Data Model version 2.1.2
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Class: Residue

The Residue constructor includes non-standard actions.
    A monomer part of a specific molecule in a specific environment (Chain)).
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link chain to class Chain
Main key: seqId
Mandatory Attributes: descriptor, linking, seqCode, seqId
Known Subclasses: None
Children:
link atoms to class Atom
link molSystemLinkEnds to class MolSystemLinkEnd
Constructor: newObj = Residue( chain,descriptor=value, linking=value, seqCode=value, seqId=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
ccpCode LongWord 1..1 Derived. ccpCode of ChemComp corresponding to Residue  
descriptor Line 1..1 descriptor of ChemCompVar corresponding to Residue. Describes topological variant, i.e. protonation state or (for Polymers) non-polymer type substitution. linking and descriptor may be changed for existing Residues, thus changing the identity of the corresponding ChemCompVar. The new chemCompVar must contain a ChemAtom to correspond to every existing Atom, and a LinkEnd to correspond to every existing MolSystemLinkEnd, as well as every existing MolResLinkEnd in the MolResidue. Note that this may require that Atom and MolSsytemLinkEnd objects be deleted before the linking and descriptor can be modified.  
details Text 0..1 free text for notes, etc.  
linking ccp.api.molecule.ChemComp.ChemCompLinking 1..1 linking (substitution pattern) of ChemCompVar corresponding to Residue. linking and descriptor may be changed for existing Residues, thus changing the identity of the corresponding ChemCompVar. The new chemCompVar must contain a ChemAtom to correspond to every existing Atom, and a LinkEnd to correspond to every existing MolSystemLinkEnd, as well as every existing MolResLinkEnd in the MolResidue. Note that this may require that Atom and MolSystemLinkEnd objects be deleted before the linking and descriptor can be modified.  
molType ccp.api.molecule.ChemComp.MolType 1..1 Derived. molType of ChemComp corresponding to Residue  
seqCode Int 1..1 Author sequence identifier. Set to MolResidue.seqCode when the Residue is created as part of the Chain constructor.  
seqId Int 1..1 Identifier corresponding to the molResidue identifier (self.molResidue.serial)  
seqInsertCode Line 1..1 Author insertion code. Defaults to MolResidue.seqInsertCode (which again defaults to a single white space ' ') when the Residue is created as part of the Chain constructor..  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
atoms Atom 0..* (Child link). child link  
chain Chain 1..1 (Parent link). parent link  
chainFragment ChainFragment 0..1 ChainFragment to which Residue belongs. When Chains are created, each Residue will automatically be linked to a ChainFragment, so that the Chain is divided in Fragments of uniform molType.  
chainStateSets ccp.api.nmr.Nmr.ChainStateSet 0..* ChainStateSets relevant for Residue  
chemCompVar ccp.api.molecule.ChemComp.ChemCompVar 1..1 Derived. ChemCompVar (that is, specific protonation state etc.) of the chemComp corresponding to this particular residue.  
dangleResidues cambridge.api.Dangle.DangleResidue 0..* DangleResidue with predicted angles  
molResidue ccp.api.molecule.Molecule.MolResidue 1..1 Derived. MolResidue (Residue in Molecule Sequene) corresponding to Residue  
molSysResidueValidations ccp.api.molecule.Validation.MolSysResidueValidation 0..* Validation results for Residue  
molSystemLinkEnds MolSystemLinkEnd 0..* (Child link). child link to class MolSystemLinkEnd  
parent Chain 1..1 link to parent object - synonym for chain  
residueProbs ccp.api.nmr.Nmr.ResidueProb 0..* ResidueProb describing ResonanceGroups with a probability of corresponding to this residue.  
resonanceGroups ccp.api.nmr.Nmr.ResonanceGroup 0..* ResonanceGroups that are definitely assigned to this residue  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
ccpCode
getCcpCode LongWord - non-std.
descriptor
getDescriptor Line -
setDescriptor - Line
details
getDetails Text -
setDetails - Text
linking
getLinking ccp.api.molecule.ChemComp.ChemCompLinking -
setLinking - ccp.api.molecule.ChemComp.ChemCompLinking
molType
getMolType ccp.api.molecule.ChemComp.MolType - non-std.
seqCode
getSeqCode Int -
setSeqCode - Int
seqId
getSeqId Int -
setSeqId - Int
seqInsertCode
getSeqInsertCode Line -
setSeqInsertCode - Line

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atoms
getAtoms Atom Set -
sortedAtoms Atom List -
findFirstAtom Atom keyword=value pairs
findAllAtoms Atom Set keyword=value pairs
chain
getChain Chain -
chainFragment
getChainFragment ChainFragment -
setChainFragment - ChainFragment
chainStateSets
getChainStateSets ccp.api.nmr.Nmr.ChainStateSet Set -
setChainStateSets - ccp.api.nmr.Nmr.ChainStateSet Set
sortedChainStateSets ccp.api.nmr.Nmr.ChainStateSet List -
addChainStateSet - ccp.api.nmr.Nmr.ChainStateSet
removeChainStateSet - ccp.api.nmr.Nmr.ChainStateSet
findFirstChainStateSet ccp.api.nmr.Nmr.ChainStateSet keyword=value pairs
findAllChainStateSets ccp.api.nmr.Nmr.ChainStateSet Set keyword=value pairs
chemCompVar
getChemCompVar ccp.api.molecule.ChemComp.ChemCompVar - non-std.
dangleResidues
getDangleResidues cambridge.api.Dangle.DangleResidue Set -
setDangleResidues - cambridge.api.Dangle.DangleResidue Set
sortedDangleResidues cambridge.api.Dangle.DangleResidue List -
findFirstDangleResidue cambridge.api.Dangle.DangleResidue keyword=value pairs
findAllDangleResidues cambridge.api.Dangle.DangleResidue Set keyword=value pairs
molResidue
getMolResidue ccp.api.molecule.Molecule.MolResidue - non-std.
molSysResidueValidations
getMolSysResidueValidations ccp.api.molecule.Validation.MolSysResidueValidation Set -
setMolSysResidueValidations - ccp.api.molecule.Validation.MolSysResidueValidation Set
sortedMolSysResidueValidations ccp.api.molecule.Validation.MolSysResidueValidation List -
addMolSysResidueValidation - ccp.api.molecule.Validation.MolSysResidueValidation
removeMolSysResidueValidation - ccp.api.molecule.Validation.MolSysResidueValidation
findFirstMolSysResidueValidation ccp.api.molecule.Validation.MolSysResidueValidation keyword=value pairs
findAllMolSysResidueValidations ccp.api.molecule.Validation.MolSysResidueValidation Set keyword=value pairs
molSystemLinkEnds
getMolSystemLinkEnds MolSystemLinkEnd Set -
sortedMolSystemLinkEnds MolSystemLinkEnd List -
findFirstMolSystemLinkEnd MolSystemLinkEnd keyword=value pairs
findAllMolSystemLinkEnds MolSystemLinkEnd Set keyword=value pairs
parent
getParent Chain -
residueProbs
getResidueProbs ccp.api.nmr.Nmr.ResidueProb Set -
setResidueProbs - ccp.api.nmr.Nmr.ResidueProb Set
sortedResidueProbs ccp.api.nmr.Nmr.ResidueProb List -
findFirstResidueProb ccp.api.nmr.Nmr.ResidueProb keyword=value pairs
findAllResidueProbs ccp.api.nmr.Nmr.ResidueProb Set keyword=value pairs
resonanceGroups
getResonanceGroups ccp.api.nmr.Nmr.ResonanceGroup Set -
setResonanceGroups - ccp.api.nmr.Nmr.ResonanceGroup Set
sortedResonanceGroups ccp.api.nmr.Nmr.ResonanceGroup List -
addResonanceGroup - ccp.api.nmr.Nmr.ResonanceGroup
removeResonanceGroup - ccp.api.nmr.Nmr.ResonanceGroup
findFirstResonanceGroup ccp.api.nmr.Nmr.ResonanceGroup keyword=value pairs
findAllResonanceGroups ccp.api.nmr.Nmr.ResonanceGroup Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Residue 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
newAtom Atom name, ...
newMolSystemLinkEnd MolSystemLinkEnd linkCode, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:54_00030

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

clazz = ccp.api.molecule.ChemComp.ChemAtom
ccv = self.chemCompVar
for chemAtom in ccv.chemAtoms:
  if isinstance(chemAtom, clazz):
    Atom(self, name=chemAtom.name)

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

linking_and_descriptor_must_be_consistent_with_Atoms_and_LinkEnds
Constraint code: isValid = True

molResidue = self.getByNavigation(
'chain',
'molecule',
('molResidues', self.seqId),
)
chemCompVar = molResidue.getByNavigation(
'chemComp',
('chemCompVars', (self.linking,  self.descriptor))
)

linkCodes = set(x.linkCode for x in chemCompVar.linkEnds)

for le in self.molSystemLinkEnds:
  if le.linkCode not in linkCodes:
    isValid = False
    
for le in molResidue.molResLinkEnds:
  if le.linkCode not in linkCodes:
    isValid = False

clazz = ccp.api.molecule.ChemComp.ChemAtom
aset = set(ca.name for ca in chemCompVar.chemAtoms if isinstance(ca, clazz))
  
for atom in self.atoms:
  if atom.name not in aset:
    isValid = False
Known inward one-way links: ccp.api.molecule.MolStructure.Residue.residueccp.api.nmr.NmrCalc.MolResidueData.residuesccpnmr.api.Analysis.ResidueMapping.residueccpnmr.api.AnalysisV3.ResidueMapping.residuemolsim.api.Symmetry.Segment.residuesutrecht.api.Haddock.Residue.residue
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:25 2014    from data model package  ccp.api.molecule.MolSystem.Residue   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk