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Class: ChemComp


Abstract Class

    Chemical Component. E.g. GLU (glutamate). Describes the topology of templates that serve as building block for molecules. The ChemComp holds information valid for all toploigical variants, as well as all Atoms, Bonds, Angles etc. for the different ChemCompVars (e.g. 'start','protonated'; 'end','deprotonated', etc.). For this reason the Atoms, Bonds etc. linked to do not form a consistent set.
Attributes
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Attribute Methods
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Class Methods
Factory Methods
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Appendix

Inheritance:


Details:

Parent: link memopsRoot to class memops.api.Implementation.MemopsRoot
Main key: molType, ccpCode
Mandatory Attributes: None
Partitions Children: True
Known Subclasses: NonStdChemComp, StdChemComp
Children:
link chemAngles to class ChemAngle
link chemAtomSets to class ChemAtomSet
link chemAtoms to class AbstractChemAtom
link chemBonds to class ChemBond
link chemCompVars to class ChemCompVar
link chemTorsions to class ChemTorsion
link linkEnds to class LinkEnd
link namingSystems to class NamingSystem
link stereochemistries to class Stereochemistry

Attributes (in package)

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Attribute Type Multiplicity Description
baseGlycoCtCode String 0..1 base glycoCT description code. For carbohydrates. The full glycoCtCode is only defined at the ChemCompVar level, but htis gives the base code that is exanded on in the vars.  
beilsteinCode Word 0..1 Beilstein compound code  
casRegCode Word 0..1 CAS code  
ccpCode LongWord 1..1 ccp Code of ChemComp. Part of the class key  
code1Letter Word 0..1 Derived. One-letter code  
code3Letter ThreeLetterCode 0..1 PDB three letter code of ChemComp.  
commonNames Text 0..* Common names of ChemComp  
details Text 0..1 Free text, for notes, explanatory comments, etc.  
hasStdChirality Boolean 0..1 Does ChemComp have standard chirality? Serves to flag molecules containing ChemComps with non-standard chirality, such as D amino acids. Note that the attribute may not be set, for cases where no standard is defined.  
isLinearPolymer Boolean 1..1 Derived. Is ChemComp a component of a linear polymer?  
keywords Line 0..* Keywords for searching ChemComp. E.g. 'saccharide', ...  
merckCode Word 0..1 Merck compound code  
molType MolType 1..1 molecule Type of ChemComp (part of the class key)  
name Text 0..1 name of AbstractChemComp  
sigmaAldrichCode Word 0..1 SigmaAldrich compound code  
stdChemCompCode LongWord 0..1 ccpCode of standard ChemComp corresponding to a given (non-standard) ChemComp. E.g. bromo-tyrosine would have stdChemCompCode 'TYR'. StdChemComps have stdChemCompCode equal to ccpCode. Key for derived link stdChemComp.  

Inherited Attributes (not in package): applicationDataclassNamecreatedByfieldNamesguidinConstructorisDeletedisLoadedisModifiableisModifiedisReadinglastUnlockedBymetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
chemAngles ChemAngle 0..* (Child link). child link to class ChemAngle  
chemAtomSets ChemAtomSet 0..* (Child link). child link to class ChemAtomSet  
chemAtoms AbstractChemAtom 0..* (Child link). child link to class AbstractChemAtom  
chemBonds ChemBond 0..* (Child link). child link to class ChemBond  
chemCompVars ChemCompVar 0..* (Child link). child link to class ChemCompVar  
chemTorsions ChemTorsion 0..* (Child link). child link to class ChemTorsion  
linkEnds LinkEnd 0..* (Child link). child link to class LinkEnd  
memopsRoot memops.api.Implementation.MemopsRoot 1..1 (Parent link). parent link  
namingSystems NamingSystem 0..* (Child link). child link to class NamingSystem  
parent memops.api.Implementation.MemopsRoot 1..1 link to parent object - synonym for memopsRoot  
residueTypeProbs ccp.api.nmr.Nmr.ResidueTypeProb 0..* ResidueTypeProb describing ResonanceGroups with a probability of corresponding to this ChemComp.  
stdChemComp StdChemComp 0..1 Derived. Standard ChemComp corresponding to ChemComp. If ChemComp is a StdChemComp points to the ChemComp itself.  
stereochemistries Stereochemistry 0..* (Child link). child link to class Stereochemistry  

Inherited Attributes (not in package): accessactiveAccessactiveRepositoriespackageLocatorroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
baseGlycoCtCode
getBaseGlycoCtCode String -
setBaseGlycoCtCode - String
beilsteinCode
getBeilsteinCode Word -
setBeilsteinCode - Word
casRegCode
getCasRegCode Word -
setCasRegCode - Word
ccpCode
getCcpCode LongWord -
setCcpCode - LongWord
code1Letter
getCode1Letter Word - non-std.
code3Letter
getCode3Letter ThreeLetterCode -
setCode3Letter - ThreeLetterCode
commonNames
getCommonNames Text Tuple -
setCommonNames - Text List
addCommonName - Text
removeCommonName - Text
details
getDetails Text -
setDetails - Text
hasStdChirality
getHasStdChirality Boolean -
setHasStdChirality - Boolean
isLinearPolymer
getIsLinearPolymer Boolean - non-std.
keywords
getKeywords Line Tuple -
setKeywords - Line List
addKeyword - Line
removeKeyword - Line
merckCode
getMerckCode Word -
setMerckCode - Word
molType
getMolType MolType -
setMolType - MolType
name
getName Text -
setName - Text
sigmaAldrichCode
getSigmaAldrichCode Word -
setSigmaAldrichCode - Word
stdChemCompCode
getStdChemCompCode LongWord -
setStdChemCompCode - LongWord

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chemAngles
getChemAngles ChemAngle Set -
sortedChemAngles ChemAngle List -
findFirstChemAngle ChemAngle keyword=value pairs
findAllChemAngles ChemAngle Set keyword=value pairs
chemAtomSets
getChemAtomSets ChemAtomSet Set -
sortedChemAtomSets ChemAtomSet List -
findFirstChemAtomSet ChemAtomSet keyword=value pairs
findAllChemAtomSets ChemAtomSet Set keyword=value pairs
chemAtoms
getChemAtoms AbstractChemAtom Set -
sortedChemAtoms AbstractChemAtom List -
findFirstChemAtom AbstractChemAtom keyword=value pairs
findAllChemAtoms AbstractChemAtom Set keyword=value pairs
chemBonds
getChemBonds ChemBond Set -
sortedChemBonds ChemBond List -
findFirstChemBond ChemBond keyword=value pairs
findAllChemBonds ChemBond Set keyword=value pairs
chemCompVars
getChemCompVars ChemCompVar Set -
sortedChemCompVars ChemCompVar List -
findFirstChemCompVar ChemCompVar keyword=value pairs
findAllChemCompVars ChemCompVar Set keyword=value pairs
chemTorsions
getChemTorsions ChemTorsion Set -
sortedChemTorsions ChemTorsion List -
findFirstChemTorsion ChemTorsion keyword=value pairs
findAllChemTorsions ChemTorsion Set keyword=value pairs
linkEnds
getLinkEnds LinkEnd Set -
sortedLinkEnds LinkEnd List -
findFirstLinkEnd LinkEnd keyword=value pairs
findAllLinkEnds LinkEnd Set keyword=value pairs
memopsRoot
getMemopsRoot memops.api.Implementation.MemopsRoot -
namingSystems
getNamingSystems NamingSystem Set -
sortedNamingSystems NamingSystem List -
findFirstNamingSystem NamingSystem keyword=value pairs
findAllNamingSystems NamingSystem Set keyword=value pairs
parent
getParent memops.api.Implementation.MemopsRoot -
residueTypeProbs
getResidueTypeProbs ccp.api.nmr.Nmr.ResidueTypeProb Set -
setResidueTypeProbs - ccp.api.nmr.Nmr.ResidueTypeProb Set
sortedResidueTypeProbs ccp.api.nmr.Nmr.ResidueTypeProb List -
findFirstResidueTypeProb ccp.api.nmr.Nmr.ResidueTypeProb keyword=value pairs
findAllResidueTypeProbs ccp.api.nmr.Nmr.ResidueTypeProb Set keyword=value pairs
stdChemComp
getStdChemComp StdChemComp - non-std.
stereochemistries
getStereochemistries Stereochemistry Set -
sortedStereochemistries Stereochemistry List -
findFirstStereochemistry Stereochemistry keyword=value pairs
findAllStereochemistries Stereochemistry Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
getByKey ChemComp memops.api.Implementation.MemopsRoot, Any List static
getFullKey Any List Boolean
getLocalKey Any -

Factory Methods (in package)

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Method Return Parameters
newChemAngle ChemAngle chemAtoms, ...
newChemAtom ChemAtom elementSymbol, name, ...
newChemAtomSet ChemAtomSet isProchiral, name, ...
newChemBond ChemBond chemAtoms, ...
newChemCompVar ChemCompVar descriptor, formalCharge, isAromatic, isParamagnetic, linking, ...
newChemTorsion ChemTorsion chemAtoms, ...
newLinkAtom LinkAtom name, ...
newLinkEnd LinkEnd linkCode, boundChemAtom, boundLinkAtom, ...
newNamingSystem NamingSystem name, ...
newStereochemistry Stereochemistry stereoClass, value, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:51_00047

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

Each_set_of_ChemAtoms_may_have_only_one_Stereochemistry
Constraint code: ll = self.stereochemistries
isValid = (len(ll) == len(set(frozenset(x.chemAtoms) for x in ll)))

Constraint name:

protein_DNA_RNA_are_linear_polymers
Constraint code: self.isLinearPolymer or not self.chemCompVars or self.molType not in ('protein', 'DNA', 'RNA')
Known inward one-way links: ccp.api.molecule.ChemCompCharge.ChemCompCharge.chemCompccp.api.molecule.ChemCompCoord.ChemCompCoord.chemCompccp.api.molecule.ChemCompLabel.ChemCompLabel.chemCompccp.api.molecule.Molecule.MolResidue.chemCompccp.api.nmr.Nmr.ResonanceGroup.chemCompccp.api.nmr.NmrReference.ChemAtomShiftCorr.chemCompccp.api.nmr.NmrReference.NmrReferenceStore.chemCompmemops.api.Implementation.MemopsRoot.currentChemComp
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:30 2015    from data model package  ccp.api.molecule.ChemComp.ChemComp   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk