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Class: ChemAtomNmrRef


    Information about refrence chemical shift for a ChemAtom. The information may apply to a ChemAtom in all ChemCompVars (linking and descriptor both 'any'), in some ChemCompVars (either linking or descriptor 'any') or in a specific ChemCompVar (all other cases). Either the meanValue or the randomCoilValue attribute must be set.
Attributes
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Attribute Methods
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Class Methods
Factory Methods
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Appendix

Inheritance:


Details:

Parent: link chemCompNmrRef to class ChemCompNmrRef
Main key: serial
Mandatory Attributes: name, chemCompVarNmrRefs
Known Subclasses: None
Children:
link chemAtomShiftCorrs to class ChemAtomShiftCorr
Constructor: newObj = ChemAtomNmrRef( chemCompNmrRef,name=value, chemCompVarNmrRefs=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
distribution Float 0..* histogram of frequency distribution. Normalised - must sum to 1.0. The shifts to which the individual points belong are defined so that point i collects the shifts from refValue + valuePerPoint*( i-refPoint) to refValue + valuePerPoint*( i+1-refPoint).  
meanValue Float 0..1 Average predicted chemical shift value (in ppm)  
name Word 1..1 Name of ChemAtom. Part of key for object.  
numPoints Int 1..1 Derived. Number of points in shift distribution  
randomCoilValue Float 0..1 Chemical shift for random coil conformation. Need not be the same as the mean value over the known distribution.  
refPoint Float 1..1 Reference point number (in floating point, first point is 0.0) for referencing chemical shift axis of distribution.  
refValue Float 1..1 Reference value (in ppm) for setting chemical shift axis of distribution.  
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  
stdDev Float 0..1 Standard deviation (in ppm) over the chemical shift distribution  
subType Int 1..1 subType of ChemAtom referred to.  
valuePerPoint Float 0..1 The value per point on the histogram axis, equivalent to the width of a column.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
chemAtomShiftCorrs ChemAtomShiftCorr 0..* (Child link). child link to class ChemAtomShiftCorr  
chemAtoms ccp.api.molecule.ChemComp.AbstractChemAtom 1..* Derived. ChemAtom to which reference information applies.  
chemCompNmrRef ChemCompNmrRef 1..1 (Parent link). parent link  
chemCompVarNmrRefs ChemCompVarNmrRef 1..* ChemCompNmrRefs that contain this ChemAtomNmrRef.  
parent ChemCompNmrRef 1..1 link to parent object - synonym for chemCompNmrRef  
shiftDistributions ChemAtomNmrDistrib 0..* Chemicasl shift distribution records involving ChemAtomNmrRef  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
distribution
getDistribution Float Tuple -
setDistribution - Float List
addDistribution - Float non-std.
removeDistribution - Float non-std.
meanValue
getMeanValue Float -
setMeanValue - Float
name
getName Word -
setName - Word
numPoints
getNumPoints Int - non-std.
randomCoilValue
getRandomCoilValue Float -
setRandomCoilValue - Float
refPoint
getRefPoint Float -
setRefPoint - Float
refValue
getRefValue Float -
setRefValue - Float
serial
getSerial Int -
setSerial - Int
stdDev
getStdDev Float -
setStdDev - Float
subType
getSubType Int -
setSubType - Int
valuePerPoint
getValuePerPoint Float -
setValuePerPoint - Float

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chemAtomShiftCorrs
getChemAtomShiftCorrs ChemAtomShiftCorr Set -
sortedChemAtomShiftCorrs ChemAtomShiftCorr List -
findFirstChemAtomShiftCorr ChemAtomShiftCorr keyword=value pairs
findAllChemAtomShiftCorrs ChemAtomShiftCorr Set keyword=value pairs
chemAtoms
getChemAtoms ccp.api.molecule.ChemComp.AbstractChemAtom Set - non-std.
sortedChemAtoms ccp.api.molecule.ChemComp.AbstractChemAtom List -
findFirstChemAtom ccp.api.molecule.ChemComp.AbstractChemAtom keyword=value pairs
findAllChemAtoms ccp.api.molecule.ChemComp.AbstractChemAtom Set keyword=value pairs
chemCompNmrRef
getChemCompNmrRef ChemCompNmrRef -
chemCompVarNmrRefs
getChemCompVarNmrRefs ChemCompVarNmrRef Set -
setChemCompVarNmrRefs - ChemCompVarNmrRef Set
sortedChemCompVarNmrRefs ChemCompVarNmrRef List -
addChemCompVarNmrRef - ChemCompVarNmrRef
removeChemCompVarNmrRef - ChemCompVarNmrRef
findFirstChemCompVarNmrRef ChemCompVarNmrRef keyword=value pairs
findAllChemCompVarNmrRefs ChemCompVarNmrRef Set keyword=value pairs
parent
getParent ChemCompNmrRef -
shiftDistributions
getShiftDistributions ChemAtomNmrDistrib Set -
setShiftDistributions - ChemAtomNmrDistrib Set
sortedShiftDistributions ChemAtomNmrDistrib List -
findFirstShiftDistribution ChemAtomNmrDistrib keyword=value pairs
findAllShiftDistributions ChemAtomNmrDistrib Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey ChemAtomNmrRef 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
newChemAtomShiftCorr ChemAtomShiftCorr ccpCode, molType, seqOffset, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:25:09_00002

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

Distribution_is_normalised
Constraint code: isValid = True

ll = self.distribution
if ll:
  floatTolerance = 1.0e-5

  if abs(sum(ll)-1.0) > floatTolerance:
    isValid = False

Constraint name:

meanValue_or_randomCoilValue_must_be_set
Constraint code: self.meanValue is not None or self.randomCoilValue is not None
Known inward one-way links: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:35 2015    from data model package  ccp.api.nmr.NmrReference.ChemAtomNmrRef   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk