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Class: AbstractChemAtom


Abstract Class

    Atom in topology sense. E.g. Arg CB.

    The AbstractChemAtoms within a ChemComp comprise all atomds (including link atoms) contained in any form of the ChemComp. The ChemCompVars then select the appropriate subset of AbstractChemAtoms. Bonds, angles, Stereochemistry etc. are relevant only for the ChemCompVars that contain all AbstractChemAtoms involved.

    ChemAtom names are (should be) IUPAC and follow from the nature of the ChemComp. LinkAtom names (should) reflect the linkCode of the LinkEnd they are part of; the recommended style is that a LinkEnd with a linkCode 'prev' should have link atoms named 'prev_1' for the LinkAtom partaking in the bond and 'prev_2' for the other LinkAtom.
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: name
Known Subclasses: ChemAtom, LinkAtom
Children: None

Attributes (in package)

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Attribute Type Multiplicity Description
name Word 1..1 name of ChemAtom  
subType Int 1..1 Subtype of AbstractChemAtom, used to distinguish Atoms with the same names but different characteristics, to be used in diferent ChemCompVars.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
chemAngles ChemAngle 0..* ChemAngles involving AbstractChemAtom  
chemBonds ChemBond 0..* ChemBonds involving AbstractChemAtom  
chemComp ChemComp 1..1 (Parent link). parent link  
chemCompVars ChemCompVar 0..* ChemCompVars that contain AbstractChemAtom  
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  
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
name
getName Word -
setName - Word
subType
getSubType Int -
setSubType - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chemAngles
getChemAngles ChemAngle Set -
setChemAngles - ChemAngle Set
sortedChemAngles ChemAngle List -
findFirstChemAngle ChemAngle keyword=value pairs
findAllChemAngles ChemAngle Set keyword=value pairs
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
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 -
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
getByKey AbstractChemAtom memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey 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_00001

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.ChemCompCoord.ChemAtomCoord.chemAtomccp.api.nmr.NmrReference.ChemAtomNmrRef.chemAtoms
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:29 2015    from data model package  ccp.api.molecule.ChemComp.AbstractChemAtom   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk