mmLib.Structure.AtomOverwrite:
Raised by Structure.add_atom() or Fragment.add_atom() when an Atom
added to a Structure or Fragment has the same chain_id,
fragment_id, name, and alt_loc as an Atom already in the Structure
or Fragment.
mmLib.Structure.ChainOverwrite:
Raised by Structure.add_chain() or by Model.add_chain() when a
Chain added to a Structure has the same chain_id of a Chain already
in the Structure.
mmLib.Structure.FragmentOverwrite:
Raised by Chain.add_fragment() when a Fragment added to a Chain has
the same fragment_id as a Fragment already in the Chain.
mmLib.Structure.ModelOverwrite:
Raised by Structure.add_model() when a Model added to a Structure
has the same model_id of a Model already in the Structure.
dict:
dict() -> new empty dictionary
dict(mapping) -> new dictionary initialized from a mapping object's
(key, value) pairs
dict(iterable) -> new dictionary initialized as if via:
d = {}
for k, v in iterable:
d[k] = v
dict(**kwargs) -> new dictionary initialized with the name=value pairs
in the keyword argument list.
mmLib.Structure.Altloc:
Container holding the same atom, but for different conformations
and occupancies.
mmLib.PDB.DBREF:
The DBREF record provides cross-reference links between PDB
sequences and the corresponding database entry or entries.
mmLib.PDB.END:
The END record marks the end of the PDB file.
mmLib.PDB.ENDMDL:
The ENDMDL records are paired with MODEL records to group
individual structures found in a coordinate entry.
mmLib.PDB.EXPDTA:
The EXPDTA record presents information about the experiment.
mmLib.PDB.FORMUL:
The FORMUL record presents the chemical formula and charge of a
non-standard group.
mmLib.PDB.HEADER:
This section contains records used to describe the experiment and
the biological macromolecules present in the entry: HEADER, OBSLTE,
TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT,
SPRSDE, JRNL, and REMARK records.
mmLib.PDB.HELIX:
HELIX records are used to identify the position of helices in the
molecule.
mmLib.PDB.HET:
The HET records are used to describe non-standard residues, such as
prosthetic groups, inhibitors, solvent molecules, and ions for
which coordinates are supplied.
mmLib.PDB.HETNAM:
This record gives the chemical name of the compound with the given
hetID.
mmLib.PDB.HETSYN:
This record provides synonyms, if any, for the compound in the
corresponding (i.e., same hetID) HETNAM record.
mmLib.PDB.HYDBND:
The HYDBND records specify hydrogen bonds in the entry.
mmLib.PDB.JRNL:
The JRNL record contains the primary literature citation that
describes the experiment which resulted in the deposited coordinate
set.
mmLib.PDB.KEYWDS:
The KEYWDS record contains a set of terms relevant to the entry.
mmLib.PDB.LINK:
The LINK records specify connectivity between residues that is not
implied by the primary structure.
mmLib.PDB.MASTER:
The MASTER record is a control record for bookkeeping.
mmLib.PDB.MODEL:
The MODEL record specifies the model serial number when multiple
structures are presented in a single coordinate entry, as is often
the case with structures determined by NMR.
mmLib.PDB.MODRES:
The MODRES record provides descriptions of modifications (e.g.,
chemical or post-translational) to protein and nucleic acid
residues.
mmLib.PDB.MTRIXn:
The MTRIXn (n = 1, 2, or 3) records present transformations
expressing non-crystallographic symmetry.
mmLib.PDB.OBSLTE:
OBSLTE appears in entries which have been withdrawn from
distribution.
mmLib.PDB.ORIGXn:
The ORIGXn (n = 1, 2, or 3) records present the transformation from
the orthogonal coordinates contained in the entry to the submitted
coordinates.
mmLib.PDB.REMARK:
REMARK records present experimental details, annotations, comments,
and information not included in other records.
mmLib.PDB.REVDAT:
REVDAT records contain a history of the modifications made to an
entry since its release.
mmLib.PDB.SCALEn:
The SCALEn (n = 1, 2, or 3) records present the transformation from
the orthogonal coordinates as contained in the entry to fractional
crystallographic coordinates.
mmLib.PDB.SEQADV:
The SEQADV record identifies conflicts between sequence information
in the ATOM records of the PDB entry and the sequence database
entry given on DBREF.
mmLib.PDB.SEQRES:
The SEQRES records contain the amino acid or nucleic acid sequence
of residues in each chain of the macromolecule that was studied.
mmLib.PDB.SHEET:
SHEET records are used to identify the position of sheets in the
molecule.
mmLib.PDB.SIGATM:
The SIGATM records present the standard deviation of atomic
parameters as they appear in ATOM and HETATM records.
mmLib.PDB.SIGUIJ:
The SIGUIJ records present the standard deviations of anisotropic
temperature factors scaled by a factor of 10**4 (Angstroms**2).
mmLib.PDB.SITE:
The SITE records supply the identification of groups comprising
important sites in the macromolecule.
mmLib.PDB.SLTBRG:
The SLTBRG records specify salt bridges in the entry.
mmLib.PDB.SOURCE:
The SOURCE record specifies the biological and/or chemical source
of each biological molecule in the entry.
mmLib.PDB.SPRSDE:
The SPRSDE records contain a list of the ID codes of entries that
were made obsolete by the given coordinate entry and withdrawn from
the PDB release set.
mmLib.PDB.SSBOND:
The SSBOND record identifies each disulfide bond in protein and
polypeptide structures by identifying the two residues involved in
the bond.
mmLib.PDB.TER:
The TER record indicates the end of a list of ATOM/HETATM records
for a chain.
mmLib.PDB.TITLE:
The TITLE record contains a title for the experiment or analysis
that is represented in the entry.
mmLib.PDB.TURN:
The TURN records identify turns and other short loop turns which
normally connect other secondary structure segments.
mmLib.PDB.TVECT:
The TVECT records present the translation vector for infinite
covalently connected structures.
mmLib.mmCIF.mmCIFFileParser:
Stateful parser which uses the mmCIFElementFile tokenizer to read a
mmCIF file and convert it into the mmCIFData/mmCIFTable/mmCIFRow
data hierarchy.