it's required for extensions to get the current GLWidget.  Also fixed up
  all the GAMESS EFP stuff so that it works correctly.   

2007-08-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h: Some small updates to the POVPainter. Added
  drawLine and drawSpline to the Painters, but spline is commented out as it
  still requires more work. Started some very early work on the ribbon view but
  it is far from working right now. Depends on implementing a spline function
  to draw B-splines.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed regression with bond
  picking.  

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Added the computeClickedPrimitive/Atom/Bond functions to the GLWidget class
  as these functions have been used in several tools and are quite generic.
  Ported the tools to use the new computeClicked* functions and removed the
  local ones.  

2007-08-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h, libavogadro/src/tools/navigate.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Added a new navigation class with
  static member functions to perform the navigation functions common to three
  tools right now. Ported the tools to use the new Navigate class and removed
  all duplicated code.  

2007-08-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp: Added the display of
  the angle sector under consideration with the current selection of atoms.  

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp: Added units to the
  output.  

2007-08-16  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/action.cpp,
  avogadro/src/action.h, avogadro/src/extension.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h, avogadro/src/mainwindow.cpp:
  Removed action.cpp/h all together and replaced with ::menuPath(QAction
  *action) in the Extension class 

2007-08-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h, avogadro/src/main.cpp: Progress on
  the EFP dialog.  Saves the previous selection and interactivley displays the
  current group in the dialog.  Still modal but I believe that works the best. 
  It's a complicated process and might get more complicated with multiple
  dialogs being open.  Plus if the molecule is modified the EFP group
  information becomes invalid. 

  * avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h: More EFP Additions.  Still more
  needed.   

  * ChangeLog, avogadro/src/editcommands.cpp,
  avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Refactored
  clearSelection -> clearSelected (needs to be clearSelectedPrimitives
  eventually but it seems wordy.  I prefer wordy and clear over short and
  unclear.  Added some more EFP mechanisms to the GAMESS plugin but it needs
  some more work.   

2007-08-13  Shahzad Ali <saky.org@gmail.com>

  * libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/skeletontree.h: Comments added - Documentation 

2007-08-11  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: I updated Krazy to the
  latest generation of checks. Several issues have now been found 

2007-08-10  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitivelist.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autorotate.png,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.qrc,
  libavogadro/src/tools/clickmeasuretool.qrc, libavogadro/src/tools/draw.qrc,
  libavogadro/src/tools/drawtool.qrc, libavogadro/src/tools/manipulate.qrc,
  libavogadro/src/tools/manipulatetool.qrc, libavogadro/src/tools/measure.qrc,
  libavogadro/src/tools/navigate.qrc, libavogadro/src/tools/navigatetool.qrc,
  libavogadro/src/tools/select.qrc, libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.qrc: Minor file renaming to match
  correctly, might still need some work.  Also changed the auto-rotate icon
  which could also use some work.   

2007-08-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/navigatetool.cpp: Added visual
  representation of atom centred translation. Needs extra features adding to
  the painter and porting. Also need to add something for zoom/tilt.  

2007-08-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h: Added
  multiCylinder support thanks to help from Benoit with the maths. Also tweaked
  the default material parameters in order to improve the look of default
  renders. Still need to improve the translation from OpenGL to POV-Ray coords.
   

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Add visual representation of atom
  centred molecule rotation. Open up modifiers to all - we always planned to
  add this for all architectures. Alt seems to be taken in KDE for Window
  movement though - possibly need an alternate.  

2007-08-07  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/quaternion.h, libavogadro/src/tools/skeletontree.h:
  Added comments to various functions that I wrote. 

2007-08-07  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentric.png,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/bondcentrictool.qrc,
  libavogadro/src/tools/quaternion.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h:
  Added the bondcentric tool.  Added a few procedures needed by this tool to
  the painters, and a new signal to the widget that signals when the molecule
  is changed.   

2007-08-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h:
  * libavogadro/src/glwidget.cpp: GLWidget is not initialized until it is
  actually called to render.  This hopefully fixes a race condition that
  existed somewhere with makeCurrent().  Not sure why this was happening but I
  believe it had something to do with the fact that we were calling ->run()
  within the constructor and we don't know what magic TT is doing behind the
  scenes.  * libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitiveitemmodel.cpp: there was an issue with the engine
  views when deleting certain atoms which has been fixed.  Basically the model
  needs to notify the view that it's just taking from the end of the list but
  has reordered the contents (just the way we happen to change things in the
  engines).     

2007-08-05  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Reran Krazy. Still no
  issues. Great 

2007-07-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/action.cpp,
  avogadro/src/action.h, avogadro/src/extension.h,
  avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h, avogadro/src/mainwindow.cpp,
  libavogadro/src/primitivelist.h: Made Avogadro::Action so that each action
  also has a menuPath where it should go.  It will also help later, i think we
  can emit signals easier.   

2007-07-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/camera.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/textrenderer.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/navigatetool.cpp: resolved PR 1759321 and 1742953  see
  bug reports for more information and future updates.   

  * libavogadro/src/camera.cpp, libavogadro/src/engines/bsdyengine.cpp:
  camera.cpp: Fixed PR #1759321 bsdyengine.cpp: removed extraneous sorting
  calls (previously inserted to help with transparency)    

2007-07-21  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html, krazy/runkrazy.rb: Now
  Krazy is run with --exclude qclasses,license,copyright. This means those
  three scripts are not used which leads to a --tara-- error-free Avogadro! 

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Updating the HTML files
  after I fixed most issues found by Krazy 

  * avogadro/src/flowlayout.cpp, avogadro/src/mainwindow.cpp: Krazy-fixes:  Fix
  include order and "" → <>  

  * avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.h,
  avogadro/src/enginesetupwidget.h, avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/flattabwidget.cpp, avogadro/src/flattabwidget.h,
  avogadro/src/flowlayout.h, avogadro/src/primitivetreeview.h: Krazy fixes: -
  Many explicit ctors - One more const QString& instead of QString in the API  

  * avogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt:
  Do not use TRUE in CMake, use true. The TRUE/FALSE macros are obsolete since
  CMake 2.4.2 or something like that. 

  * libavogadro/src/CMakeLists.txt, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/toolgroup.cpp: Krazy fixes
  for libavogadro/src/*:  - Make two ctors explicit - Use #include <config.h>
  and not "config.h" - Marcus forgot a const QString&   (was just a QString) 
  Question:  ../libavogadro/src/painterengine.h: line#38 (1)
  ../libavogadro/src/painter.h: line#39 (1)  Those two clases are derived from
  QObject but are missing the Q_OBJECT macro... Is there a reason for that? If
  not I will add the macro.   

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Updating the Krazy files
  after installing the latest Krazy-version. Also, this is against the latest
  svn trunk 

2007-07-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/elementcombobox.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/include/avogadro/povpainter.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/painterdevice.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/painterengine.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/tool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: MERGE OF MULTITHREADED_OPENGL
  BRANCH INTO TRUNK.  svn merge -r 535:572  *** do not work on
  multithreaded_opengl any longer ***   

2007-06-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: *
  libavogadro/src/tools/drawtool.cpp (DrawTool::mousePress): Fix bugs with
  "alchemy" mode -- clicking on an atom to change the element. PR#1741653 and
  PR#1720879.   

  * ChangeLog, avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp: * avogadro/src/editcommands.[h,cpp]: Support for
  selecting new atoms when pasting. Fixes PR#1739837.  *
  avogadro/src/mainwidnow.cpp: Pass along the widget when creating a paste
  command. Fix minor crashes when copy/cut with selected bonds. (Now we can
  select more than just atoms).   

2007-06-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/navigatetool.cpp:
  Add initial one-button Mac support for draw tool and navigate tool.  

2007-06-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h: *
  avogadro/src/extensions/h2methylextension.cpp: New extension for "sculpting"
  hydrogen atoms to methyl groups. Works also on selected hydrogens.   

  * ChangeLog, avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h: *
  avogadro/src/extensions/hydrogens*: Fix PR#1739841. Only add or remove
  hydrogens for selected atoms if some atoms are selected.   

2007-06-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/glwidget.cpp: let GLWidget::setUnitCells auto-update the
  geometry, reinitialize the camera for the new geometry, and update the view. 
   

2007-06-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extension.h, libavogadro/src/painter.h: removed some function
  definitions that were never implemented. 

2007-06-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/glwidget.cpp:
  Initialise the painter at the start of the GLWidget render function, removed
  all calls to painter begin and end from the engines.  

2007-06-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/glwidget.cpp: *
  avogadro/src/extensions/ghemicalextension.cpp: Added threading so that a
  progress dialog is displayed.  Also removed some debuggin code that was left
  over.   

  * avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: ghemical optimization is now
  threaded 

2007-06-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: * libavogadro/src/glwidget.*: Added
  ::radius function to the GLWidget that way tools and engines only need to ask
  the GLWidget the radius rather than actually going through all engines on
  their own.  Also, engines more accurately give radius.  *
  libavogadro/src/engine.*: updated ::radius function to take the GLWidget as a
  parameter.  * libavogadro/src/engines/*: updated engines to not maintain an
  internal pointer to the GLWidget that was last called.   

2007-06-19  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/navigatetool.cpp: Updated tooltip to
  reflect current behaviour of this tool.  

  * ChangeLog, libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: Added the ability to initiate
  rotation using mouse movements. Left for x/y, middle for z.  

2007-06-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/glwidget.cpp: * libavogadro/src/glwidget.cpp
  (updateGeometry): Initial attempt at updating geometry based on unit cell
  parameters. This *seems* like the correct approach, but I have not checked
  with Benoit or fully tested. This tracks PR#1739844.   

2007-06-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: move buttonStartStop to member
  pointer so that name can change.   

2007-06-19  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/spheresettingswidget.ui: Removed the skeleton
  rendering functions - use the other engines thanks to changes in engine
  rendering order made by Donald. Much simpler implementation that can use any
  engine for the backbone now.  

2007-06-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/glwidget.cpp: cleaned up debug code. 

2007-06-18  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/extensions/gamessextension.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.h: *
  libavogadro/src/engine.*: added some engine flags for transparency atoms,
  bonds, molecules so that the glwidget has a better idea of the capabilities
  of the engines.  also added the transparencyDepth relative to others.  this
  needs a conceptual update just because i don't think it's intuitive.  if
  people define theirs higher than other engines they get priority.  i still
  believe this should be dependent on the ::radius response for the specific
  primitive type we're trying to compare.  * libavogadro/src/glwidget.*:
  engines are now sorted on load based on their flags and their
  transparencyDepth.  * libavogadro/src/engines/*: updated engines. 

  * ChangeLog, avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/gamessinputdialog.ui, avogadro/src/mainwindow.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/tools/selectrotatetool.cpp: *
  libavogadro/src/glwidget.*: Fixed a bug in mass selection where	the pointer
  was going past the end of the buffer.  Had to make sure	our pointer stays
  sane.  * libavogadro/src/primitive.*: Removed old selection code.  *
  libavogadro/src/selectrotate.cpp: Updated so that if there are       
  multiple engines, the toggling of selection only happens once per       
  primitive.  * avogadro/src/extensions/gamessinputdialog.cpp: Fixed bug
  1720467. 

2007-06-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: *
  avogadro/src/mainwindow.*: Remove quit() event -- Mac clients should receive
  a closeEvent for every window (advice from Trolltech).   

  * ChangeLog, avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/extensions/unitcellparamdialog.ui: *
  avogadro/src/extensions/unitcell*: Add support for controlling unit cell
  dimensions and angles. Add a warning if the molecule does not yet have a unit
  cell record -- extension will suggest a possible box dimenison.   

2007-06-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/axesengine.cpp: Improvements to the axes
  engine rendering - all axes should be of equal length now.  

  * ChangeLog, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/spheresettingswidget.ui: Some improvements to the
  rendering code and the setup widget, as suggested by Benoit.  

  * ChangeLog, avogadro/src/settingsdialog.ui, libavogadro/src/painter.cpp:
  Added some higher detail levels, probably only useful on accelerated systems.
  Kept the default level at 2.  

2007-06-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: Added a start/stop button and a reset
  button to the config widget.  

  * ChangeLog, cmake/modules/FindOpenBabel2.cmake: Added more verbosity to the
  cmake messages about the required version.  

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Added undo/redo support to the
  manipulation tool.  

2007-06-14  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: update the krazy status 

  * libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.h, libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h, libavogadro/src/engines/wireengine.h:
  remove 23 includes from the engine headers... We really need a script to do
  this! 

  * CMakeLists.txt, ChangeLog, INSTALL: Require Qt 4.3.0 now. Marcus told me
  with 4.2.x Avo doesn't even compile right now because of some .ui-files.  Ok,
  I have *no* clue whatsoever what these lines are all about... Shall I simple
  s/4.2.3/4.3.0/?  File C:\Qt\4.2.3\lib\QtGui4.dll File
  C:\Qt\4.2.3\lib\QtCore4.dll File C:\Qt\4.2.3\lib\QtOpenGL4.dll    

2007-06-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/extensions/unitcellparamdialog.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added full unit cell display support -- new
  extension can allow you to specify how many unit cells in each direction to
  display. (Still need to fix selection.)  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Add a small random
  vector offset to pasted molecules, so they do not fall on top of each other.
  (Best solution would be to mirror drawing programs, a small increasing offset
  with every paste.)  

2007-06-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: Added new auto rotation tool. The
  rotation speed about the x, y and z axes can be set using sliders. It needs
  an icon.  

2007-06-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h:
  Added an axes engine - draws the x, y and z axes in the bottom left of the
  GLWidget. Added new transformedAxis() functions for x, y and z to the camera
  class. Thanks to Benoit for his help in figuring this one out - still need to
  add drawing of axis labels.  

2007-06-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/stickengine.cpp: Added support for bond labels too.
  They are not drawn for engines that do not draw bonds or the wireframe engine
  - they both return a zero bond radius. Also updated the engines that needed
  it to return the radius of their bonds.  

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/spheresettingswidget.ui: A few small optimisations of
  the OpenGL code and the settings widget.  

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/spheresettingswidget.ui: Extend the VdW sphere engine
  for transparent rendering of the VdW spheres and draw a ball and stick
  structure inside if the VdW spheres are transparent. Added setAlpha function
  to the Color class to accomplish this.  

2007-06-05  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/engineconfigurationwidget.ui,
  avogadro/src/enginetabwidget.cpp, avogadro/src/enginetabwidget.h,
  avogadro/src/mainwindow.cpp: Minor class refactoring / cleanup 

2007-06-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/periodictabledialog.cpp: Update draw tool to update
  periodic table when visible. (e.g., if element is picked from menu, table
  will update correctly).  

  * libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/periodictabledialog.ui: Make the periodic table more
  like a palette -- no "ok" or "cancel" buttons -- can leave it open on the
  screen while changing elements.  

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h: Add periodic table which
  actually sets elements! (What a concept.)  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/periodictabledialog.ui: Minor periodic table fixes  

2007-05-31  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/periodicTable.ui,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/periodictabledialog.ui: Added slim periodic table
  widget to draw tool, but does not yet set custom elements.  

2007-05-26  Marcus D. Hanwell <marcus@cryos.org>

  * AUTHORS, ChangeLog, authors.xml, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Updated my details in the author
  files. Added bond selection support to the stick engine, small clean ups in
  bsdyengine and sphereengine.  

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Fix a bug where the 0 indexed
  bond is not selectable. 

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Use left mouse button for rotation
  and right mouse button for translation.  

2007-05-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extension.h,
  avogadro/src/extensions/ghemicalextension.h, avogadro/src/mainwindow.cpp: *
  avogadro/src/extension.h, avogadro/src/mainwindow.cpp: Add
  Extension::menuPath() which defines menus and submenus for extensions.
  Default is to use "&Tools" -- existing Tools menu.  *
  avogadro/src/extensions/ghemicalextension.h: Use above for a "Molecular
  Mechanics" submenu for all actions.   

2007-05-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Extended code to
  support bond selection for selection boxes too.  

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/global.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added some initial bond selection
  support in bsdyengine, refactored the engine a little. Added some support to
  selectrotatetool to pick bonds and some extra checks in manipulatetool as it
  previously assumed all selected items were atoms. Also added
  SEL_BOND_EXTRA_RADIUS for rendering selected bonds.  

2007-05-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/application.cpp, avogadro/src/mainwindow.cpp: *
  avogadro/src/application.cpp: Fix bug 1717423 -- Mac interface fix for
  opening files from Finder.  

  * avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h: Remove undo/redo support for
  selection extensions. Selections are handled by views, which are volatile.
  There's no way to reliably undo a selection and people probably don't care.  

2007-05-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: * avogadro/src/mainwindow.*: Mac interface fixes.
  Duplicate menu and toolbar actions for  new, open, save, close, quit. Remove
  icons from menu items. Fix bug 1720872: don't close the last MainWindow, hide
  it and disable menu items. Restore upon open or new.   

2007-05-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/editcommands.cpp,
  avogadro/src/engineconfigurationwidget.ui, avogadro/src/engineitemmodel.cpp,
  avogadro/src/enginetabwidget.cpp, avogadro/src/enginetabwidget.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/flattabwidget.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/settingsdialog.cpp,
  libavogadro/src/color.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: * libavogadro/src/glwidget.*: Did a
  bunch of API cleanup.  I know i know. How you guys loath my long function
  names.  Moved from ::selection to ::selectedPrimitives.  Now have
  ::setSelected and ::isSelect.  Thanks KDevelop for nice refactoring.  This
  naming method follows more of the Qt style "view" naming conventions (ie
  ::selectedItems).  * .: Fixed a few compiler warnings.   

2007-05-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/extension.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitivelist.cpp,
  libavogadro/src/primitivelist.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp: Fix selection to use new
  PrimitiveList. The selectrotate tool still needs some updating to properly
  handle non-atom selections and hits. Eliminate duplicate
  GLWidget::selection() and selectedItems() calls.  

2007-05-23  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/color.cpp, libavogadro/src/glwidget.cpp: Fine-tune
  materials and light: The black background suggests that we're in deep space,
  so there's no wall around to reflect the light, so the "ambient" component of
  the light is lowered (0.4 -> 0.2). To sharpen this effect, the "ambient"
  component of materials is also lowered (1/2 -> 1/3). Another change is that
  the "diffuse" light is increased to 1.0 (from 0.8) so that the effective
  color is as saturated as the color given by openbabel for the atom. There was
  no good reason not to set it to 1.0 and it's also visually more beautiful.   

2007-05-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/ChangeLog, avogadro/src/CMakeLists.txt,
  avogadro/src/avogadro.qrc, avogadro/src/engineconfigurationwidget.ui,
  avogadro/src/enginetabwidget.cpp, avogadro/src/enginetabwidget.h,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/icons/edit_add.png,
  avogadro/src/icons/edit_remove.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui, avogadro/src/primitivetreeview.cpp,
  avogadro/src/primitivetreeview.h,
  libavogadro/include/avogadro/primitiveitemmodel.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: *
  avogadro/src/enginetabwidget.*: Now uses a .ui file to design the widget. 
  this is much easier.  * avogadro/src/primitivetreeview.*: Added the
  PrimitiveTreeView class as a helper class for displaying PrimitiveItemModels.
   Just looks a bit prettier.  * libavogadro/src/primitivelist.*: Added the
  ::contains(Primitive *) operator for checking if a primitive is already in
  the list.  * .: Lots of other stuff for doing selective rendering.   

2007-05-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp: Fix
  bug 1722691. Show preferences in the correct spot on Mac.   

2007-05-22  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: improvement in drawtool: when creating an
  atom by dragging from an existing atom, the newly created atom is placed and
  moved within the plane passing through the existing atom, and parallel to the
  window. This feels more intuitive than the former behavior, where the new
  atom was placed and moved within the plane passing through the molecule
  center.  Also fix a comment in camera.cpp.   

2007-05-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.h: Small clean up in variable
  initialisation order.  

2007-05-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Some more code clean ups. Deleted
  old code and fixed some compiler warnings.  

  * libavogadro/src/engine.cpp, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/painter.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Various small clean ups for compiler
  warnings - unused variables etc.  

2007-05-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/include/avogadro/primitivelist.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h:
  Refactored PrimitiveQueue -> PrimitiveList.  Within the class renamed
  ::primitiveQueue to ::subList which returns a subList based on type.  Fixed
  changes due to refactoring in various files.   

  * ChangeLog, avogadro/src/enginelistview.cpp, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.h: *
  libavogadro/src/primitive.h: Fixed compiler warnings. *
  libavogadro/src/glwidget.cpp: Fixed compiler warnings. *
  libavogadro/src/color.cpp: Added virtual deconstructor and reformatted. *
  libavogadro/src/engines/bsdyengine.cpp: Fixed compiler warnings. *
  avogadro/src/enginelistview.cpp: Cleaned commented code and fixed bug caused
  by previous approach.   

2007-05-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Added confguration for label
  settings. Can now display atom number as before, element symbol or element
  name.  

2007-05-21  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Update the krazy issues 

2007-05-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h: Merge
  TextRenderer improvements made in the Kalzium branch: -- simplifications --
  3D-text is now centered around the specified position. This makes the atom
  labels look better, especially the longer ones (like full element names). 2D
  text (as in debugengine) is left unchanged.   

2007-05-20  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/color.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/painter.cpp: Silence Krazy: We can #include <config.h>
  because of the way CMake works. 

2007-05-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/elementcombobox.cpp,
  avogadro/src/elementcombobox.h, avogadro/src/engineitemmodel.cpp,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.cpp,
  avogadro/src/enginelistview.h, avogadro/src/enginetabwidget.cpp,
  avogadro/src/enginetabwidget.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/tools/manipulatetool.cpp: Added a item model for managing
  engines for a GLWidget.  This will make it easier whenw e need to add /
  remove / edit engines.  Updated the engine interface for name and
  description.  Added new configuration widget layout.  Now there is a dock
  widget for for configuring an engines, this includes engine settings plus
  *eventually* the primitives that are rendered by an engine.  Created the
  EngineTabWidget that will display the configuration for a GLWidget (one
  engine at a time).  It is possible that it should be called a
  GLWidgetStackedWidget but it does some weird stuff to save GUI memory.  The
  tab for settings is a stack, but when we add a tab for editing primitive,
  this will be a single widget for all engines.   

2007-05-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: Added Setup Force Field dialog,
  Calculate Energy and Rotor Search  

2007-05-18  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Added a settings dialog.  Updated the
  painter class to use ::begin ::end all the time.  This is good but needs to
  be better.  It needs to check to make sure it's in the correct context, if a
  painter is used in more than one context it should probably at least give a
  warning.  Can lead to data corruption.  (check email to list)  Updated
  engines to use the new painter class.   

2007-05-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Updates of the html files

  * krazy/libavo-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-tools.html, krazy/libavogadro-src.html: some new files 

  * avogadro/src/extensions/issues.html, avogadro/src/issues.html,
  krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavo-src.html: They files should go in one directory 

  * libavogadro/src/moleculetreeview.cpp, testfiles/2-aminoethanol.cml,
  testfiles/2-thioethanol.cml, testfiles/2_2_2-trifluoroethanol.cml,
  testfiles/COPYING, testfiles/but-2-yne-1_4-diol.cml, testfiles/butane.cml,
  testfiles/ethane-1_2-diol.cml, testfiles/ethane.cml, testfiles/ethanol.cml,
  testfiles/methane.cml, testfiles/methanol.cml, testfiles/porphyrin.cml,
  testfiles/propan-1-ol.cml, testfiles/propan-2-ol.cml, testfiles/propane.cml,
  testfiles/thiophene.cml: Adding a couple of deme/test molecules  

2007-05-18  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: this slot is
  needed in Kalzium, and it's needed anyway.   

2007-05-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/engine.h, libavogadro/src/primitive.h,
  libavogadro/src/tool.h, libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: Ok, doing funny ";" fixes. GCC 4.3
  is issuing a million warning it seems and Stephan Binner is fixing them in
  Kalziums copy of avogadro. I am forward porting all fixes now so that they
  are not lost!  Example: -Q_DECLARE_INTERFACE(Avogadro::ToolFactory,
  "net.sourceforge.avogadro.toolfactory/1.0");
  +Q_DECLARE_INTERFACE(Avogadro::ToolFactory,
  "net.sourceforge.avogadro.toolfactory/1.0")   

  * libavogadro/src/camera.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitive.h, libavogadro/src/tool.cpp: Several EBN fixes: 
  explit ctors newer compare a QString to == "" but use ".isEmpty"  

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/sphereengine.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h:
  Fixing a couple of EBN issues. Benoit ack'ed the explicit patch  

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.h, libavogadro/src/tools/manipulatetool.cpp: Fix several
  typos found by 
  
  ex.html   

2007-05-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * AUTHORS, CMakeLists.txt, COPYING, ChangeLog, INSTALL, authors.xml,
  avogadro/src/extensions/CMakeLists.txt,
  cmake/modules/cmake_uninstall.cmake.in, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt:
  Merged all changes from tag loschmidt/0.1.0.  Final merge. (r407, r409, r410,
  r411, r412, r413) 

2007-05-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp: Fix for issue 1719080 

  * avogadro.nsi, avogadro/src/CMakeLists.txt, avogadro/src/application.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/gamessextension.h,
  avogadro/src/icons/avogadro.ico, avogadro/src/mainwindow.cpp,
  avogadro/src/windows/avogadro.rc, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/manipulatetool.cpp, libavogadro/src/undosequence.h:
  Merging changes from 0.1.0 tag; r400, r401, r402, r403, r404 

2007-05-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.h, libavogadro/src/painter.h: Clarify/add
  documentation; remove my copyright from glwidget.h because really I only
  edited a few lines in it.   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/labelengine.cpp, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: add documentation and internal
  comments for Painter class rename Camera::backTransformed* to
  Camera::backtransformed*, add documentation, make a bit more use of them in
  labelengine. clarify tooltip of manipulatetool   

2007-05-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Few UI bugs and
  removed debugging line that was unneeded.   

2007-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added function to
  easily determine if a Primitive is selected in the GLWidget. Modified the
  toggleSelected function to behave as expected with multiple views. Found and
  fixed a subtle crash in the engines when radius was called before render and
  ported all engines to render correctly with multiple views.  

2007-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/extension.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h: Extension cleanup. Base Extension
  class is not QObject, but extensions are.  

  * avogadro/src/extension.h, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h, avogadro/src/mainwindow.cpp: Pass
  a GLWidget to extensions (so selection can be modified, auto-rotate, etc.)
  Add example SMARTS selection extension -- select atoms by SMARTS pattern.  

2007-05-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, Doxyfile, Doxyfileext, avogadro/src/extension.h,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  libavogadro/src/CMakeLists.txt, libavogadro/src/camera.cpp,
  libavogadro/src/camera.h, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/global.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/internal/cylinder.cpp,
  libavogadro/src/internal/cylinder.h, libavogadro/src/internal/sphere.cpp,
  libavogadro/src/internal/sphere.h, libavogadro/src/internal/textrenderer.cpp,
  libavogadro/src/internal/textrenderer.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h, libavogadro/src/undosequence.cpp,
  libavogadro/src/undosequence.h: Updated documentation.  Removed dependancy on
  4.3 (make sure you do editing of .ui files with designer of qt4.2)  Added
  documentation.  Updated copyright information on all files.  There is now a
  Doxyfileext which generates external docs.   

2007-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/tools/manipulatetool.cpp: Fix inconsistencies between what is
  drawn and what the manipulate tool does when using multiple views. The other
  engines still need their behaviour to be fixed.  

2007-05-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Minor API improvements; make use
  of these at various places; close bug 1717437 in clickmeasuretool.   

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/internal/textrenderer.cpp: fix bug in dynamic-bs where the
  separation between the two colors of a bond was not made at the middle of the
  bond. Also don't draw the portion of the bond that's inside the sphere.   

2007-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Fix a bug with atoms selected using
  the selection box. Performed some clean up in the selectrotatetool code.  

2007-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add support for
  setting the number of unit cells to display. Not exposed in the user
  interface, but it's now in the library. Just need to build the window for the
  extension (after this beta release).  

  * libavogadro/src/tools/manipulate.png, libavogadro/src/tools/manipulate.qrc,
  libavogadro/src/tools/manipulatetool.cpp: Add "hand" icon for manipulate
  tool.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add "select all" and "select none" edit menu
  actions.  

2007-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added some shortcut keys for the
  tools. These may not be optimal and probably need further discussion. Also
  added the drawing of the selection centroid sphere for the manipulate tool.  

2007-05-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Support for cut/copy
  of just selected atoms.  

2007-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Adapted the methods implemented by
  Geoff in the selectrotatetool source. Now translation (LMB) and rotation
  (RMB) of selected atoms works. Currently uses the selection list maintained
  by GLWidget.  

2007-05-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/application.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Improve behavior when
  opening files while launching on Mac.  

2007-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/manipulate.qrc,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Initial version of the manipulation
  tool. Currently only operates on single atoms. Currently the left mouse
  button translates the atom position in x and y. The middle mouse button moves
  the atom into and out of the screen (zoom). This tool needs its own icon.  

2007-05-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Add initial cut
  support, as well as undo/redo for clear.  

2007-05-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * Doxyfile, libavogadro/src/CMakeLists.txt,
  libavogadro/src/internal/sphere.h: Updated indenting in CMakeLists.txt,
  corrected some comments in sphere.h, updated Doxygen configuration.   

2007-05-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/glwidget.cpp: remove some useless
  OpenGL commands. Make sure GL_TEXTURE_RECTANGLE_ARB is defined.   

  * libavogadro/src/internal/textrenderer.cpp,
  libavogadro/src/internal/textrenderer.h: some cleanup in TextRenderer   

2007-05-10  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h:
  Remove old bsengine code  

2007-05-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h: add method needed by
  cryos (and needed anyway): Camera::backTransformedZAxis()   

2007-05-10  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Add some initial support for
  "selection modes" and tracking selected atoms (in the GLWidget). Probably
  needs some work.  

2007-05-09  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.h: remove outdated #include that were
  breaking compilation. Sorry rbraith :)   

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/CMakeLists.txt, libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/sphere.h,
  libavogadro/include/avogadro/textrenderer.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/internal/cylinder.cpp, libavogadro/src/internal/cylinder.h,
  libavogadro/src/internal/sphere.cpp, libavogadro/src/internal/sphere.h,
  libavogadro/src/internal/textrenderer.cpp,
  libavogadro/src/internal/textrenderer.h, libavogadro/src/painter.cpp,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h: Move the
  Sphere, Cylinder and TextRenderer to a internal/ subdirectory, don't expose
  them publicly. These classes are only used by the Painter class. Also replace
  tabs with 2 spaces in the CMakeLists.txt files, to be consistent with the
  indenting style of the source code.   

  * libavogadro/src/sphere.cpp, libavogadro/src/textrenderer.cpp,
  libavogadro/src/textrenderer.h: In TextRenderer: quality improvements, API
  changes, indentation fixing, and most importantly, documentation (both API
  and internal code comments). Also fix indentation in Sphere.   

2007-05-08  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: In GLWidget, make the Camera live
  as a pointer and let GLWidget::camera() return this pointer instead of a
  reference. Adapt the rest of the code to that change.   

2007-05-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Added improved "manipulate" rotate
  thanks to Benoit. Shift + left mouse. Much cleaner rotation.  

2007-05-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/application.cpp,
  avogadro/src/application.h, avogadro/src/extension.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Update Extensions to separate instances per
  MainWindow.  Added true SDI functionality.  For more info see
  
  
  l  This should fix our Mac errors.   

2007-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/primitive.cpp: Copy/paste now
  prefers MDL molfile mimetype (ensures bond orders, etc. copied) Paste will
  now select atoms pasted for automatic manipulation.  

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Initial "manipulate mode" for
  select tool. Hold down the shift key: left button rotates (needs work) right
  translates  

2007-05-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitive.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Added the settings dialogs to Engines. 
  Modified the preexisting toolSettings interface to return a 0 if there is no
  settings available for the tool.  This is done to mimic the engines settings
  interface and it is done in the engines settings so that we know if we should
  create a new window or not.  It is better than testing against null QWidgets
  or whatever the alternative would be.  Also added GLWidget::setStable(bool)
  and GLWidget::isStable() to see if the GLWidget is in an unstable state. 
  This would occur as the result of some tool setting it.   

2007-05-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/tools/clickmeasuretool.cpp: Fix
  compile error (extra closing parenthesis -- sorry!) Tweak detail level of
  spheres.   

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h, libavogadro/src/global.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  rework class Cylinder; make Painter able to draw Cylinders; make use of that
  in all engines; also change Tools so they no longer have their own
  Cylinders/Spheres and use Painter instead.   

2007-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Minor fixes.
  Remove "select all" (not ready) and fudge "cut" with current copy() code.  

  * avogadro/src/CMakeLists.txt, avogadro/src/editcommands.cpp,
  avogadro/src/editcommands.h, avogadro/src/enginelistview.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add initial support for copy commands (includes
  copy to text, image, chemical/x-xyz). Still needs work tomorrow.  

2007-05-06  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h, libavogadro/src/global.h,
  libavogadro/src/painter.cpp: make use of Painter to draw spheres in all
  engines. Introduce SEL_ATOM_EXTRA_RADIUS constant to control the radius of
  selection highlighting spheres (added to the atom's radius).   

  * libavogadro/include/avogadro/painter.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/global.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h: Introduce Painter class and global quality
  setting. Currently it can only paint spheres. Make bsdyengine use it.   

  * libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: implement level 0 as
  a octahedron, d-pointerify, and many simplifications   

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h: Fix typo in Ross's name. Sorry!   

2007-05-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h: Added operator+= and copy constructor to the
  Molecule class.  Added pasting operation.  Currently only works with
  cartesian coordinates.  It is setup to work with Mime data but i pick the
  default text case (assumed to be cartesian coordinates).   

2007-05-05  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp: Add hooks for options dialog for engines.  

2007-05-05  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp: Draw outlined text in labelengine, for
  readibility on all backgrounds. Had to change the depthFunc from GL_LESS to
  GL_LEQUAL. Hope that doesn't break anything. This is very slow so I propose
  that text should be hidden while moving the camera with the mouse, to get
  smoother movement. That suggests the following: in Engine, we could have
  renderOpaque, renderTransparent and renderText. What do you think? Tools
  would inform the GLWidget that they are moving the view using callbacks
  GLWidget::beginMoveCamera() and GLWidget::endMoveCamera().   

2007-05-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Fix compile problems with radius()
  function  

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp: Add support for classes of color maps
  (subclasses of Color). This includes setting a color map for any engine.
  (e.g., color by element, color by atom type, color by reside...)  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/labelengine.cpp, libavogadro/src/global.h: fix
  position of label in the labelengine (now the label is always placed on top
  of the atom, from the camera's point of view) however there remains an issue
  caused by the fact that we still don't make sure all opaque objects have been
  drawn *before* transparent objects are drawn.   

2007-05-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Removed d-pointer stuff as it is not
  required for tools - see mailing list.  

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Improved the label engine to use the
  radius method an so labels can be seen using the sphere engine now. Still
  needs work on label placement.  

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Updated visual effects in NaviateTool
  to cover all atom centred operations. After discussion with Benoit added
  d-pointer to NavigateTool too.  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: fix #including in tools and
  engines. In particular, don't include the meta-header <QtGui> when the much
  smaller <QtPlugin> is enough. Also fix comment in debugengine.   

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h: fix copyright lines in debug engine   

2007-05-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * CMakeLists.txt, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: -- I
  moved the FindFoo instructions in the toplevel CMakeLists.txt. I see no
  reason why we should check for it twice...  -- We now officially require Qt
  4.2.0 (set(QT_MIN_VERSION)). Benoit told me that 4.1 is totally broken wrt to
  something in QtGl and all developers are using 4.2 anyway. Before we we just
  looking for "Qt4" which would even have worked for 4.0-beta I think!  

  * INSTALL, avogadro/INSTALL: Update the installation instructions  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: remove _setup : Sphere::setup is clever
  enough to notice that new_detail==old_detail and exit in that case.  remove
  some unnecessary state changes. Donald: it is possible to draw spheres with
  GL_NORMALIZE, only it's not optimally fast. But if we're only drawing one
  sphere, it's not worth the four state changes enabling GL_RESCALE_NORMAL
  instead.   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/global.h: replace
  #defines with constants in global.h remove a qDebug and other negligible
  cleanup   

2007-05-04  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/sphereengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Updated Tool interface. Now there is a ::paint function which gets called
  after the engines render allowing Tools a better way to render to the
  GLWidget (as opposed to using a displayList).  I updated the NavigateTool and
  ClickMeasure tool (it now shows proper colors).  Also added the ::radius
  function to the dynamic ball and stick engine.  As a note if an atom is
  selected, radius(Primitive *) needs to reflect that.   

2007-05-03  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Made the changes that Benoit recommended, code in
  the glwidget was removed and new code was put into the debug engine.  When
  the debug engine is turned on now it repeatedly calles gl->update() thereby
  makeing the glwidget constantly re-render.  This gives FPS a reasonably
  accurate value.  

2007-05-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: Added radius function to Engine,
  ported bsengine and sphereengine to use the new function. 

2007-05-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/avogadro.qrc, avogadro/src/icons/navigate.png,
  avogadro/src/icons/navigateN.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, gpltemplate,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/navigate.png,
  libavogadro/src/tools/navigate.qrc, libavogadro/src/tools/navigatetool.cpp:
  Added template for licensing.  Added navigate icon taken from the crystal
  clear office set.  Added "Center View" action.  There are times things are
  not updateing the glwidget's geometry info.  we need to fix this so that
  things are required to call it.  there is a callback from primitiveAdded /
  primitiveUpdate / primitiveRemoved that should be sufficient to set a flag
  that the geometry data needs to be updated.  I'll look at this more tomorrow,
  tomorrow, i'll love ya, tomorrow, you're only a day away.   

  * avogadro/src/extensions/CMakeLists.txt, avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamess.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemical.cpp, avogadro/src/extensions/ghemical.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogens.cpp, avogadro/src/extensions/hydrogens.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h: Refactored classes so that
  extensions are named *Extension (GamessExtension, etc etc)  Renamed source
  files accordingly.   

  * avogadro/src/application.cpp, avogadro/src/enginelistview.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamess.h, avogadro/src/extensions/ghemical.cpp,
  avogadro/src/extensions/ghemical.h, avogadro/src/extensions/hydrogens.cpp,
  avogadro/src/extensions/hydrogens.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  libavogadro/include/avogadro/undosequence.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h, libavogadro/src/undosequence.cpp,
  libavogadro/src/undosequence.h: ****Big Huge Changes****  Undo/Redo is
  implemented and all of the extensions and tools have been updated. The
  interface to tools and extensions now requires that you return a
  QUndoCommand* or 0 (NULL).  The only important things to remember when
  creating QUndoCommands is to make sure that the state after undo is exactly
  how it was before you performed your action.  Worst case you need to
  duplicate all the Molecule data.  This is somewhat intense but it runs quite
  quickly as there are no calls to NewAtom meaning no callbacks.  There is a
  new class UndoSequence which is essentially a list of QUndoCommands which are
  all compiled into one.  This is handy for our drawing tool.  I apologize as i
  haven't had time to document any of this code.   

2007-05-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/elementcombobox.h, avogadro/src/extension.h,
  avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamessinputdata.h,
  avogadro/src/extensions/ghemical.cpp, avogadro/src/extensions/hydrogens.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/include/avogadro/primitive.h,
  libavogadro/include/avogadro/primitives.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: primtives.h was defining the
  Primitive class.  Minor refactoring that was buggin me.  *sigh*.   

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added new Debug Engine which lists the number of
  atoms and molcules along with the FPS.  Contributed by James, Ross and
  Shahzad.  I modified to only perform one division.  As a result there are
  some added hooks to GLWidget to keep track of time to render a scene. 
  Hopefully we can say this is trivial.   

2007-05-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Added stick engine  

2007-05-01  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/CMakeLists.txt, avogadro/config.h.in, avogadro/src/CMakeLists.txt,
  avogadro/src/config.h.in, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/CMakeLists.txt, libavogadro/config.h.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/config.h.in,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/CMakeLists.txt: tools,
  engines, extensions are now installed and loaded by default to their correct
  locations: ${CMAKE_INSTALL_PREFIX}/lib/avogadro/{tools|engines|extensions} 
  added the define INSTALL_PREFIX to the CMAKE_INSTALL_PREFIX path.  this does
  not get installed with the other header files.  modified the environment
  variables:  AVOGADRO_{ENGINES|TOOLS|EXTENSIONS}  AVOAGDOR_EXTENSIONS was
  previously AVOGADRO_PLUGINS   

2007-05-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/ResidueSphereEngine.cpp,
  libavogadro/src/engines/ResidueSphereEngine.h,
  libavogadro/src/engines/StickEngine.cpp,
  libavogadro/src/engines/StickEngine.h,
  libavogadro/src/engines/WireframeEngine.cpp,
  libavogadro/src/engines/WireframeEngine.h: Remove old engines to allow
  updated stick engine.  

  * libavogadro/src/engines/SphereEngine.cpp,
  libavogadro/src/engines/SphereEngine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: Remove old SphereEngine code --
  conflicts on capitalization-sensitive file systems. Clean up class names,
  etc. in new sphere engine.  

2007-04-29  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.cpp, libavogadro/src/sphere.cpp,
  libavogadro/src/sphere.h: Fix errors (not leaks) found by valgrind:
  "Conditional jump or move depends on uninitialised value(s)"   

2007-04-27  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/tools/navigatetool.cpp: add another missing {} after a
  one-line if in my code :)  simplification in navigatetool  more clever
  handling of the selection buffer. Instead of resizing at molecule loading (as
  done before), resize in GLWidget::hits(). To prevent too frequent resizing,
  add some margin to the buffer size. The advantages are: -- new approach never
  fails, the user may add as many atoms as he likes (like when doing "add
  hydrogens"). -- old approach required a large margin in order to let user add
  atoms; this is no longer needed. Old margin was 256*8=2048 ints. New margin
  is 128 ints only.    

2007-04-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/tools/clickmeasuretool.cpp:
  Added check for correct hit type (AtomType)   

2007-04-26  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: -- introduce defines in global.h
  for the size of the small selection boxes used in tools. The former size,
  5x5, was too small in wireframe mode (selection-wise, the atoms were single
  pixels regardless of the "point size"). We now use 9x9 boxes. -- cleanup in
  drawtool   

  * libavogadro/src/cylinder.cpp, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/sphere.cpp: minor cleanup in
  bsdyengine; only toggle client state inside Sphere and Cylinder, since it's
  not needed elsewhere.   

  * libavogadro/src/camera.cpp, libavogadro/src/tools/navigatetool.cpp:
  simplification in Camera::normalize(), remove qDebug()   

  * avogadro/ChangeLog, avogadro/src/enginelistview.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/tools/navigatetool.cpp:
  complete the updateGL() -> update() move   

  * avogadro/src/enginelistview.cpp, libavogadro/src/engine.cpp: start with
  only dynbs engine enabled. That's pretty much a hack as I don't really
  understand how avogadro (the app) works. So I did it in enginelistview. Sorry
  if that's not the right place.  CCMAIL:Donald Ephraim Curtis
  <donald-curtis@uiowa.edu>   

  * libavogadro/src/global.h, libavogadro/src/glwidget.cpp: dynamically resize
  the selection buffer at molecule loading, to adapt to any number of atoms. At
  mol loading, a margin is added in case the user creates new atoms (current
  margin is for 256 new atoms).   

  * libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: updateGL() -> update()   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/global.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Hey, the Navigate Tool now feels
  very solid, even when cruising through very large proteins!! 
  -simplifications and improvements in Camera wrt clipping planes
  -reorganization in NavigateTool: -- move much code to helper functions -- fix
  at last the problem with zoom-in passing beyond the goal -- swap left and
  right buttons -- use a member glwidget pointer to reduce argument-passing.
  the pointer is obtained from the mouse callbacks. - move numeric constants to
  #defines in global.h   

2007-04-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: have the camera auto-normalize
  after each rotation. no need to explicitly normalize anymore.   

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Now mouse wheel is also sensitive to
  the atom below mouse pointer.   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Solve a numerical instability
  issue : after a large number of rotations, the camera matrix got more and
  more corrupt, eventually resulting in a blank GLwidget.  Solved by adding
  method Camera::normalizeRotation(), to be called after each frequent rotation
  (typically in user input handling). Already used in navigatetool and
  selectrotatetool.    

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/navigatetool.cpp: much improved right-button movement
  in navigatetool. Now the molecule precisely follows the mouse movement. This
  required further tweaking of the unProject API.   

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: change
  prototype of unProject(double, double) to unProject(const QPoint&).  This
  simplifies some code since this method is always being called on QPoint
  coordinates.   

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Rework
  API and documentataion for project/unproject, const-correctify, make use of
  class Vector3d. Move to GLWidget the special unproject method from DrawTool
  taking only x and y coords and unprojecting to the plane of the mol center
  parallel to the screen. Will be useful in NavigateTool.    

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: fixes and simplifications in mid-button
  zoom. No longer center on atom; instead keep atom center at fixed position on
  screen. Centering is no longer needed since right-button allows to center
  manually. Keeping atom at fixed position is also more consistent with
  left-button rotation.   

2007-04-24  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: simplifications   

2007-04-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/clickmeasure.cpp, libavogadro/src/tools/clickmeasure.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigate.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h, libavogadro/src/tools/selectrotate.cpp,
  libavogadro/src/tools/selectrotate.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Renamed tool filenames to match
  their class names.   

  * libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/clickmeasure.cpp, libavogadro/src/tools/clickmeasure.h,
  libavogadro/src/tools/draw.cpp, libavogadro/src/tools/draw.h,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h,
  libavogadro/src/tools/selectrotate.cpp, libavogadro/src/tools/selectrotate.h:
  Updated Engine interface to recieve the GLWidget as a pointer.  This as
  opposed to using the ::parent() for two reasons: 1) we can duplicate
  GLWidgets (so that they share engines) 2) we may also want to allow programs
  using libavogadro to load their own engines and pass them to the GLWidget. 
  Updated Tools so that they are named correctly.  ie. DrawTool
  SelectRotateTool ...  This to match the *Engine form with engines. renaming
  coming soon.   

2007-04-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: MainWindow now has functionality to create
  multiple views.  View->New View / View->Close View.  GLWidget optimized
  functionality so that unactive GLContexts to not get rendered.  This will
  need to be updated if/when we allow two views to be shown at once. 
  EngineListView now handles enabling and disabling engines for the current
  GLWidget. (opposed to MainWindow binding to the signals).  

2007-04-23  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h:
  cleanup and bugfixing in the navigate tool. -- fix molecule-centered rotation
  when center is not at origin -- don't recompute GL hits at every mouse move  

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp: Fix camera bug cause by
  miscalculation of distance to molecule. Fix comment explaining how this is
  computed. Introduce Camera::distance(Vector&) method performing this
  computation in the correct way. Make use of this new method in bsdynengine
  and labelengine, and do cleanup there. Remove method
  Camera::translationVector().   

2007-04-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engine.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Added d-pointer to Cylinder class + formatting
  updated.  Primitive and Molecule now share d-pointer.   

  * avogadro/src/application.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: new / open now
  perform correctly; ie, check for modified status (handled by the QMainWindow)
  and ask to save if changes have been made.  also, 'new' simply clears our the
  editor rather than creating a new window.   

2007-04-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Updating to qt
  style d-ptrs.   

  * libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h: more updates based off the new tool interface. 

  * libavogadro/src/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h, libavogadro/src/tools/navigate.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/selectrotate.cpp,
  libavogadro/src/tools/selectrotate.h:
  libavogadro/src/tool.h,libavogadro/src/tool.cpp; updated interface. removed
  ::initialize() and ::cleanup() functions.  Unneeded.  If plugins need to use
  these functions they can attach functions to the signals of the
  ::activateAction().  libavogadro/src/toolgroup.cpp; we can now use
  Tool::parent() to get the plugin which it belongs to, rather than relying on
  the Tool::data() to do the same.  libavogadro/src/CMakeLists.txt; added the
  tool.cpp file so that the tool object gets compiled into libavogadro. 
  libavogadro/src/glwidget.cpp; tool interface was updated.  Updated interface
  to all tools.  

2007-04-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/select.png,
  libavogadro/src/tools/select.qrc, libavogadro/src/tools/selectrotate.cpp: Add
  pointer icon for selectrotate tool  

2007-04-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h: libavogadro/src/tools/draw.h,
  libavogadro/src/tools/draw.cpp; updated tooltip to include how the tool
  works.  added code to replace atoms and bonds if they are different. 
  clicking on a lone atom will change it to the new type.. drawing bonds over
  preexisting bonds updates them. 
  libavogadro/src/tools/clickmeasure.cpp,libavogadro/src/tools/clickmeasure.h;
  updated tooltip to include how the tool works.  renamed the tag so that as
  you select you get atom 1,2,3 rather than 0,1,2.  

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/tools/clickmeasure.cpp:
  libavogadro/src/engines/labelengine.cpp; push all GL attribute bits and use
  white text.  libavogadro/src/tools/clickmeasure.cpp; push all GL attributes,
  give feedback on initial click (marked with *0) for now.  

  * libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/tool.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h, libavogadro/src/tools/selectrotate.cpp:
  libavogadro/src/glwidget.h libavogadro/src/glwidget.cpp : added unProject and
  project functions, also fixed the ::hits function so it restore the previous
  projection and modelview matrices  libavogadro/src/engines/bsdyengine.cpp :
  fixed compiler warning  libavogadro/src/tools/selectrotate.cpp : free the
  display list  libavogadro/src/tools/clickmeasure.cpp
  libavogadro/src/tools/clickmeasure.h : new click to measure tool.  Displays
  results in the GL Widget.  libavogadro/src/tools/CMakeLists.txt : added
  clickmeasure build instructions  libavogadro/src/tools/draw.cpp
  libavogadro/src/tools/draw.h : make use of the new GLWidget::project and
  GLWidget::unProject functions  libavogadro/src/tool.h : renamed ::init to
  ::initialize.  can't be sure we actually need these functions.  we have the
  option to let the tool decide what initialization it needs to do by
  connection to the action signals.  

2007-04-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp: Switch
  to use dynamic_cast instead of qobject_cast  

  * libavogadro/src/color.cpp, libavogadro/src/cylinder.cpp,
  libavogadro/src/sphere.cpp: Namespace fixes.  

2007-04-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/include/avogadro/camera.h,
  libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/engine.h, libavogadro/include/avogadro/global.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/primitives.h,
  libavogadro/include/avogadro/sphere.h, libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h: Fix "fake" includes.  

  * libavogadro/include/avogadro/camera.h,
  libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/engine.h, libavogadro/include/avogadro/global.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/primitives.h,
  libavogadro/include/avogadro/sphere.h, libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h: Moving headers from src/ to
  include/avogadro -- two pass job.  

2007-04-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h:
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h:
  added dynamics for bonds.  libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h:  when detail < 0 we generate a single line rather
  than a cylinder.  Also added constructor with default parameter to 0.  

2007-04-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/primitives.cpp,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/draw.cpp, libavogadro/src/tools/selectrotate.cpp:
  libavogadro/src/moleculetreeview.cpp: removed debug code 
  libavogadro/src/sphere.cpp: added constructor and cleaned up code 
  libavogadro/src/toolgroup.cpp: removed debug code 
  libavogadro/src/primitives.cpp: removed debug code  libavogadro/src/sphere.h:
  added constructor which takes as a parameter the detail 
  libavogadro/src/engine.h, libavogadro/src/engine.cpp : added interface
  function to inform the engine to update the primitive.  This is a cautionary
  function for optimization.  libavogadro/src/glwidget.cpp: cleaned up the
  code, added use of new engine function. 
  libavogadro/src/engines/labelengine.cpp: added clause to not label when far
  from camera libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdyengine.cpp: proof of concept for optimization of
  the ball & stick engine.  Added this as to not disturb the old code until the
  new code can be cleaned up.  I will get around to this just haven't had the
  time to think about the best way to do it. 
  libavogadro/src/engines/bsengine.cpp: removed debug code. 
  libavogadro/src/engines/CMakeLists.txt: added bsdyengine 
  libavogadro/src/tools/CMakeLists.txt: commented test tool code. 
  libavogadro/src/tools/selectrotate.cpp: added atom::update call after
  selection  libavogadro/src/tools/draw.cpp: removed debug code  

2007-04-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h:
  Minor reorganization of BS engine to improve performance. (Need to add
  "options" ability to set level of detail, etc.)  

  * avogadro/src/CMakeLists.txt, avogadro/src/mac/MacOSXBundleInfo.plist.in,
  avogadro/src/mac/atom.icns, avogadro/src/mac/avogadro.icns: Renamed Mac icon
  to avogadro.icns  

2007-04-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/aboutdialog.cpp, avogadro/src/avogadro.qrc,
  avogadro/src/avogadro.ui, avogadro/src/icons/atom2.png,
  avogadro/src/icons/avogadro.png, libavogadro/src/tools/CMakeLists.txt: Update
  logo name to avogadro.png.  Lets not get too lazy with naming it's important!
   atom2.png does not describe what the png is really of.   

2007-04-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Updated PrimitiveQueue to allocate statically
  instead of dynamically.  Changed PrimitiveQueue::primitiveList to return a
  const QList<Primitive *>  Updated the engines to use "foreach" loops.   

2007-04-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Add wireframe engine (partly to help debug label issues)   

2007-04-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Label rendering engine added.  Needs
  work.  Possibly using an overlay?   

  * avogadro/src/CMakeLists.txt, avogadro/src/application.cpp,
  avogadro/src/application.h, avogadro/src/avogadroapp.cpp,
  avogadro/src/avogadroapp.h, avogadro/src/enginelistview.cpp,
  avogadro/src/enginelistview.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Refactored AvogadroApp -> Application to maintain
  naming scheme.  Added EngineListView to list the engines and allow them to be
  enabled/disabled accordingly.  Engines now maintain their own PrimitiveQueue.
   This will allow us (in the future) to allow advanced users to add/remove
  atoms/bond/residues accordingly from an engine.  (in the case that i only
  want a certain atom or set of atoms rendered.   

2007-03-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/avogadroapp.cpp,
  avogadro/src/avogadroapp.h, avogadro/src/main.cpp: Added open events for Mac
  (i.e., now can drag-and-drop files from the Finder)  

  * avogadro/src/mac/MacOSXBundleInfo.plist.in, avogadro/src/mac/atom.icns:
  Added Mac OS X resources directory  

2007-03-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/tools/draw.cpp: Refactored SetVector3d and GetVector3d to
  setPos and pos after discussing with Benoit.  We agreed that this sticks with
  our Avogadro API convention.   

  * avogadro/include/avogadro/extension.h, avogadro/include/avogadro/plugin.h,
  avogadro/src/CMakeLists.txt, avogadro/src/extension.h,
  avogadro/src/extensions/CMakeLists.txt, avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamess.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdata.h,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/gamessinputdialog.ui,
  avogadro/src/extensions/ghemical.cpp, avogadro/src/extensions/ghemical.h,
  avogadro/src/extensions/hydrogens.cpp, avogadro/src/extensions/hydrogens.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/plugin.h,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/draw.h, avogadro/src/plugins/draw.png,
  avogadro/src/plugins/draw.qrc, avogadro/src/plugins/gamess.cpp,
  avogadro/src/plugins/gamess.h, avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h,
  avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h,
  avogadro/src/plugins/gamessinputdialog.ui, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/ghemical.h, avogadro/src/plugins/hydrogens.cpp,
  avogadro/src/plugins/hydrogens.h, avogadro/src/plugins/navigate.cpp,
  avogadro/src/plugins/navigate.h, avogadro/src/plugins/selectrotate.cpp,
  avogadro/src/plugins/selectrotate.h,
  avogadro/src/plugins/ui_gamessinputdialog.h,
  libavogadro/include/avogadro/molgeominfo.h,
  libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h,
  libavogadro/include/avogadro/toolmanager.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/draw.cpp, libavogadro/src/tools/draw.h,
  libavogadro/src/tools/draw.png, libavogadro/src/tools/draw.qrc,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h,
  libavogadro/src/tools/selectrotate.cpp, libavogadro/src/tools/selectrotate.h:
  Moved tools to libavogadro: - Added ToolGroup which manages a group of tools.
  - Moved avogadro "plugins" to "extensions".  (removed tools)   

2007-03-24  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: In Draw:
  standardize on passing GLWidget *widget to the various methods, from which
  both the molecule and the center can be retrieved. Maybe evaluate letting the
  Tool know which GLWidget it's operating in, gettable with glwidget()? That
  would spare much argument-passing.  Add API documentation and explanatory
  code comments to unProject().   

  * avogadro/src/plugins/draw.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: In class Atom:
  Rename position() to GetVector3d() and setPosition() to SetVector3d(). This
  underlines the fact that they're just wrappers for GetVector() and
  SetVector() from OBAtom, doing casts with Eigen::Vector3d.  Rewrite these
  functions to make sure they don't cause copies, and inline them. Add
  documentation. A "rationale for inlining" is provided in comment, to justify
  that inlining isn't dangerous here.   

2007-03-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/aboutdialog.cpp, avogadro/src/avogadro.qrc,
  avogadro/src/icons/atom2.png: Add contributed icon to about dialog  

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/ui_gamessinputdialog.h:
  Add full third-row elements (e.g., sulfur, phosphorus...)  

2007-03-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/navigate.cpp,
  avogadro/src/plugins/navigate.h: Commiting cryo's patch for the navigate
  plugin.  (ie. importing navigation functionality from Kalzium.   

2007-03-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/glwidget.cpp: Document class Camera   

2007-03-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/plugin.h, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/draw.h, avogadro/src/plugins/selectrotate.cpp,
  avogadro/src/plugins/selectrotate.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added wheel function to plugins to allow handling
  of wheel events on the GLWidget.   

2007-03-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/plugins/draw.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engine.h, libavogadro/src/glwidget.h: Fix compilation (after
  removal of molgeominfo.*).   

2007-03-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  avogadro/src/plugins/selectrotate.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molgeominfo.cpp,
  libavogadro/src/molgeominfo.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Removed the MolGeomInfo class.  It's really not
  needed as all this info can happily exist in the Molecule class and
  techincally should.  The GLWidget makes it's own copies of this info when it
  wants to by GLWidget::updateGeometry().  I believe this class was most likely
  introduced as a way to get the info to the Engines, but really they should
  know their parent.   

2007-03-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engine.h, libavogadro/src/engines/StickEngine.cpp,
  libavogadro/src/engines/StickEngine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp: fix the
  auto-multiple-bonds-oritentation feature from kalzium That is, now when you
  load a molecule the double bonds are automatically oriented to face the
  camera in the default viewpoint. So that they don't look like single bonds. 
  This implied API changes in engines: now render must be passed the
  molGeomInfo structure, as it needs to know the normal vector of the
  molecule's fitting plane.   

  * avogadro/src/plugins/draw.cpp, libavogadro/src/camera.cpp: adjust initial
  viewpoint on loaded molecule. remove unused define.   

  * avogadro/src/plugins/draw.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/molgeominfo.cpp: Fix bug where atoms created on an empty
  molecule were not shown. The problem was twofold: -molGeomInfo wasn't getting
  updated -with an empty molecule, applyPerspective set nearPlane==farPlane,
  thus nothing would be drawn until molGeomInfo would be updated.   

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  avogadro/src/plugins/selectrotate.cpp,
  libavogadro/include/avogadro/molgeominfo.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/camera.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molgeominfo.cpp,
  libavogadro/src/molgeominfo.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: - much improved Draw::moveAtom: now moves the
  atom within the iso-z-distance of the molecule's center - introduce
  MolGeomInfo class, stores the geometric info of a molecule - take geom info
  out of class Molecule - remove Molecule's d-pointer (nothing left there) -
  remove mutex stuff in Molecule - add d->molGeomInfo member to GLWidget, MUST
  BE UPDATED BY HAND - fix Atom::position() (interfacing coord vectors with
  Eigen)   

2007-03-18  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/plugins/selectrotate.cpp, avogadro/src/plugins/selectrotate.h:
  Unscrew the selectrotate tool, after migration to the Camera class caused
  some damage. Donald: I hope I reproduced the original behavior, if not, just
  tell me.   

2007-03-16  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Make
  Primitive's d-pointer private Move Molecule's data to a d-pointer Cache the
  molecule geometric info. Still need to evaluate potential thread-safeness
  issues.   

2007-03-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Removed
  _vatom / _vbond from Molecule class (not needed) and fixed up the iterator
  stuff in primitives.cpp for Benoit.  (specifically the computGeometricInfo
  function).   

  * Doxyfile, avogadro/src/main.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/engine.h, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Document
  Changes. Merged in Benoit's changes.    

2007-03-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Implement computation and storage of geometric
  information in the Molecule class, replacing the former approach consisting
  in changing molecule coordinates.   

2007-03-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/aboutdialog.cpp,
  avogadro/src/flattabwidget.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/gamess.cpp, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/hydrogens.cpp, avogadro/src/plugins/selectrotate.cpp,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/primitives.cpp:
  Converted cmake files to use qt4_automoc format.  More KDE like.   

  * avogadro/src/CMakeLists.txt, avogadro/src/aboutdialog.cpp: about dialog
  compilation fixed.  thanks carsten.   

2007-03-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/CMakeLists.txt, avogadro/src/aboutdialog.cpp,
  avogadro/src/aboutdialog.h, avogadro/src/mainwindow.cpp: New about dialog.
  Here it works but I think the moc-thing is wrong. Could somebody with more
  moc-foo check this, please?  

2007-03-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/sphere.cpp: Add Molecule::centerAndFitInXYPlane() method.
  Just to demonstrate it, call it from GLWidget::setMolecule(). Some sparse
  cleanup in Cylinder and Sphere.   

2007-03-09  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Misspelled
  USING_DYNAMIC_LIBS.  What a mistake.  Fixed the CMakeLists.txt files. 

2007-03-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/plugins/gamessinputdialog.ui: Updated mainwindow.ui.  TODO:
  Refactor so that variables are named descriptionType instead of
  typeDescription.  All mainwindow actions need to be renamed.   

2007-03-08  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h: Remove a lot unused includes.
  Includes shouldn't be in .h-files, use forward declaration here 

2007-03-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.ui: Minor misspellings and added units
  to the recalculate hessian spin box.   

  * avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h,
  avogadro/src/plugins/gamessinputdialog.ui: Done with ui and working.   

2007-03-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/gamess.cpp,
  avogadro/src/plugins/gamess.h, avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputbuilder.ui,
  avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h,
  avogadro/src/plugins/gamessinputdialog.ui: Refactoring GamessInputBuilder ->
  GamessInputDialog.  More appropriately named.   

  * avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputbuilder.ui: My version of the dialog.  With
  tree and tabs etc etc.  Widgets named accordingly.  

  * libavogadro/src/cylinder.h, libavogadro/src/sphere.h: Needed Qt4OpenGL
  include so that GLuint named a type.   

  * avogadro/src/CMakeLists.txt, avogadro/src/plugins/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt: Updated include precedence.  Should fix some
  compile errors.  Just so that when you build you are getting the header files
  from your build directory and not the installed ones.   

2007-03-07  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Commit my patch: No
  inludes in the .h-file if possible 

2007-03-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.h, libavogadro/src/sphere.h: don't include
  QGLWidget when not needed; documentation fixes   

  * libavogadro/src/cylinder.cpp, libavogadro/src/sphere.cpp: Remove all
  mentions of the USE_DISPLAY_LISTS define, always use display lists (instead
  of never) for the sphere and cylinder.  This fixes an issue with the way avo
  reused the sphere/cylinder code from Kalzium: avo used a display list for the
  whole molecule, but not for the spheres and cylinders, which caused the
  geometric data and the opengl traffic of each sphere/cylinder to be
  replicated into the molecule display list. This caused the rendering to be
  unnecessarily slow and memory-consuming.   

2007-03-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/flattabwidget.cpp, avogadro/src/plugins/CMakeLists.txt:
  flattabwidget.cpp: return proper integer CMakeLists.txt: remove garbage left
  over from initial testing of gamess plugin. 

2007-03-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/gamess.cpp,
  avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h: GAMESS Input Deck Plugin Complete.
   Non-Modal Dialog.  

  * avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h: Gamess Interface Updates.  Still not
  incorporated into the plugin.  This will happen tomorrow.   

2007-03-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp: More changes to the GAMESS Input
  Deck Generator.  Almost finished.  Need to add some more specific
  information.  At some point a lot of the callbacks need to be refactored to
  another class.  For now they are alright.  This is very big and complex.  Not
  fun.   

  * avogadro/src/plugins/gamess.cpp, avogadro/src/plugins/gamess.h,
  avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h: Working good so far.  Not yet a
  plugin.   

2007-03-01  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamess.cpp, avogadro/src/plugins/gamess.h,
  avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h: Backing up before deleteing a bunch
  of unnecisary functions. Code taken from WxMacMolPlt GNU Licensed.   

2007-02-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * cmake/modules/FindAvogadro.cmake, cmake/modules/FindEigen.cmake: cmake
  files needed updating for finding paths correctly.   

2007-02-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.h, avogadro/src/plugins/ghemical.cpp: Tim
  Vandermeersch's Patch for ghemical.  Cleaned up mainwindow.h so it'd compile.
   

  * avogadro/src/CMakeLists.txt, avogadro/src/flattabwidget.cpp,
  avogadro/src/flattabwidget.h, avogadro/src/flowlayout.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Added new
  FlatTabWidget for Messages.  Needs working on but will be really sweet.   

2007-02-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/plugin.h,
  avogadro/src/plugins/ghemical.cpp, avogadro/src/plugins/ghemical.h,
  avogadro/src/plugins/hydrogens.cpp, avogadro/src/plugins/hydrogens.h:
  Messages are now printed to the messages window.  It's very hard to see but
  it's at the bottom of the GL area.  You can see a small dotten line, which
  you can drag up and see the messages.  I'm working on a better interface for
  this, unfortanly it's not built into the default QT widgets.  More to come.  

2007-02-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h: Some repeated
  code.  Factored out into the newBond function.   

2007-02-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt: Update build
  environment  

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/hydrogens.cpp: Update
  to fix draw and hydrogen problems from Begin/EndModify in OBMol.  

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/ghemical.h: Add support for Ghemical minimization using
  Open Babel OBForceField  

2007-02-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, avogadro/src/plugin.h,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/hydrogens.cpp,
  avogadro/src/plugins/hydrogens.h, libavogadro/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Fixed bug in
  glwidget.h with GLHit constructure being ill-defined. Updated cmake files to
  incorporated dependancy (multi-threaded make now works). Added plugin to
  Add/Removed Hydrogens.  Having problems which i believe are in OpenBabel.   

2007-02-09  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi, avogadro/avogadro.nsi: moved nsis file 

2007-02-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/selectrotate.cpp,
  libavogadro/src/engines/bsengine.cpp: corrected names. 

2007-02-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h: Add bond order
  to draw tool.   

2007-02-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/avogadro.nsi, avogadro/src/CMakeLists.txt,
  avogadro/src/icons/avogadro.ico, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/draw.h, avogadro/src/plugins/selectrotate.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitives.h: Updated WIN32
  compiling parameters, added icons/avogadro.ico and nsis installer file. 

  * libavogadro/CMakeLists.txt, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp: more WIN32 changes.  Added some GL defines that
  were missing.  added return value on GLHit = operator. 

  * avogadro/config.h.in, libavogadro/config.h.in: Cleaned up config.h 
  config.h should contain the install paths and version and package name. 
  Needs updating.   

  * avogadro/CMakeLists.txt, avogadro/config.h.in, libavogadro/CMakeLists.txt:
  Rather than using an include file for WIN32 we should just define it as a
  compile time definition.   

  * libavogadro/CMakeLists.txt, libavogadro/config-libavogadro.h.in,
  libavogadro/config.h.in, libavogadro/global.h.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/engine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: Done with changes. 
  Defines are properly setup.   

2007-02-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/CMakeLists.txt, libavogadro/config-libavogadro.h.in,
  libavogadro/config.h.in, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.h, libavogadro/src/cylinder.h,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.h, libavogadro/src/sphere.h: Broken for two min.  

  * libavogadro/src/moleculetreeview.h, libavogadro/src/sphere.cpp:
  MoleculeTreeView no longer has ambiguous constructor. Sphere no longer has
  ambiguous call to sqrt. 

  * libavogadro/CMakeLists.txt, libavogadro/config.h.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.h,
  libavogadro/src/cylinder.h, libavogadro/src/engine.h,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h, libavogadro/src/sphere.h: Update for WIN32
  defines for compilation on windows.  Exporting of DLL classes.  

2007-02-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: Updated plugin
  paths: split by colon...  PATH=/usr/bin:/bin:/usr/sbin (etc)  

2007-01-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/plugins/CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/moleculetreeview.cpp: Updated link commands to work on Mac OS
  X.  

2007-01-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Changed names /
  added QT_PROPERTIES.  Bulked up the lib.   

  * avogadro/include/avogadro/tool.h, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/plugin.h, avogadro/src/plugins/CMakeLists.txt,
  avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  avogadro/src/plugins/draw.png, avogadro/src/plugins/draw.qrc,
  avogadro/src/plugins/selectrotate.cpp, avogadro/src/plugins/selectrotate.h,
  avogadro/src/tool.h, avogadro/src/tools/CMakeLists.txt,
  avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  avogadro/src/tools/draw.png, avogadro/src/tools/draw.qrc,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h,
  libavogadro/src/glwidget.cpp: Merged Tools + Extensions = Plugins.   

2007-01-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/plugin.h: Fixed plugin.h to
  compile.   

2007-01-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/include/avogadro/plugin.h, avogadro/include/avogadro/tool.h,
  avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, avogadro/src/plugin.h,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/ghemical.h, avogadro/src/tool.cpp,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.h,
  avogadro/src/tools/selectrotate.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp: Added
  plugin interface (incomplete).  Added tabs at bottom for messages and other
  information we wish to have.   

  * avogadro/src/elementcombobox.cpp, avogadro/src/elementcombobox.h,
  libavogadro/src/elementcombobox.cpp, libavogadro/src/elementcombobox.h: Moved
  combobox to avogadro app.    

  * libavogadro/src/elementcombobox.cpp, libavogadro/src/elementcombobox.h:
  Modifications... will be moved.   

  * libavogadro/src/elementbox.cpp, libavogadro/src/elementbox.h,
  libavogadro/src/elementcombobox.cpp, libavogadro/src/elementcombobox.h:
  Rename   

  * avogadro/src/CMakeLists.txt, avogadro/src/flowlayout.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/tool.h, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/draw.h, avogadro/src/ui_mainwindow.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/elementbox.cpp,
  libavogadro/src/elementbox.h: Using generated ui.  Added tool properties. 
  adding ElementComboBox   

2007-01-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/selectrotate.cpp, libavogadro/CMakeLists.txt,
  libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/engine.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/primitives.h,
  libavogadro/include/avogadro/sphere.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.cpp, libavogadro/src/cylinder.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/sphere.cpp: Updated cmake
  files and added psuedo include dir.   

  * avogadro/src/flowlayout.cpp, avogadro/src/flowlayout.h: Missing files!   

  * avogadro/src/tool.h, avogadro/src/tools/draw.cpp: updated tooltip / text
  minor change.   

  * avogadro/src/CMakeLists.txt, avogadro/src/tool.h,
  avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h:
  Updated name() and description() to const functions.  Made it so that if a
  tool doesn't defined an Icon / Text / Tooltip it will be correctly populated
  using name() and description().   

  * avogadro/src/CMakeLists.txt, avogadro/src/avogadro.qrc,
  avogadro/src/icons/colorize.png, avogadro/src/icons/exit.png,
  avogadro/src/icons/fileclose.png, avogadro/src/icons/fileexport.png,
  avogadro/src/icons/filenew.png, avogadro/src/icons/fileopen.png,
  avogadro/src/icons/filesave.png, avogadro/src/icons/filesaveas.png,
  avogadro/src/icons/help.png, avogadro/src/icons/redo.png,
  avogadro/src/icons/revert.png, avogadro/src/icons/tool.png,
  avogadro/src/icons/undo.png, avogadro/src/icons/window_fullscreen.png,
  avogadro/src/icons/window_nofullscreen.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, avogadro/src/tool.h,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/draw.h, avogadro/src/tools/draw.png,
  avogadro/src/tools/draw.qrc, avogadro/src/tools/selectrotate.cpp,
  avogadro/src/tools/selectrotate.h, avogadro/src/ui_mainwindow.h,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: ui_mainwindow.h defines Ui::MainWindow which is
  a private member of Avogadro::MainWindow.  QTDesigner does a crappy job with
  naming the layouts and embedding widgets within widgets that don't need to be
  that way.  There is a bit of renaming done so that we can use our FlowLayout
  (ripped from the tutorials).  Added icons to actions.  Images are from
  CrystalClear collection.  Made libavogadro const-correct as well as
  implementing the d-pointer technique in glWidget and Primitives classes. 
  Figured out a memory leak in OpenBabel.  Updated the TreeView to match
  pointers rather than indexes.  This could become a bottleneck if we have to
  delete a lot of primitives from a big molecule. We'll tackle that when we
  cross that bridge.  Would give us something like O(n^2) when we should really
  have O(n).  Although that could be wrong i was never good with big O.  Added
  resource files.  Plugins now define an action which selects them.  They can
  connect to the callback but it doesn't them little good.  The MainWindow
  decides what tool gets called.  This just gives the plugin the ability to
  define it's own tooltips / icon.  tool.h defines a default action but this
  action doesn't get any information from the implemented plugin.   

2007-01-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitives.h: Added const
  correctness.   

2007-01-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  avogadro/src/tools/selectrotate.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp: Draw
  tools done.  Fixed some bugs.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Can now draw
  atoms into the model.  No bonds yet but it also updates the treewidget
  through callbacks.  However, primitiveAdded(Primitive *) should actually be
  admitted *after* the primitive has been added to the model. Otherwise we
  would need to overload everytime that the indexes change.  Need to discuss
  further with Geoff and crew.   

  * avogadro/src/avogadro.pro, avogadro/src/src.pro,
  avogadro/src/tools/SelectRotate.pro, avogadro/src/tools/tools.pro: Cleanup. 
  Old Project files we don't need.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Rather than using a view on top of a model i
  created a custom view widget for our Primitive::Molecule.  I haven't updated
  all the signals but this is now what we will use.  It looks better and is
  easier to manage.  Plus I got it looking sweeet.   

2007-01-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/primitives.cpp: New Molecule is Working... signal to GLWidget
  needs to be updated.   

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/projectmodel.cpp,
  avogadro/src/projectmodel.h: Updated to use new Molecule which has
  QAbstractItemModel.   

  * libavogadro/src/moleculemodel.cpp, libavogadro/src/moleculemodel.h:
  Cleanup!   

  * libavogadro/src/moleculemodel.cpp, libavogadro/src/moleculemodel.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/projectmodel.cpp, libavogadro/src/projectmodel.h: Moved
  MoleculeModel *into* Molecule.  Thus, a Molecule acts as a
  QAbstractItemModel.   

  * libavogadro/src/CMakeLists.txt, libavogadro/src/projectmodel.cpp,
  libavogadro/src/projectmodel.h: Moved ProjectModel to library.   

  * avogadro/src/mainwindow.cpp, avogadro/src/projectmodel.cpp,
  avogadro/src/projectmodel.h, avogadro/src/tools/selectrotate.cpp,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.h: Updated the primitives enum.  Also reworked
  ProjectModel so that it works directly with the molecule.  Should be moved to
  the library.  The view needs to be updated so that it subgroups.  This should
  not be part of the model.  (ie. the model should not contain "dummy" nodes
  just so that we have groupings of Atoms, Bonds, Residues.). 
  Avogadro::GLWidget needs to be updated to use the MoleculeModel instead of
  working on the Molecule itself.   

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/projectmodel.cpp,
  avogadro/src/projectmodel.h, avogadro/src/projecttree.cpp,
  avogadro/src/projecttree.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Added Docks for
  Tools and for the Project Layout.  The project layout is model/view. 
  ProjectModel, given a molecule, sets up the model for the molecular view. 
  I'm not sure if this is the correct place for this.  I believe it could go
  into the libavogadro.  It's a tossup because we may want to have our Model be
  the basis for interaction with the library but the way the GL engine is
  setup, it takes primitives directly to render them. This isn't a problem as
  we can setup our primitives to act as nodes of the model.  Will think about
  this more.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/projecttree.cpp, avogadro/src/projecttree.h: Adding project
  model.   

2007-01-05  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp: Minor
  Changes   

  * avogadro/src/tools/draw.cpp, avogadro/src/tools/selectrotate.cpp,
  avogadro/src/tools/selectrotate.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Draw tool now
  draws.  Need to refine these tools.  Also need configuration system
  implemented for the tools.  TODO: create a Tool Properties Dialog.   

  * CMakeLists.txt, avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/draw.h, avogadro/src/tools/selectrotate.cpp,
  avogadro/src/tools/selectrotate.h, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/vertexarray.cpp,
  libavogadro/src/engines/vertexarray.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Added the drawing tool but it doesn't work. 
  There is no code.  Had an issue where the header files were included from the
  wrong location.  Should be easy to implement the drawing tool in the next
  day.  Also need to build an extension for other plugins (gamess /
  libghemical).  Should be interesting then.   

2007-01-04  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/tool.h,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h,
  libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitives.h: Should compile and run.  bsengine is Ball and
  Stick and currently works.  Need to bring the other stuff up to date.  the
  select&rotate tool now works too.  haven't finished cleaning up the functions
  and working on creating the drawing tool.   

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/tools/SelectRotate.cpp, avogadro/src/tools/SelectRotate.h,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h,
  libavogadro/CMakeLists.txt, libavogadro/FindOpenBabel.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/sphere.cpp: Should compile now.
   Must checkout the whole trunk to build the cmake files.   

2007-01-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, avogadro/FindAvogadro.cmake,
  cmake/modules/FindAvogadro.cmake, cmake/modules/FindEigen.cmake,
  cmake/modules/FindOpenBabel2.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: Added cmake/modules for
  CMAKE building.   

  * AUTHORS, COPYING, ChangeLog, Doxyfile, INSTALL, NEWS, README, avogadro.pro,
  avogadro/AUTHORS, avogadro/CMakeLists.txt, avogadro/COPYING,
  avogadro/ChangeLog, avogadro/Doxyfile, avogadro/FindAvogadro.cmake,
  avogadro/FindOpenBabel.cmake, avogadro/INSTALL, avogadro/NEWS,
  avogadro/README, avogadro/avogadro.pro, avogadro/src/avogadro.pro,
  avogadro/src/avogadro.ui, avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/src.pro, avogadro/src/tool.cpp,
  avogadro/src/tool.h, avogadro/src/tools/SelectRotate.cpp,
  avogadro/src/tools/SelectRotate.h, avogadro/src/tools/SelectRotate.pro,
  avogadro/src/tools/tools.pro, avogadro/untitled01.gpr,
  libavogadro/CMakeLists.txt, libavogadro/FindOpenBabel.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/engine.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ResidueSphereEngine.cpp,
  libavogadro/src/engines/ResidueSphereEngine.h,
  libavogadro/src/engines/SphereEngine.cpp,
  libavogadro/src/engines/SphereEngine.h,
  libavogadro/src/engines/StickEngine.cpp,
  libavogadro/src/engines/StickEngine.h,
  libavogadro/src/engines/WireframeEngine.cpp,
  libavogadro/src/engines/WireframeEngine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/vertexarray.cpp,
  libavogadro/src/engines/vertexarray.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h, src/Engine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/Primitives.cpp, src/Primitives.h,
  src/Renderer.h, src/Tool.cpp, src/Tool.h, src/Views.cpp, src/Views.h,
  src/avogadro.pro, src/avogadro.ui, src/color.cpp, src/color.h,
  src/engines/BSEngine.cpp, src/engines/BSEngine.h, src/engines/BSEngine.pro,
  src/engines/ResidueSphereEngine.cpp, src/engines/ResidueSphereEngine.h,
  src/engines/ResidueSphereEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/SphereEngine.pro,
  src/engines/StickEngine.cpp, src/engines/StickEngine.h,
  src/engines/StickEngine.pro, src/engines/WireframeEngine.cpp,
  src/engines/WireframeEngine.h, src/engines/WireframeEngine.pro,
  src/engines/engines.pro, src/engines/vertexarray.cpp,
  src/engines/vertexarray.h, src/main.cpp, src/src.pro,
  src/tools/SelectRotate.cpp, src/tools/SelectRotate.h,
  src/tools/SelectRotate.pro, src/tools/tools.pro: Moving things around. 
  Conforming to a more KDE-like layout in SVN.  I'm going nuts.  SOrry  

2007-01-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLWidget.cpp, src/GLWidget.h, src/Tool.cpp, src/Tool.h,
  src/avogadro.pro, src/src.pro, src/tools/SelectRotate.cpp,
  src/tools/SelectRotate.h, src/tools/SelectRotate.pro, src/tools/tools.pro:
  Added Tool interface and SelectRotate tool.   

  * src/engines/BSEngine.cpp, src/engines/StickEngine.cpp,
  src/engines/WireframeEngine.cpp: Changed GetBgn to GetBeginAtom   

2006-09-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/MainWindow.cpp, src/MainWindow.h, src/main.cpp: Change QMessageWindowEx
  to QMessageWindow (for rc1 snapshot)  

2006-09-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/Engine.h, src/GLWidget.cpp, src/GLWidget.h, src/Primitives.h,
  src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/StickEngine.cpp, src/engines/StickEngine.h: Added PrimitiveQueue
  class to Engine.h which is now instanciated for each Engine.   

2006-09-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, src/Engine.h, src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/Primitives.cpp, src/Primitives.h,
  src/Views.cpp, src/Views.h, src/engines/BSEngine.h,
  src/engines/ResidueSphereEngine.h, src/engines/SphereEngine.h,
  src/engines/StickEngine.h, src/engines/WireframeEngine.h: Refactored GLEngine
  to Engine.   

2006-09-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/GLWidget.cpp, src/GLWidget.h, src/SphereRender.cpp,
  src/SphereRender.h, src/StickRender.cpp, src/StickRender.h, src/avogadro.pro,
  src/color.cpp, src/color.h, src/engines/BSEngine.cpp,
  src/engines/BSEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.pro, src/engines/StickEngine.cpp,
  src/engines/StickEngine.pro, src/engines/WireframeEngine.cpp,
  src/engines/WireframeEngine.pro, src/engines/vertexarray.cpp,
  src/engines/vertexarray.h: * src/color.h, src/color.cpp: Migrate Color class
  out of vertexarray files, to allow further colormaps (e.g., color by other
  atomic or residue properties).  * src/*: Use Color() class.  

2006-08-31  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, src/GLWidget.cpp, src/GLWidget.h: Added group selection.  see
  GLWidget::selectRegion()   

  * ChangeLog, src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/Primitives.cpp, src/Primitives.h, src/Views.cpp, src/Views.h,
  src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/ResidueSphereEngine.cpp, src/engines/SphereEngine.cpp,
  src/engines/StickEngine.cpp, src/engines/WireframeEngine.cpp: *
  src/Primitives.h: moved the glnametypeing enum to here as enum primativeType 
  * src/Primitives.cpp: Overwrote OBMol::CreateResidue (trunk version of OB)  *
  src/GLWidget.cpp: _hits now containts both .type and .name corresponding to
  the type if hit and the name of the hit.   

2006-08-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/Primitives.h, src/Views.cpp,
  src/Views.h, src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/ResidueSphereEngine.cpp, src/engines/ResidueSphereEngine.h,
  src/engines/ResidueSphereEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h, src/engines/WireframeEngine.cpp,
  src/engines/WireframeEngine.h, src/engines/engines.pro: * src/MainWindow.h,
  src/MainWindow.cpp, src/GLWidget.h, src/GLWidget.cpp: Move molecule storage
  (for now) to the GL widget to allow atom selection.  * src/Primitives.h: Add
  marker to indicate that a particular object was selected by the user.  *
  src/Views.h, src/Views.cpp: Add support for ResidueView, as well as
  whole-molecule rendering.  * src/engines/ResidueSphereEngine.*: New render
  engine drawing spheres for residues in PDB files. Illustrates whole molecule
  render option.  * src/GLEngine.h: Add glSelection enum for glPushName()
  entries to deliniate between molecule, atom, bond, residue, etc. picking.
  Render engines are responsible for using these as appropriate for a
  particular user view.  * src/engines/*: Update for glPushName() for atoms and
  hilights when an atom is selected.   

2006-08-29  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, src/GLWidget.cpp, src/GLWidget.h: * src/GLWidget.cpp: Initial
  group selection code.  Needs work still.  When you double-click to open a
  file it registers the mouse as having moved.  This generates a selection box.
    

  * ChangeLog, src/GLWidget.cpp: Updated the perspective code and added
  "picking".  Will work on drag to select also.   

2006-08-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h, src/Primitives.h,
  src/avogadro.pro, src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/BSEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h, src/engines/StickEngine.pro,
  src/engines/WireframeEngine.cpp, src/engines/WireframeEngine.h,
  src/engines/WireframeEngine.pro, src/engines/vertexarray.h, src/main.cpp:
  Updates to use vertex array classes for rendering. Much, much faster.  

  * ChangeLog, src/MainWindow.cpp, src/MainWindow.h: * src/MainWindow.h,
  src/MainWindow.cpp: Add full screen rendering and background color. (Needed
  for upcoming ACS presentations.)   

  * src/engines/SphereEngine.cpp, src/engines/SphereEngine.h: Minor update to
  actually show atoms. Not sure why previous version shows nothing.  

  * ChangeLog, src/GLWidget.cpp, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/SphereEngine.pro,
  src/engines/WireframeEngine.cpp, src/engines/WireframeEngine.h,
  src/engines/WireframeEngine.pro, src/engines/engines.pro,
  src/engines/vertexarray.cpp, src/engines/vertexarray.h: * src/GLWidget.cpp:
  Make sure to enable vertex arrays (for Benoit's sphere/cylinder classes.  *
  src/engines/vertextarray.cpp, src/engines/vertexarray.h: Moved Benoit's
  vertex array sphere and cylinder from Kalzium.  *
  src/engines/WireframeEngine.*: New class for a wireframe view. (Should be
  made a static plugin and the default view, but don't have time right now.)  *
  src/engines/SphereEngine.*: New class for van der Waals spheres using
  Benoit's classes. Very fast.   

2006-08-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLEngine.h, src/engines/BSEngine.h, src/engines/StickEngine.h: More
  documentation updates.   

  * Doxyfile, src/GLEngine.h, src/engines/BSEngine.h,
  src/engines/StickEngine.h: Added Doxyfile for documentation generation
  through doxygen and added comments to the Engine files.   

2006-08-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/MainWindow.cpp: * src/MainWindow.cpp: Make sure to update
  recent file list when creating a new window, and make sure to call updateGL
  after reading a file. Fixes minor bugs.  

2006-08-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLWidget.cpp, src/GLWidget.h, src/engines/BSEngine.h,
  src/engines/StickEngine.h: Updated Description (should not include "Engine"
  Added slots for setting the GLWidget renderer.   

  * src/MainWindow.cpp, src/MainWindow.h: Added engine selection ComboBox.   

2006-08-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h, src/Primatives.cpp,
  src/Primatives.h, src/Primitives.cpp, src/Primitives.h, src/Renderer.h,
  src/Views.cpp, src/Views.h, src/avogadro.pro, src/engines/BSEngine.cpp,
  src/engines/BSEngine.h, src/engines/BSEngine.pro,
  src/engines/StickEngine.cpp, src/engines/StickEngine.h,
  src/engines/StickEngine.pro: Rename Prim-a-tive to Primitive (correct
  spelling). Add a fallback for finding plugins to environment variable:
  AVOGADRO_PLUGINS  This enables plugin support on Mac OS X.  

2006-08-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLEngine.h, src/Views.cpp, src/engines/BSEngine.cpp,
  src/engines/BSEngine.h, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h: Updated GLEngine interface to only implement
  .render(<subclass of Primative> *).   

  * src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h, src/MainWindow.cpp,
  src/MainWindow.h, src/Primatives.cpp, src/Primatives.h, src/Views.cpp,
  src/Views.h, src/avogadro.pro, src/engines/BSEngine.cpp,
  src/engines/BSEngine.h, src/engines/SBSEngine.cpp, src/engines/SBSEngine.h,
  src/engines/SBSEngine.pro, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h, src/engines/StickEngine.pro,
  src/engines/engines.pro: Refactored Renderer -> GLEngine  StickEngine &
  BSEngine both run. (although they need some fixes).  Major Modifications. 
  See mailing list.   

  * src/engines/BSEngine.cpp, src/engines/BSEngine.h, src/engines/BSEngine.pro,
  src/engines/BSRenderer.cpp, src/engines/BSRenderer.h,
  src/engines/BSRenderer.pro, src/engines/SBSEngine.cpp,
  src/engines/SBSEngine.h, src/engines/SBSEngine.pro,
  src/engines/SBSRenderer.cpp, src/engines/SBSRenderer.h,
  src/engines/SBSRenderer.pro, src/engines/engines.pro: Refactoring: Renderer
  -> Engine   

2006-08-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * autogen.sh, configure.ac: Cleaning up old GNU stuff from the main
  directory.   

  * src/MainWindow.cpp, src/MainWindow.h: MainWindow now dynamically loads
  rendering engines.  There is currently no way to select the default and there
  is not NULL check as of yet.  Thats is to come.   

  * src/avogadro.pro, src/src.pro: src is now a qmake that does recursive
  building.  avogadro.pro builds the binary.   

  * src/Primatives.cpp, src/Primatives.h: These are molecule primatives; ie.
  wrappers around the OBAtom / OBBond / OBMol classes.  They are used to set
  graphical attributes of the primatives and allows us to call render on the
  individuals.   

  * src/BSRender.cpp, src/BSRender.h: These have been moved to the pluggable
  engines directory.   

  * src/engines/BSRenderer.cpp, src/engines/BSRenderer.h,
  src/engines/BSRenderer.pro, src/engines/SBSRenderer.cpp,
  src/engines/SBSRenderer.h, src/engines/SBSRenderer.pro,
  src/engines/engines.pro: Rendering Engines have been added.   

2006-08-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/MainWindow.cpp, src/MainWindow.h: * src/MainWindow.h,
  src/MainWindow.cpp: Fix saveFile -- make sure to call SetOutFormat() not
  SetInFormat()! Works great now. Added code to save settings for window
  position and size.  

2006-08-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLWidget.cpp, src/MainWindow.cpp, src/main.cpp: * MainWindow (see line
  82 TODO) - Temporarily fixed the open bug. * GLWidget - Modified the rotate
  so that the molecule rotates more normal. Also did some reformatting.   

2006-08-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/MainWindow.cpp, src/MainWindow.h: * src/MainWindow.cpp:
  Check to see if a file is already in a window -- raise it if needed, rather
  than opening another copy. Implement exportGraphics with
  QGLWidget::grabFrameBuffer. Doesn't allow oversampling, but works.  

  * src/GLWidget.cpp, src/GLWidget.h: * src/GLWidget.cpp: Improved scale/zoom
  feature and added calls for adding screen coordinates (e.g., for seelction
  rectangle).   

2006-08-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/BSRender.cpp, src/BSRender.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/SphereRender.cpp,
  src/SphereRender.h, src/StickRender.cpp, src/StickRender.h, src/main.cpp:
  Merge of current development code. Sometimes buggy, as explained in message. 

2006-08-18  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/ABSRender.cpp, src/ABSRender.h, src/AGLWidget.cpp, src/AGLWidget.h,
  src/AMainWindow.cpp, src/AMainWindow.h, src/ASphereRender.cpp,
  src/ASphereRender.h, src/AStickRender.cpp, src/AStickRender.h,
  src/BSRender.cpp, src/BSRender.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/SphereRender.cpp,
  src/SphereRender.h, src/StickRender.cpp, src/StickRender.h, src/avogadro.pro:
  Renamed files.  We user the 'Avogadro' namespace.  Naming the files with A*
  is redundant.   

2006-08-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/ABSRender.cpp, src/ABSRender.h, src/AGLWidget.cpp, src/AGLWidget.h,
  src/AMainWindow.cpp, src/AMainWindow.h, src/AStickRender.cpp,
  src/AStickRender.h, src/avogadro.pro, src/avogadro.ui, src/main.cpp: Added
  additional rendering options. Moving towards a more full-featured GUI.  

2006-08-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/AGLWidget.cpp, src/AGLWidget.h, src/AMainWindow.cpp,
  src/ASphereRender.cpp: Added initial support for rotation.  

  * ChangeLog, src/AGLWidget.cpp, src/AMainWindow.cpp, src/AMainWindow.h,
  src/ASphereRender.cpp, src/ASphereRender.h, src/avogadro.pro: Sample renderer
  (still OpenGL glitches). When a molecule is opened, a set of VdW spheres is
  rendered with the appropriate colors.  

2006-08-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/AGLWidget.cpp, src/ASphereRender.cpp, src/ASphereRender.h: More
  experiments.  

  * src/AGLWidget.cpp, src/AMainWindow.cpp, src/AMainWindow.h,
  src/avogadro.pro: More experiments.  

  * ChangeLog, src/AGLWidget.cpp, src/AGLWidget.h: * src/AGLWidget.h,
  src/AGLWidget.cpp: Add support for rendering GL display lists -- renderer
  classes should generate a display list and pass it off to the widget.  

  * src/AMainWindow.cpp, src/AMainWindow.h, src/main.cpp: Switch back to custom
  main window -- easier to add slots for commands. (Not sure why menu doesn't
  show up on Mac OS X.)  

2006-08-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/AMainWindow.cpp, src/avogadro.pro, src/avogadro.ui,
  src/main.cpp: * src/avogadro.ui: Use QDesigner to layout some menu items and
  toolbar.  * src/main.cpp, src/AMainWindow.cpp, src/avogadro.pro: Use it.  

2006-05-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/AGLWidget.cpp, src/AGLWidget.h, src/AMainWindow.cpp, src/AMainWindow.h,
  src/avogadro.pro, src/main.cpp: Demo includes a toolbar and GL widget.   

2006-04-28  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * AUTHORS, COPYING, ChangeLog, INSTALL, NEWS, src/main.cpp: Tutorial time.   

  * src/AWindow.cpp, src/AWindow.h: Fixed   

  * src/AWindow.cpp, src/AWindow.h, src/main.cpp, src/main.h: Bad Changes.   

  * Makefile.am, autogen.sh, configure.ac, src/Makefile.am, src/defines.h,
  src/main.cpp, src/main.h: GNU Basics 
