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Class: AtomSite


    An Atom site on the graph of atoms through which magnetisation passes in an experiment. If there is more than one ExpGraph, each AtomSite may be relevant for one or more of these. The AtomSite may be given even if it is never a carrier of magnetisation, for instance to show that coupling to a given nucleus is used for filtering during an experiment.
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Attribute Methods
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Appendix

Inheritance:


Details:

Parent: link nmrExpPrototype to class NmrExpPrototype
Main key: serial
Mandatory Attributes: isotopeCode
Known Subclasses: None
Children: None
Constructor: newObj = AtomSite( nmrExpPrototype,isotopeCode=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
isotopeCode Word 1..1 Isotope code for Isotope making up the ExpAtomSite  
maxNumber NonNegativeInt 0..1 Maximum number of occurrences of atom corresponding to atomSite. maxNumber 2 would mena no more than two atoms could appear in this position. If, for instance a carbon atomSite has a J coupling transfer to a proton AtomSite with maxNumber=2, it means that this ExpGraph will give no observable result for CH3 groups. May be set to zero, which indicates that no atoms of this type are allowed.  
maxShift Float 0..1 maximum value of shift allowed for AtomSite, in ppm. Is not set in normal cases. Together with minShift serves to distinguish frequency-selective sites. For some common cases it is recommended to use standard limits : Aliphatic carbon: <90ppm Aromatic carbon: 90-150ppm CO carbon: > 150ppm CA (for proteins): 40-90ppm  
minNumber NonNegativeInt 1..1 Minimum number of occurrences of atom corresponding to atomSite. MinNumber two wiould mean at least two atoms. If, for instance a carbon atomSite has a J coupling transfer to a proton AtomSite with minNumber=2, it means that this ExpGraph will give observable results only for CH2 and CH3 groups.  
minShift Float 0..1 minimum value of shift allowed for AtomSite, in ppm. Is not set in normal cases. Together with maxShift serves to distinguish frequency-selective sites. The most common use is for distinguishing CO, aliphatic carbon, and 'just' carbon. Aliphatic carbon: <90ppm Aromatic carbon: 90-150ppm CO carbon: > 150ppm CA (for proteins): 40-90ppm  
name Word 0..1 A short string to be used in generating experiment names. If the attribute is not set, the nucleus symbol should be used. Examples of names would be 'CO', 'CA', for e.g. HNCOCA.Note that the name does not have to match with protein or any other naming conventions (proteins use 'C', where we might use 'CO').  
numberStep PositiveInt 1..1 Integer step between allowed number of occurrences of atoms corresponding to this atomSite. If, for instance a carbon atomSite has a J coupling transfer to a proton AtomSite with minNumber=1 and numberStep = 2, there must be 1, 3, 5, ... atoms corresponding to the AtomSite. Uased for instance to indicate 'carbon coupled to an odd number of protons', where you would have a carbon AtomSite, with a JCoupling ExpTransfer to a proton AtomSite witn minNumber 1 and numberStep 2.  
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
expGraphs ExpGraph 0..* Derived. ExpGraphs whre AtomSite appears  
expMeasurements ExpMeasurement 0..* ExpMeasurements involving AtomSite  
expTransfers ExpTransfer 0..* Magnetisation transfer (non-directional) connecting two AtomSites  
isotope ccp.api.molecule.ChemElement.Isotope 0..1 Derived. Isotope making up ExpAtomSite.  
nmrExpPrototype NmrExpPrototype 1..1 (Parent link). parent link  
parent NmrExpPrototype 1..1 link to parent object - synonym for nmrExpPrototype  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
isotopeCode
getIsotopeCode Word -
setIsotopeCode - Word
maxNumber
getMaxNumber NonNegativeInt -
setMaxNumber - NonNegativeInt
maxShift
getMaxShift Float -
setMaxShift - Float
minNumber
getMinNumber NonNegativeInt -
setMinNumber - NonNegativeInt
minShift
getMinShift Float -
setMinShift - Float
name
getName Word -
setName - Word
numberStep
getNumberStep PositiveInt -
setNumberStep - PositiveInt
serial
getSerial Int -
setSerial - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
expGraphs
getExpGraphs ExpGraph Set - non-std.
sortedExpGraphs ExpGraph List -
findFirstExpGraph ExpGraph keyword=value pairs
findAllExpGraphs ExpGraph Set keyword=value pairs
expMeasurements
getExpMeasurements ExpMeasurement Set -
setExpMeasurements - ExpMeasurement Set
sortedExpMeasurements ExpMeasurement List -
addExpMeasurement - ExpMeasurement
removeExpMeasurement - ExpMeasurement
findFirstExpMeasurement ExpMeasurement keyword=value pairs
findAllExpMeasurements ExpMeasurement Set keyword=value pairs
expTransfers
getExpTransfers ExpTransfer Set -
setExpTransfers - ExpTransfer Set
sortedExpTransfers ExpTransfer List -
findFirstExpTransfer ExpTransfer keyword=value pairs
findAllExpTransfers ExpTransfer Set keyword=value pairs
isotope
getIsotope ccp.api.molecule.ChemElement.Isotope - non-std.
nmrExpPrototype
getNmrExpPrototype NmrExpPrototype -
parent
getParent NmrExpPrototype -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey AtomSite 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_2006-08-16-14:22:45_00023

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: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:28 2015    from data model package  ccp.api.nmr.NmrExpPrototype.AtomSite   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk