Data Model version 2.0.6
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Class: Atom


    Atom in Coordinate description - local equivalent of MolSystem.Atom for a given set of coordinates.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link residue to class Residue
Main key: name
Mandatory Attributes: name
Known Subclasses: None
Children:
link coords to class Coord
Constructor: newObj = Atom( residue,name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
elementSymbol Word 1..1 Derived. Element Symbol (e.g. 'C', 'He', 'Sn').  
name Word 1..1 Atom Name - identical to Molsystem.Atom.name of corersponding Molsysterm Atom. Part of object key, and foreign key used for deriving the link to MolSystem.Atom  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
atom ccp.api.molecule.MolSystem.Atom 1..1 Derived. MolSystem Atom, coresponding to Coordinate Atom  
atomValidations ccp.api.molecule.Validation.AtomValidation 0..* Validation results that include Atom  
chemAtom ccp.api.molecule.ChemComp.ChemAtom 1..1 Derived. ChemAtom corresponding to Atom  
coords Coord 0..* (Child link). child link to class Coord  
parent Residue 1..1 link to parent object - synonym for residue  
residue Residue 1..1 (Parent link). parent link  

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

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atom
getAtom ccp.api.molecule.MolSystem.Atom - non-std.
atomValidations
getAtomValidations ccp.api.molecule.Validation.AtomValidation Set -
setAtomValidations - ccp.api.molecule.Validation.AtomValidation Set
sortedAtomValidations ccp.api.molecule.Validation.AtomValidation List -
addAtomValidation - ccp.api.molecule.Validation.AtomValidation
removeAtomValidation - ccp.api.molecule.Validation.AtomValidation
findFirstAtomValidation ccp.api.molecule.Validation.AtomValidation keyword=value pairs
findAllAtomValidations ccp.api.molecule.Validation.AtomValidation Set keyword=value pairs
chemAtom
getChemAtom ccp.api.molecule.ChemComp.ChemAtom - non-std.
coords
getCoords Coord Set -
sortedCoords Coord List -
findFirstCoord Coord keyword=value pairs
findAllCoords Coord Set keyword=value pairs
parent
getParent Residue -
residue
getResidue Residue -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Atom 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
newCoord Coord model, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:55_00004

isImplicit:

False

Tag

Value
repositoryId $Id: Atom.xml,v 1.57 2011-01-13 14:40:34 rhfogh Exp $

Tag

Value
repositoryTag $Name: not supported by cvs2svn $

Special constructor code:

None

Special destructor code:

None

Constraints:

None
Known inward one-way links: None
  Data Model Version 2.0.6
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Wed Aug 7 15:06:38 2013    from data model package  ccp.api.molecule.MolStructure.Atom   revision 1.57  
  Work done by the CCPN team.
www.ccpn.ac.uk