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Class: LinkAtom


    Atom used to specify LinkEnds. Serves as a placeholder for ChemAtoms that are not part of the present ChemComp but of other ChemComps linked to it. As such allows the definition of bonds, Torsions, Stereochemistry etc. involving ChemAtoms from several ChemComps. The key element in the definition of LinkEnds.
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: None
Children: None
Constructor: newObj = LinkAtom( chemComp,name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
elementSymbol Word 0..1 Derived. There for compatibility - is always None  
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
boundLinkEnd LinkEnd 0..1 linkEnd with link directly bound to LinkAtom  
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  
remoteLinkEnd LinkEnd 0..1 LinkEnd where LinkAtom is remoteLinkAtom  
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
elementSymbol
getElementSymbol Word - non-std.
name
getName Word -
setName - Word
subType
getSubType Int -
setSubType - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
boundLinkEnd
getBoundLinkEnd LinkEnd -
setBoundLinkEnd - LinkEnd
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 -
remoteLinkEnd
getRemoteLinkEnd LinkEnd -
setRemoteLinkEnd - LinkEnd
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 LinkAtom 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_00038

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

subtype_must_be_one
Constraint code: self.subType == 1
Known inward one-way links: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Fri Mar 28 11:18:04 2014    from data model package  ccp.api.molecule.ChemComp.LinkAtom   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk