Data Model version 2.1.2
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Class: AtomSetMapping

The AtomSetMapping constructor includes non-standard actions.
    Stores (pseudo)atom and residue name to use for display, graphical user interfaces etc., and links to appropriate Residue, AtomSets, and ChemAtomSet.

    NB the various links are not independent, and the API does *not* guarantee consistency. It is up to CcpNmr Analysis to make sure the information is up-to-date. This behaviour is only tolerated because this is a program-specific part of the model.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link residueMapping to class ResidueMapping
Main key: name
Mandatory Attributes: name
Known Subclasses: None
Children: None
Constructor: newObj = AtomSetMapping( residueMapping,name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
atomSetSerials Int 0..* serial numbers of atomSets represented by the mapping  
elementSymbol Word 1..1 Element symbol of element corresponding to AtomSets. Automatically calculated at creation time.  
mappingType ccpnmr.api.Analysis.MappingType 1..1 whether the mapping is simple, ambiguous (points to multiple other mappings), nonstereo (non-stereospecific prochiral like Hba or Hbb) or stereo (like Hb2 or Hb3)  
name Word 1..1 (pseudo)atom name.  
resonanceSerials Int 0..* serial numbers of resonances represented by the mapping, keys for derived link  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
atomSetMappings AtomSetMapping 0..* the AtomSetMappings contained by the AtomSetMapping, often used to specify that an ambiguous mapping contains non-ambiguous mappings  
atomSets ccp.api.nmr.Nmr.AtomSet 0..* Derived. the AtomSet represented by the AtomSetMapping  
chemAtomSet ccp.api.molecule.ChemComp.ChemAtomSet 0..1 the ChemAtomSet represented by the AtomSetMapping  
parent ResidueMapping 1..1 link to parent object - synonym for residueMapping  
residueMapping ResidueMapping 1..1 (Parent link). parent link  
resonances ccp.api.nmr.Nmr.Resonance 0..* Derived. Resonances that AtomSetMapping is associated with. This link does not have to be filled in.  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atomSetSerials
getAtomSetSerials Int Set -
setAtomSetSerials - Int Set
addAtomSetSerial - Int
removeAtomSetSerial - Int
elementSymbol
getElementSymbol Word -
setElementSymbol - Word
mappingType
getMappingType ccpnmr.api.Analysis.MappingType -
setMappingType - ccpnmr.api.Analysis.MappingType
name
getName Word -
setName - Word
resonanceSerials
getResonanceSerials Int Set -
setResonanceSerials - Int Set
addResonanceSerial - Int
removeResonanceSerial - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atomSetMappings
getAtomSetMappings AtomSetMapping Set -
setAtomSetMappings - AtomSetMapping Set
sortedAtomSetMappings AtomSetMapping List -
addAtomSetMapping - AtomSetMapping
removeAtomSetMapping - AtomSetMapping
findFirstAtomSetMapping AtomSetMapping keyword=value pairs
findAllAtomSetMappings AtomSetMapping Set keyword=value pairs
atomSets
getAtomSets ccp.api.nmr.Nmr.AtomSet Set - non-std.
sortedAtomSets ccp.api.nmr.Nmr.AtomSet List -
findFirstAtomSet ccp.api.nmr.Nmr.AtomSet keyword=value pairs
findAllAtomSets ccp.api.nmr.Nmr.AtomSet Set keyword=value pairs
chemAtomSet
getChemAtomSet ccp.api.molecule.ChemComp.ChemAtomSet -
setChemAtomSet - ccp.api.molecule.ChemComp.ChemAtomSet
parent
getParent ResidueMapping -
residueMapping
getResidueMapping ResidueMapping -
resonances
getResonances ccp.api.nmr.Nmr.Resonance Set - non-std.
sortedResonances ccp.api.nmr.Nmr.Resonance List -
findFirstResonance ccp.api.nmr.Nmr.Resonance keyword=value pairs
findAllResonances ccp.api.nmr.Nmr.Resonance Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey AtomSetMapping 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
None

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2011-12-01-15:00:56_00003

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

# automatic set self.elementSymbol.
# Based on all atoms in an atomSet being of the same type.
if not self.elementSymbol:
  ll = [self]
  elements = set()
  for x in ll:
    for y in x.atomSetMappings:
      ll.append(y)
    for z in x.atomSets:
      elements.add(z.findFirstAtom().chemAtom.elementSymbol)

  element = elements.pop()
  if elements:
    raise ApiError("creating AtomSetMapping combining different chemical elements")

  self.elementSymbol = element

Special destructor code:

None

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: atomSetMappings
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:25:17 2015    from data model package  ccpnmr.api.AnalysisV3.AtomSetMapping   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk