Data Model version 2.1.2
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Class: AtomSet


    Group of Atoms for use in Assignment. Connects Resonance and Atom records. All Atoms connected to an AtomSet are by definition equivalent and in fast exchange throughout the project. Atoms in an atomSet could be e.g. the protons of any -CH3 or -NH3 group, or HD1/HD2 in a fast-flipping Phe, or free water protons with either bound water protons (molecular exchange) or Ser OH protons (proton exchange). Atoms that can not be in an AtomSet are e.g. a Lys epsilon CH2 (not in fast exchange) or Phe HD1/HD2 if the Phe is in slow exchange under any circumstances within the project.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link nmrProject to class NmrProject
Main key: serial
Mandatory Attributes: atoms
Known Subclasses: None
Children: None
Constructor: newObj = AtomSet( nmrProject,atoms=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
name Line 0..1 name of AtomSet  
serial Int 1..1 Serial number of object. Serves as object main key. Serial numbers of deleted objects are not re-used. Serial numbers can only be set by the implementation. Values are in practice always positive, since negative values are interpreted as a signal to set the next free serial  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
atoms ccp.api.molecule.MolSystem.Atom 1..* Atoms making up the AtomSet. Atoms that are part of the same AtomSet are by definition equivalent and in fast exchange on the NMR time scale throughout the project.  
nmrProject NmrProject 1..1 (Parent link). parent link  
parent NmrProject 1..1 link to parent object - synonym for nmrProject  
resonanceSets ResonanceSet 0..* ResonanceSets corresponding to AtomSet. Part of assigning Atoms to Resonances  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
name
getName Line -
setName - Line
serial
getSerial Int -
setSerial - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atoms
getAtoms ccp.api.molecule.MolSystem.Atom Set -
setAtoms - ccp.api.molecule.MolSystem.Atom Set
sortedAtoms ccp.api.molecule.MolSystem.Atom List -
findFirstAtom ccp.api.molecule.MolSystem.Atom keyword=value pairs
findAllAtoms ccp.api.molecule.MolSystem.Atom Set keyword=value pairs
nmrProject
getNmrProject NmrProject -
parent
getParent NmrProject -
resonanceSets
getResonanceSets ResonanceSet Set -
setResonanceSets - ResonanceSet Set
sortedResonanceSets ResonanceSet List -
addResonanceSet - ResonanceSet
removeResonanceSet - ResonanceSet
findFirstResonanceSet ResonanceSet keyword=value pairs
findAllResonanceSets ResonanceSet Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey AtomSet 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_2006-08-16-14:22:46_00015

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

all_atoms_must_be_same_element
Constraint code: isValid = True
atoms = self.atoms
if len(atoms) > 1:
  element = self.findFirstAtom().chemAtom.elementSymbol
  for atom in self.atoms:
    if atom.chemAtom.elementSymbol != element:
      isValid = False
      break
Known inward one-way links: ccpnmr.api.Analysis.AtomSetMapping.atomSetsccpnmr.api.AnalysisV3.AtomSetMapping.atomSets
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:53 2015    from data model package  ccp.api.nmr.Nmr.AtomSet   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk