Data Model version 2.1.2
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Class: Atom


    Atom in a specific location in a specific molecule in specific surroundings (Chain).

    Atoms can *not* be deleted while they are linked to FixedAtomSets. If this is desired the fixedAtomSets link must be cleared first.
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: None
Constructor: newObj = Atom( residue,name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
name Word 1..1 name of Atom.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
atomSet ccp.api.nmr.Nmr.AtomSet 0..1 Set of atoms in fast exchange with Atom.  
chainStateSets ccp.api.nmr.Nmr.ChainStateSet 0..* ChainStateSets involving Atom.  
chemAtom ccp.api.molecule.ChemComp.ChemAtom 1..1 Derived. ChemAtom corresponding to Atom.  
fixedAtomSets ccp.api.nmr.NmrConstraint.FixedAtomSet 0..* FixedAtomSets (part of Nmr Assignment for Nmr Constraint Lists) involving Atom  
molSysAtomValidations ccp.api.molecule.Validation.MolSysAtomValidation 0..* Validation results for Atom  
nonCovalentBonds NonCovalentBond 0..* Non-covalent bonds in which the atom takes part.  
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
name
getName Word -
setName - Word

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atomSet
getAtomSet ccp.api.nmr.Nmr.AtomSet -
setAtomSet - ccp.api.nmr.Nmr.AtomSet
chainStateSets
getChainStateSets ccp.api.nmr.Nmr.ChainStateSet Set -
setChainStateSets - ccp.api.nmr.Nmr.ChainStateSet Set
sortedChainStateSets ccp.api.nmr.Nmr.ChainStateSet List -
addChainStateSet - ccp.api.nmr.Nmr.ChainStateSet
removeChainStateSet - ccp.api.nmr.Nmr.ChainStateSet
findFirstChainStateSet ccp.api.nmr.Nmr.ChainStateSet keyword=value pairs
findAllChainStateSets ccp.api.nmr.Nmr.ChainStateSet Set keyword=value pairs
chemAtom
getChemAtom ccp.api.molecule.ChemComp.ChemAtom - non-std.
fixedAtomSets
getFixedAtomSets ccp.api.nmr.NmrConstraint.FixedAtomSet Set -
setFixedAtomSets - ccp.api.nmr.NmrConstraint.FixedAtomSet Set
sortedFixedAtomSets ccp.api.nmr.NmrConstraint.FixedAtomSet List -
addFixedAtomSet - ccp.api.nmr.NmrConstraint.FixedAtomSet
removeFixedAtomSet - ccp.api.nmr.NmrConstraint.FixedAtomSet
findFirstFixedAtomSet ccp.api.nmr.NmrConstraint.FixedAtomSet keyword=value pairs
findAllFixedAtomSets ccp.api.nmr.NmrConstraint.FixedAtomSet Set keyword=value pairs
molSysAtomValidations
getMolSysAtomValidations ccp.api.molecule.Validation.MolSysAtomValidation Set -
setMolSysAtomValidations - ccp.api.molecule.Validation.MolSysAtomValidation Set
sortedMolSysAtomValidations ccp.api.molecule.Validation.MolSysAtomValidation List -
addMolSysAtomValidation - ccp.api.molecule.Validation.MolSysAtomValidation
removeMolSysAtomValidation - ccp.api.molecule.Validation.MolSysAtomValidation
findFirstMolSysAtomValidation ccp.api.molecule.Validation.MolSysAtomValidation keyword=value pairs
findAllMolSysAtomValidations ccp.api.molecule.Validation.MolSysAtomValidation Set keyword=value pairs
nonCovalentBonds
getNonCovalentBonds NonCovalentBond Set -
setNonCovalentBonds - NonCovalentBond Set
sortedNonCovalentBonds NonCovalentBond List -
findFirstNonCovalentBond NonCovalentBond keyword=value pairs
findAllNonCovalentBonds NonCovalentBond 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
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_2006-08-16-14:22:54_00029

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.MolStructure.Atom.atom
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:24 2014    from data model package  ccp.api.molecule.MolSystem.Atom   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk