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Class: ChemAtomSet


    Group of chem atoms that may form a pseudoatom. A ChemAtomSet may consist of either other ChemAtomSets or of ChemAtoms, but not both. All ChemAtomSets are relevant for all ChemCompVars, but they (or some of the ChemAtomSets they consist of) may contain fewer or even no atoms in some ChemCompVars.
Attributes
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Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link chemComp to class ChemComp
Main key: name, subType
Mandatory Attributes: isProchiral, name
Known Subclasses: None
Children: None
Constructor: newObj = ChemAtomSet( chemComp,isProchiral=value, name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
distCorr Float 1..1 Distance Restraint Correction (in A) applied when making restraints to the pseudoatom defined here.  
elementSymbol Word 1..1 Derived. ELement symbol for all ChemAtoms ultimately making up the ChemAtomSet.  
isEquivalent Boolean 0..1 Indicates whether the atoms in the ChemAtomSet are chemically equivalent (set to true, e.g. for a methyl group), non-equivalent (set to false, e.g. for a methylene group or for the NH2 protons of a glutamine side chain), or sometimes equivalent (not set, e.g. for the HD1/HD2 protons of a a Phe or Tyr aromatic ting)..  
isProchiral Boolean 1..1 Indicates whether the two atoms or chemAtomSets in the ChemAtomSet form a prochiral pair, such as the b methylene group of serine..  
name Word 1..1 Pseudo atom name.  
subType Int 1..1 Subtype of ChemAtomSet, used to distinguish ChemAtomSets with the same names but different characteristics, to be used in diferent ChemCompVars.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
chemAtomSet ChemAtomSet 0..1 ChemAtomSet that ChemAtoms are part of  
chemAtomSets ChemAtomSet 0..* ChemAtomSets that make up ChemAtomSet  
chemAtoms ChemAtom 0..* ChemAtoms that make up ChemAtomSet.  
chemComp ChemComp 1..1 (Parent link). parent link  
parent ChemComp 1..1 link to parent object - synonym for chemComp  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
distCorr
getDistCorr Float -
setDistCorr - Float
elementSymbol
getElementSymbol Word - non-std.
isEquivalent
getIsEquivalent Boolean -
setIsEquivalent - Boolean
isProchiral
getIsProchiral Boolean -
setIsProchiral - Boolean
name
getName Word -
setName - Word
subType
getSubType Int -
setSubType - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chemAtomSet
getChemAtomSet ChemAtomSet -
setChemAtomSet - ChemAtomSet
chemAtomSets
getChemAtomSets ChemAtomSet Set -
setChemAtomSets - ChemAtomSet Set
sortedChemAtomSets ChemAtomSet List -
addChemAtomSet - ChemAtomSet
removeChemAtomSet - ChemAtomSet
findFirstChemAtomSet ChemAtomSet keyword=value pairs
findAllChemAtomSets ChemAtomSet Set keyword=value pairs
chemAtoms
getChemAtoms ChemAtom Set -
setChemAtoms - ChemAtom Set
sortedChemAtoms ChemAtom List -
addChemAtom - ChemAtom
removeChemAtom - ChemAtom
findFirstChemAtom ChemAtom keyword=value pairs
findAllChemAtoms ChemAtom Set keyword=value pairs
chemComp
getChemComp ChemComp -
parent
getParent ChemComp -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey ChemAtomSet 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_2006-08-16-14:22:52_00014

isImplicit:

False

Tag

Value
repositoryId $Id: ChemAtomSet.xml,v 1.57 2011-01-13 14:40:33 rhfogh Exp $

Tag

Value
repositoryTag $Name: not supported by cvs2svn $

Special constructor code:

None

Special destructor code:

None

Constraint name:

all_chemAtoms_must_be_same_chemElement
Constraint code: ll = [self]
elements = set()
for x in ll:
  ll.extend(x.chemAtomSets)
  for z in x.chemAtoms:
    elements.add(z.elementSymbol)

isValid = (len(elements) == 1)

Constraint name:

chemAtomSet_has_chemAtoms_xor_chemAtomSets
Constraint code: (not self.chemAtoms) != (not self.chemAtomSets)

Constraint name:

nested_chemAtomSets_cannot_be_equivalent
Constraint code: self.chemAtoms or not self.isEquivalent

Constraint name:

prochirals_are_not_equivalent
Constraint code: not (self.isProchiral and self.isEquivalent != False)

Constraint name:

prochirals_must_be_pairs
Constraint code: not self.isProchiral or len(self.chemAtoms) == 2 or len(self.chemAtomSets) == 2
Known inward one-way links: ccp.api.molecule.ChemComp.ChemCompVar.chemAtomSetsccpnmr.api.Analysis.AtomSetMapping.chemAtomSet
  Data Model Version 2.0.6
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Wed Aug 7 15:06:22 2013    from data model package  ccp.api.molecule.ChemComp.ChemAtomSet   revision 1.57  
  Work done by the CCPN team.
www.ccpn.ac.uk