Data Model version 2.1.2
Acknowledgements
Diagram | Class Map | Attribute Map | Method Map | Help | License
Home | Package | Class: { prev | next } | Attribute | Method

Class: Chain

The Chain constructor includes non-standard actions.
    A specific instance of a given molecule in a specific environment. E.g. one of the chains for a homodimer.

    The Chain corresponds to a specific Molecule, but may differ in some ways.

    Creating a Chain automatically creates the Residue and Atom objects corresponding to it.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link molSystem to class MolSystem
Main key: code
Mandatory Attributes: code, molecule
Known Subclasses: None
Children:
link chainFragments to class ChainFragment
link residues to class Residue
Constructor: newObj = Chain( molSystem,code=value, molecule=value, ... )

Attributes (in package)

Go to Top
Attribute Type Multiplicity Description
chemExchangeState Line 0..1 for NMR spectroscopy. Short text describing the chemical exchange state.  
code Line 1..1 ChainCode - key for the Chain class. Should ideally be a single letter, if possible.  
conformationalIsomer Line 0..1 short text describing the conformational isomer  
details Text 0..1 Free text, for notes, explanatory comments, etc.  
empiricalFormula Line 1..1 Derived. empirical molecular formula for Chain (may be different from that of the corresponding molecule  
formalCharge Int 1..1 Derived. formal charge of Chain (may differ from that of the corresponding molecule).  
magnEquivalenceCode Line 0..1 For NMR data. Chains with the same magnEquivalenceCode are magnetically equivalent within the MolSystem. If not set no chains are magnetically equivalent.  
molecularMass Float 1..1 Derived. molecular mass of Chain (may differ from that of the corresponding molecule).  
pdbOneLetterCode Line 1..1 One letter chain identifier. Will be used by PDB (and programs that use similar conventions). WARNING: having same oneLetterCode for different chains is legal but may cause serious confusion.  
physicalState Line 0..1 e.g. folded/unfolded  
role Line 0..1 Role of Chain within MolSystem  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

Go to Top
Attribute Type Multiplicity Description
analysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout 0..* AnalysisLayouts referring to chains  
analysisPanel ccpnmr.api.AnalysisV3.AnalysisPanel 0..1 AnalysisPanels referring to chains  
chainFragments ChainFragment 0..* (Child link). child link to class ChainFragment  
chainInteractions ChainInteraction 0..* An interaction of a given type between a pair of Chains  
chainStateSets ccp.api.nmr.Nmr.ChainStateSet 0..* ChainStateSets belonging to Chain  
dangleChains cambridge.api.Dangle.DangleChain 0..* Chains with Dangle dihedral angle predictions  
molSysChainValidations ccp.api.molecule.Validation.MolSysChainValidation 0..* Validation results for Chain  
molSystem MolSystem 1..1 (Parent link). parent link  
molecule ccp.api.molecule.Molecule.Molecule 1..1 Molecule to which Chain corresponds  
parent MolSystem 1..1 link to parent object - synonym for molSystem  
residues Residue 0..* (Child link). child link  
resonanceGroups ccp.api.nmr.Nmr.ResonanceGroup 0..* ResonanceGroups that may be relevant to Chain  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

Go to Top
Attribute Method Return Parameters Comment
chemExchangeState
getChemExchangeState Line -
setChemExchangeState - Line
code
getCode Line -
setCode - Line
conformationalIsomer
getConformationalIsomer Line -
setConformationalIsomer - Line
details
getDetails Text -
setDetails - Text
empiricalFormula
getEmpiricalFormula Line - non-std.
formalCharge
getFormalCharge Int - non-std.
magnEquivalenceCode
getMagnEquivalenceCode Line -
setMagnEquivalenceCode - Line
molecularMass
getMolecularMass Float - non-std.
pdbOneLetterCode
getPdbOneLetterCode Line -
setPdbOneLetterCode - Line
physicalState
getPhysicalState Line -
setPhysicalState - Line
role
getRole Line -
setRole - Line

Link Attribute Methods (in package)

Go to Top
Attribute Method Return Parameters Comment
analysisLayouts
getAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout Set -
setAnalysisLayouts - ccpnmr.api.AnalysisV3.AnalysisLayout Set
sortedAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout List -
addAnalysisLayout - ccpnmr.api.AnalysisV3.AnalysisLayout
removeAnalysisLayout - ccpnmr.api.AnalysisV3.AnalysisLayout
findFirstAnalysisLayout ccpnmr.api.AnalysisV3.AnalysisLayout keyword=value pairs
findAllAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout Set keyword=value pairs
analysisPanel
getAnalysisPanel ccpnmr.api.AnalysisV3.AnalysisPanel -
setAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
chainFragments
getChainFragments ChainFragment Set -
sortedChainFragments ChainFragment List -
findFirstChainFragment ChainFragment keyword=value pairs
findAllChainFragments ChainFragment Set keyword=value pairs
chainInteractions
getChainInteractions ChainInteraction Set -
setChainInteractions - ChainInteraction Set
sortedChainInteractions ChainInteraction List -
findFirstChainInteraction ChainInteraction keyword=value pairs
findAllChainInteractions ChainInteraction Set keyword=value pairs
chainStateSets
getChainStateSets ccp.api.nmr.Nmr.ChainStateSet Set -
setChainStateSets - ccp.api.nmr.Nmr.ChainStateSet Set
sortedChainStateSets ccp.api.nmr.Nmr.ChainStateSet List -
findFirstChainStateSet ccp.api.nmr.Nmr.ChainStateSet keyword=value pairs
findAllChainStateSets ccp.api.nmr.Nmr.ChainStateSet Set keyword=value pairs
dangleChains
getDangleChains cambridge.api.Dangle.DangleChain Set -
setDangleChains - cambridge.api.Dangle.DangleChain Set
sortedDangleChains cambridge.api.Dangle.DangleChain List -
findFirstDangleChain cambridge.api.Dangle.DangleChain keyword=value pairs
findAllDangleChains cambridge.api.Dangle.DangleChain Set keyword=value pairs
molSysChainValidations
getMolSysChainValidations ccp.api.molecule.Validation.MolSysChainValidation Set -
setMolSysChainValidations - ccp.api.molecule.Validation.MolSysChainValidation Set
sortedMolSysChainValidations ccp.api.molecule.Validation.MolSysChainValidation List -
addMolSysChainValidation - ccp.api.molecule.Validation.MolSysChainValidation
removeMolSysChainValidation - ccp.api.molecule.Validation.MolSysChainValidation
findFirstMolSysChainValidation ccp.api.molecule.Validation.MolSysChainValidation keyword=value pairs
findAllMolSysChainValidations ccp.api.molecule.Validation.MolSysChainValidation Set keyword=value pairs
molSystem
getMolSystem MolSystem -
molecule
getMolecule ccp.api.molecule.Molecule.Molecule -
setMolecule - ccp.api.molecule.Molecule.Molecule
parent
getParent MolSystem -
residues
getResidues Residue Set -
sortedResidues Residue List -
findFirstResidue Residue keyword=value pairs
findAllResidues Residue 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)

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

Factory Methods (in package)

Go to Top
Method Return Parameters
newChainFragment ChainFragment isLinearPolymer, molType, ...
newResidue Residue descriptor, linking, seqCode, seqId, ...

Other Methods (in package)

Go to Top
Method Return Parameters Comment
createChainFragments - - non-std. Creates ChainFragments for all Residues that do not already have them, while making no modification to existing ChainFragments or their contents. Is called automatically on Chain creation. Any program that modifies the automatically created ChainFragments should call this function at the end, to ensure that every Residue belongs to a  ChainFragment.

The function  divides the residues in four molTypes: protein, carbohydrate, DNA/RNA ,and other. Within each molType, stretches of linear polymer of two or more residues are identified without regard to the seqId value of the residues. These are put in separate ChainFragments, with the residues ordered by sequence rather than seqID. Subsequently,  residues not part of a linear polymer are grouped in the largest directly connected fragments of uniform molType. Finally, for fragments of type DNA/RNA the molType is set to DNA or RNA if this is the only molType that happens to be present, to DNA/RNA otherwise.

Appendix

Go to Top

guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:54_00024

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

molecule = self.molecule
if molecule:
  # this should never be null, but it fails more gracefully this way

  # make Residues
  for molResidue in self.molecule.molResidues:
    Residue(self, seqId=molResidue.serial,seqCode=molResidue.seqCode, seqInsertCode=molResidue.seqInsertCode, linking=molResidue.linking, descriptor=molResidue.descriptor )

  # make ChainFragments
  self.createChainFragments()

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

seqCode_and_seqInsertCode_form_secondary_key_for_residues
Constraint code: ll = self.residues
aset = frozenset((res.seqCode, res.seqInsertCode) for res in ll)
isValid = (len(aset) == len(ll))
Known inward one-way links: ccp.api.molecule.MolStructure.Chain.chainccp.api.nmr.NmrCalc.MolResidueData.chainccp.api.nmr.NmrCalc.MolResidueData.chainsccp.api.nmr.NmrCalc.MolSystemData.chainsccpnmr.api.Analysis.ChainMapping.chainccpnmr.api.AnalysisV3.ChainMapping.chainutrecht.api.Haddock.Chain.chain
  Data Model Version 2.1.2
Go to Top  
  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:24 2014    from data model package  ccp.api.molecule.MolSystem.Chain   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk