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Class: ChemAtom


    Atom, in the sense of a part of a toplogical description of a ChemComp. ChemAtoms, unlike LinkAtoms, are part of the ChemComp itself.
Attributes
Link Attributes
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: elementSymbol, name
Known Subclasses: None
Children: None
Constructor: newObj = ChemAtom( chemComp,elementSymbol=value, name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
chirality AtomChirality 0..1 Chirality of atom according to IUPAC R/S system. Note for some chiral atoms chirality cannot be specified according to this system but only using the Stereochemistry class. An example would be a chirality that involves a LinkAtom susbstituent.  
elementSymbol Word 1..1 Chemical symbol of the atom. Strictly speaking an enum .E.g. H, C, Mg, Pt. Serves as key to derived link chemElement.  
name Word 1..1 name of ChemAtom  
nuclGroupType Word 0..1 String to determine Atom Group (for assignment purposes). Proposed possibilities: 'CH0','CH2','CH3','CHx','NH0','NH2','NH3', NHx, OH0m OH1, OH2, .. etc. 'OTHER'.  
shortVegaType Line 0..1 VegaType for atom, covering only the atom itself, e.g (100) or (451). The full Vega Type is derived from the short Vegatype of the atom and the atoms bound to it.  
subType Int 1..1 Subtype of AbstractChemAtom, used to distinguish Atoms with the same names but different characteristics, to be used in diferent ChemCompVars.  
waterExchangeable Boolean 1..1 Is this atom exchanging fast with solvent under aqueous conditions ( i.e. on a timescale of a milisecond or less)? Most atoms are not. The exceptions are e.g. protons bound to oxygen, or protons in amine groups or NH2 in guanidinium groups.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
boundLinkEnds LinkEnd 0..* linkEnds with an out-of-ChemComp bond parting directly from ChemAtom.  
chemAngles ChemAngle 0..* ChemAngles involving AbstractChemAtom  
chemAtomSet ChemAtomSet 0..1 ChemAtomSet that ChemAtom is contained in.  
chemBonds ChemBond 0..* ChemBonds involving AbstractChemAtom  
chemComp ChemComp 1..1 (Parent link). parent link  
chemCompVars ChemCompVar 0..* ChemCompVars that contain AbstractChemAtom  
chemElement ccp.api.molecule.ChemElement.ChemElement 1..1 Derived. ChemElement that corresponds to ChemAtom  
chemTorsions ChemTorsion 0..* ChemTorsions involving AbstractChemAtom  
coreStereochemistries Stereochemistry 0..* Stereochemistry objects that describe the stereochemistry at ChemAtom.  
parent ChemComp 1..1 link to parent object - synonym for chemComp  
remoteLinkEnds LinkEnd 0..* LinkEnds where ChemAtom participates as remote ChemAtom  
stereochemistries Stereochemistry 0..* StereoChemistry objects that involve AbstractChemAtom in stereochemistry definition  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chirality
getChirality AtomChirality -
setChirality - AtomChirality
elementSymbol
getElementSymbol Word -
setElementSymbol - Word
name
getName Word -
setName - Word
nuclGroupType
getNuclGroupType Word -
setNuclGroupType - Word
shortVegaType
getShortVegaType Line -
setShortVegaType - Line
subType
getSubType Int -
setSubType - Int
waterExchangeable
getWaterExchangeable Boolean -
setWaterExchangeable - Boolean

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
boundLinkEnds
getBoundLinkEnds LinkEnd Set -
setBoundLinkEnds - LinkEnd Set
sortedBoundLinkEnds LinkEnd List -
findFirstBoundLinkEnd LinkEnd keyword=value pairs
findAllBoundLinkEnds LinkEnd Set keyword=value pairs
chemAngles
getChemAngles ChemAngle Set -
setChemAngles - ChemAngle Set
sortedChemAngles ChemAngle List -
findFirstChemAngle ChemAngle keyword=value pairs
findAllChemAngles ChemAngle Set keyword=value pairs
chemAtomSet
getChemAtomSet ChemAtomSet -
setChemAtomSet - ChemAtomSet
chemBonds
getChemBonds ChemBond Set -
setChemBonds - ChemBond Set
sortedChemBonds ChemBond List -
findFirstChemBond ChemBond keyword=value pairs
findAllChemBonds ChemBond Set keyword=value pairs
chemComp
getChemComp ChemComp -
chemCompVars
getChemCompVars ChemCompVar Set -
setChemCompVars - ChemCompVar Set
sortedChemCompVars ChemCompVar List -
addChemCompVar - ChemCompVar
removeChemCompVar - ChemCompVar
findFirstChemCompVar ChemCompVar keyword=value pairs
findAllChemCompVars ChemCompVar Set keyword=value pairs
chemElement
getChemElement ccp.api.molecule.ChemElement.ChemElement - non-std.
chemTorsions
getChemTorsions ChemTorsion Set -
setChemTorsions - ChemTorsion Set
sortedChemTorsions ChemTorsion List -
findFirstChemTorsion ChemTorsion keyword=value pairs
findAllChemTorsions ChemTorsion Set keyword=value pairs
coreStereochemistries
getCoreStereochemistries Stereochemistry Set -
setCoreStereochemistries - Stereochemistry Set
sortedCoreStereochemistries Stereochemistry List -
findFirstCoreStereochemistry Stereochemistry keyword=value pairs
findAllCoreStereochemistries Stereochemistry Set keyword=value pairs
parent
getParent ChemComp -
remoteLinkEnds
getRemoteLinkEnds LinkEnd Set -
setRemoteLinkEnds - LinkEnd Set
sortedRemoteLinkEnds LinkEnd List -
findFirstRemoteLinkEnd LinkEnd keyword=value pairs
findAllRemoteLinkEnds LinkEnd Set keyword=value pairs
stereochemistries
getStereochemistries Stereochemistry Set -
setStereochemistries - 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
checkValid - Boolean
checkAllValid - Boolean
getByKey ChemAtom 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_00037

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.molecule.ChemCompCharge.ChemAtomCharge.chemAtomccp.api.molecule.ChemCompLabel.AtomLabel.chemAtomccp.api.molecule.LabeledMolecule.SingleAtomLabel.chemAtomccp.api.molecule.MolStructure.Atom.chemAtomccp.api.molecule.MolSystem.Atom.chemAtom
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Fri Mar 28 11:18:03 2014    from data model package  ccp.api.molecule.ChemComp.ChemAtom   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk