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Class: Symmetry


    Single symmetry that applies to MolSystem.Each Symmetry describes a set of chain segents that are symmetric under some symmetry operation, such as C2 or C3. You would need several Symmetry objects to describe a Symmetry group such as C3v, or even to describe a simple C2 symmetry of a multichain MolSystem.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link molSystemSymmetrySet to class MolSystemSymmetrySet
Main key: serial
Mandatory Attributes: None
Known Subclasses: None
Children:
link segments to class Segment
Constructor: newObj = Symmetry( molSystemSymmetrySet, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
segmentLength PositiveInt 0..1 Length of segments that are symmetrical  
serial Int 1..1 Serial number of object. Serves as object main key. Serial numbers of deleted objects are not re-used. Serial numbers can only be set by the implementation. Values are in practice always positive, since negative values are interpreted as a signal to set the next free serial  
symmetryCode SymmetryOpCode 0..1  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
haddockRuns utrecht.api.Haddock.Run 0..* Haddock Runs using the Symmetry  
molSystemSymmetrySet MolSystemSymmetrySet 1..1 (Parent link). parent link  
parent MolSystemSymmetrySet 1..1 link to parent object - synonym for molSystemSymmetrySet  
segments Segment 0..* (Child link). child link to class Segment  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
segmentLength
getSegmentLength PositiveInt -
setSegmentLength - PositiveInt
serial
getSerial Int -
setSerial - Int
symmetryCode
getSymmetryCode SymmetryOpCode -
setSymmetryCode - SymmetryOpCode

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
haddockRuns
getHaddockRuns utrecht.api.Haddock.Run Set -
setHaddockRuns - utrecht.api.Haddock.Run Set
sortedHaddockRuns utrecht.api.Haddock.Run List -
addHaddockRun - utrecht.api.Haddock.Run
removeHaddockRun - utrecht.api.Haddock.Run
findFirstHaddockRun utrecht.api.Haddock.Run keyword=value pairs
findAllHaddockRuns utrecht.api.Haddock.Run Set keyword=value pairs
molSystemSymmetrySet
getMolSystemSymmetrySet MolSystemSymmetrySet -
parent
getParent MolSystemSymmetrySet -
segments
getSegments Segment Set -
sortedSegments Segment List -
findFirstSegment Segment keyword=value pairs
findAllSegments Segment Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Symmetry memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey Any -
get Any String
set - String, Any

Factory Methods (in package)

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Method Return Parameters
newSegment Segment chainCode, firstSeqId, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2008-02-20-18:17:09_00002

isImplicit:

False

Tag

Value
repositoryId $Id: Symmetry.xml,v 1.17 2011-01-13 14:40:37 rhfogh Exp $

Tag

Value
repositoryTag $Name: not supported by cvs2svn $

Special constructor code:

None

Special destructor code:

None

Constraint name:

segments_do_not_overlap
Constraint code: isValid = True
segments = self.sortedSegments()
if segments:
  segLength = self.segmentLength
  chainCodes = [x.chainCode for x in segments]
  seqIds = [x.firstSeqId for x in segments]
  for ii in range(len(segments) - 1):
    if chainCodes[ii] == chainCodes[ii+1] and seqIds[ii+1] - seqIds[ii] < segLength:
      isValid = False
      break
Known inward one-way links: None
  Data Model Version 2.0.6
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Wed Aug 7 15:06:36 2013    from data model package  molsim.api.Symmetry.Symmetry   revision 1.17  
  Work done by the CCPN team.
www.ccpn.ac.uk