Data Model version 2.1.2
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Class: MolSystem


    Molecular System - a set of potentially interacting chains. Describes all components of known molecular structure considered relevant for (typically) a structure determination. May include components of a complex, components in different states (e.g. free protein, free ligand, and protein and ligand bound in a complex), and also molecules that are not part of any interaction but are considered relevant (e.g. NMR-observable impurities in an Nmr study).
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link memopsRoot to class memops.api.Implementation.MemopsRoot
Main key: code
Mandatory Attributes: code
Partitions Children: True
Known Subclasses: None
Children:
link chainInteractions to class ChainInteraction
link chains to class Chain
link molSystemLinks to class MolSystemLink
link molSystemSysNames to class MolSystemSysName
link nonCovalentBonds to class NonCovalentBond
link structureGroups to class StructureGroup
Constructor: newObj = MolSystem( memopsRoot,code=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
code Word 1..1 MolSystem key, used in links from other packages. Should be a short, name, recognisable to others.  
commonNames Text 0..* Common (non-systematic) names for MolSystem  
details Text 0..1 Free text, for notes, explanatory comments, etc.  
functions Line 0..* Keywords describing the function of the MolSystem  
hasChemExchange Boolean 0..1 Does MolSystem contain chains in chemical exchange?  
isParamagnetic Boolean 1..1 Derived. Is MolSystem paramagnetic?  
keywords Line 0..* Keywords for searching MolSystem.  
molecularMass Float 1..1 Derived. molecular mass of MolSystem  
name Text 0..1 Molecule name used for display purposes. User changeable.  
numChains Int 1..1 Derived. number of Chains  

Inherited Attributes (not in package): applicationDataclassNamecreatedByfieldNamesguidinConstructorisDeletedisLoadedisModifiableisModifiedisReadinglastUnlockedBymetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
analysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout 0..* AnalysisLayouts referring MolSystem  
analysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel 0..* AnalysisPanels referring MolSystem  
chainInteractions ChainInteraction 0..* (Child link). child link to class ChainInteraction  
chains Chain 0..* (Child link). child link to class Chain  
citations ccp.api.general.Citation.Citation 0..* Citations describing MolSystem  
dbReferences ccp.api.general.DbRef.Entry 0..* Database references describing MolSystem  
entries ccp.api.nmr.NmrEntry.Entry 0..* Bmrb Entries for MolSystem  
memopsRoot memops.api.Implementation.MemopsRoot 1..1 (Parent link). parent link  
molSystemLinks MolSystemLink 0..* (Child link). child link to class MolSystemLink  
molSystemSymmetrySets molsim.api.Symmetry.MolSystemSymmetrySet 0..* MolSystemSymmetries that may apply to this MolSystem  
molSystemSysNames MolSystemSysName 0..* (Child link). child link to class MolSystemSysName  
molSystemValidations ccp.api.molecule.Validation.MolSystemValidation 0..* Validation results for MolSystem  
nmrExperiments ccp.api.nmr.Nmr.Experiment 0..* Nmr Experiments carried out on MolSystem  
nmrScreens ccp.api.nmr.NmrScreen.NmrScreen 0..*  
nonCovalentBonds NonCovalentBond 0..* (Child link). child link to class NonCovalentBond  
parent memops.api.Implementation.MemopsRoot 1..1 link to parent object - synonym for memopsRoot  
structureEnsembles ccp.api.molecule.MolStructure.StructureEnsemble 0..* Molecular structures corresponding to MolSystem  
structureGroups StructureGroup 0..* (Child link). child link to class StructureGroup  

Inherited Attributes (not in package): accessactiveAccessactiveRepositoriespackageLocatorroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
code
getCode Word -
setCode - Word
commonNames
getCommonNames Text Tuple -
setCommonNames - Text List
addCommonName - Text
removeCommonName - Text
details
getDetails Text -
setDetails - Text
functions
getFunctions Line Tuple -
setFunctions - Line List
addFunction - Line
removeFunction - Line
hasChemExchange
getHasChemExchange Boolean -
setHasChemExchange - Boolean
isParamagnetic
getIsParamagnetic Boolean - non-std.
keywords
getKeywords Line Tuple -
setKeywords - Line List
addKeyword - Line
removeKeyword - Line
molecularMass
getMolecularMass Float - non-std.
name
getName Text -
setName - Text
numChains
getNumChains Int - non-std.

Link Attribute Methods (in package)

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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
analysisPanels
getAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel Set -
setAnalysisPanels - ccpnmr.api.AnalysisV3.AnalysisPanel Set
sortedAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel List -
addAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
removeAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
findFirstAnalysisPanel ccpnmr.api.AnalysisV3.AnalysisPanel keyword=value pairs
findAllAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel Set keyword=value pairs
chainInteractions
getChainInteractions ChainInteraction Set -
sortedChainInteractions ChainInteraction List -
findFirstChainInteraction ChainInteraction keyword=value pairs
findAllChainInteractions ChainInteraction Set keyword=value pairs
chains
getChains Chain Set -
sortedChains Chain List -
findFirstChain Chain keyword=value pairs
findAllChains Chain Set keyword=value pairs
citations
getCitations ccp.api.general.Citation.Citation Set -
setCitations - ccp.api.general.Citation.Citation Set
sortedCitations ccp.api.general.Citation.Citation List -
addCitation - ccp.api.general.Citation.Citation
removeCitation - ccp.api.general.Citation.Citation
findFirstCitation ccp.api.general.Citation.Citation keyword=value pairs
findAllCitations ccp.api.general.Citation.Citation Set keyword=value pairs
dbReferences
getDbReferences ccp.api.general.DbRef.Entry Set -
setDbReferences - ccp.api.general.DbRef.Entry Set
sortedDbReferences ccp.api.general.DbRef.Entry List -
addDbReference - ccp.api.general.DbRef.Entry
removeDbReference - ccp.api.general.DbRef.Entry
findFirstDbReference ccp.api.general.DbRef.Entry keyword=value pairs
findAllDbReferences ccp.api.general.DbRef.Entry Set keyword=value pairs
entries
getEntries ccp.api.nmr.NmrEntry.Entry Set -
setEntries - ccp.api.nmr.NmrEntry.Entry Set
sortedEntries ccp.api.nmr.NmrEntry.Entry List -
addEntry - ccp.api.nmr.NmrEntry.Entry
removeEntry - ccp.api.nmr.NmrEntry.Entry
findFirstEntry ccp.api.nmr.NmrEntry.Entry keyword=value pairs
findAllEntries ccp.api.nmr.NmrEntry.Entry Set keyword=value pairs
memopsRoot
getMemopsRoot memops.api.Implementation.MemopsRoot -
molSystemLinks
getMolSystemLinks MolSystemLink Set -
sortedMolSystemLinks MolSystemLink List -
findFirstMolSystemLink MolSystemLink keyword=value pairs
findAllMolSystemLinks MolSystemLink Set keyword=value pairs
molSystemSymmetrySets
getMolSystemSymmetrySets molsim.api.Symmetry.MolSystemSymmetrySet Set -
setMolSystemSymmetrySets - molsim.api.Symmetry.MolSystemSymmetrySet Set
sortedMolSystemSymmetrySets molsim.api.Symmetry.MolSystemSymmetrySet List -
findFirstMolSystemSymmetrySet molsim.api.Symmetry.MolSystemSymmetrySet keyword=value pairs
findAllMolSystemSymmetrySets molsim.api.Symmetry.MolSystemSymmetrySet Set keyword=value pairs
molSystemSysNames
getMolSystemSysNames MolSystemSysName Set -
sortedMolSystemSysNames MolSystemSysName List -
findFirstMolSystemSysName MolSystemSysName keyword=value pairs
findAllMolSystemSysNames MolSystemSysName Set keyword=value pairs
molSystemValidations
getMolSystemValidations ccp.api.molecule.Validation.MolSystemValidation Set -
setMolSystemValidations - ccp.api.molecule.Validation.MolSystemValidation Set
sortedMolSystemValidations ccp.api.molecule.Validation.MolSystemValidation List -
addMolSystemValidation - ccp.api.molecule.Validation.MolSystemValidation
removeMolSystemValidation - ccp.api.molecule.Validation.MolSystemValidation
findFirstMolSystemValidation ccp.api.molecule.Validation.MolSystemValidation keyword=value pairs
findAllMolSystemValidations ccp.api.molecule.Validation.MolSystemValidation Set keyword=value pairs
nmrExperiments
getNmrExperiments ccp.api.nmr.Nmr.Experiment Set -
setNmrExperiments - ccp.api.nmr.Nmr.Experiment Set
sortedNmrExperiments ccp.api.nmr.Nmr.Experiment List -
addNmrExperiment - ccp.api.nmr.Nmr.Experiment
removeNmrExperiment - ccp.api.nmr.Nmr.Experiment
findFirstNmrExperiment ccp.api.nmr.Nmr.Experiment keyword=value pairs
findAllNmrExperiments ccp.api.nmr.Nmr.Experiment Set keyword=value pairs
nmrScreens
getNmrScreens ccp.api.nmr.NmrScreen.NmrScreen Set -
setNmrScreens - ccp.api.nmr.NmrScreen.NmrScreen Set
sortedNmrScreens ccp.api.nmr.NmrScreen.NmrScreen List -
addNmrScreen - ccp.api.nmr.NmrScreen.NmrScreen
removeNmrScreen - ccp.api.nmr.NmrScreen.NmrScreen
findFirstNmrScreen ccp.api.nmr.NmrScreen.NmrScreen keyword=value pairs
findAllNmrScreens ccp.api.nmr.NmrScreen.NmrScreen Set keyword=value pairs
nonCovalentBonds
getNonCovalentBonds NonCovalentBond Set -
sortedNonCovalentBonds NonCovalentBond List -
findFirstNonCovalentBond NonCovalentBond keyword=value pairs
findAllNonCovalentBonds NonCovalentBond Set keyword=value pairs
parent
getParent memops.api.Implementation.MemopsRoot -
structureEnsembles
getStructureEnsembles ccp.api.molecule.MolStructure.StructureEnsemble Set -
setStructureEnsembles - ccp.api.molecule.MolStructure.StructureEnsemble Set
sortedStructureEnsembles ccp.api.molecule.MolStructure.StructureEnsemble List -
findFirstStructureEnsemble ccp.api.molecule.MolStructure.StructureEnsemble keyword=value pairs
findAllStructureEnsembles ccp.api.molecule.MolStructure.StructureEnsemble Set keyword=value pairs
structureGroups
getStructureGroups StructureGroup Set -
sortedStructureGroups StructureGroup List -
findFirstStructureGroup StructureGroup keyword=value pairs
findAllStructureGroups StructureGroup Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey MolSystem memops.api.Implementation.MemopsRoot, 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
newChain Chain code, molecule, ...
newChainInteraction ChainInteraction chains, ...
newMolSystemLink MolSystemLink molSystemLinkEnds, ...
newMolSystemSysName MolSystemSysName namingSystem, ...
newNonCovalentBond NonCovalentBond atoms, ...
newStructureGroup StructureGroup ...

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_00023

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: ccp.api.nmr.NmrCalc.MolResidueData.molSystemccp.api.nmr.NmrCalc.MolSystemData.molSystemmemops.api.Implementation.MemopsRoot.currentMolSystemutrecht.api.Haddock.HaddockPartner.molSystem
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Fri Mar 28 11:18:13 2014    from data model package  ccp.api.molecule.MolSystem.MolSystem   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk