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Class: ExpDimRef


    This class describes the referencing for values that can appear on an axis in an NMR spectrum. There may be several ExpDimRef for each dim, either because the experiment is the sum of several experiments with differently referenced axes (e.g. 15N/13C HSQC), or because the actual peak position is a linear combination of different contributions with different referencings (J-coupling, reduced-dimensionality, or projection experiments).The kinds of linear combiantion possible are determined by the dimensionScalings;whether the experiment is a sum of several experiments is determined by the groupingNumber. Note that ExpDimRefs are only relevant to an AbstractDataDim if they are linked with a DimensionScaling
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Attribute Methods
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Appendix

Inheritance:


Details:

Parent: link expDim to class ExpDim
Main key: serial
Mandatory Attributes: sf
Known Subclasses: None
Children:
link expDimRefMappings to class ExpDimRefMapping
Constructor: newObj = ExpDimRef( expDim,sf=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
baseFrequency Float 0..1 The nominal base frequency in MHz for the measured frequency. Instrument parameter. The actual carrier frequency (sf) can be seen as the sum of a base frequency (this attribute) and a relative offset (O1 in Bruker terms - not stored in this data model but equal to (sf minus baseFrequency) in Hz). Not relevant in all cases (see sf attribute). Should be left blank where not relevant, but set equal to sf where no separate baseFrequency is known.  
constantTimePeriod Float 0..1 Total constant-time period available; the period over which the relevant coupling constants are active rather than the maximum value of the increment (which can be calculated from other data). Alternative formulation: the time between 90 deg pulses, ignoring 180 deg pulses (normal, shaped, or composite). Note that this parameter serves for nomal NMR experiments, but may be irrelevant in some other cases.  
displayName Word 0..1 Short string e.g. 'H1',' H', 'CA', 'Ca-1' used for display annotation, for naming decomposition shapes, etc. Should be unique within an experiment, but it is up to the user to enforce the constraint  
groupingNumber PositiveInt 1..1 Divides ExpDimRefs belonging to a given ExpDim into mutually exclusive groupings. If a PeakDim is connected to several ExpDimRefs (via DataDimRefs and possible PeakDimComponents), the ExpDimRefs must all have teh same groupingNumber. Only wexperiments that have different kinds of peaks on the same axis will use more than one groupingNumber. The only practical example seems to be H[{C|N}]_H.NOESY - a 13C HSQC-NOESY and 15N HSQC-NOESY acquired together in a single dataset.  
hasAliasedFreq Boolean 1..1 Derived. is dimension aliased? If yes, maxAliasedFreq and minAliasedFeq give the regions within which signals may be found. If no, signals can be found in the region covered by the points of the spectrum, neither more nor less. By definition hasAliasedFreq is False if either maxAliasedFreq or minAliasedFreq are not set.  
isAxisReversed Boolean 1..1 Set to true if the highest value on the axis corresponds to the lowest point number, and to false otherwise. Most real cases will have isAxisReversed true, as this is how ppm axes behave.  
isFolded Boolean 1..1 Boolean defining whether the dimension is folded in the true meaning of the word (default is False, which is the case for most experiments in 2003). All regularly sampled experiments are in principle aliased (which is a different question).  
isotopeCodes Word 0..* Isotope identification strings for isotopes. NB there can be several isotopes for e.g. J-coupling or multiple quantum coherence.  
maxAliasedFreq Float 0..1 Describes aliasing - maximum value actually possible for the (unaliased) frequency in units of ExpDimRef.unit. Note that all Fourier transformed data are by definition aliased - the difference lies in which frequency regions may contain signals. This attribute serves for normal NMR spectra but may be irrelevant in some other cases.  
measurementType ccp.api.nmr.NmrExpPrototype.ExpMeasurementType 1..1 String enum for measurement type of the referenced parameter in this dimension. Describes the type of measurementList that would hold values measured on this axis. enum would include 'None' for e.g. temperature axes.  
minAliasedFreq Float 0..1 Describes aliasing - minimum value actually possible for the (unaliased) frequency in units of ExpDimRef.unit. Note that all Fourier transformed data are by definition aliased - the difference lies in which frequency regions may contain signals. This attribute serves for normal NMR spectra but may be irrelevant in some other cases.  
name Word 0..1 Name of the measurement being measured by the ExpDimRef. Equivalent to the NmrExpPrototype.AtomSite.name, but does not have to be the same. Serves for user-specific names.  
nominalRefValue Float 0..1 Reference value in ExpDimRef.unit for carrier frequency (or 0.0 for splittings), for use in DataDimRef. E.g. 4.7ppm for protons in water. This value describes the nominal referencing; actual referencing used may include various correction factors, internal referencing etc. and is set in the individual DataDimRef. This attribute serves for normal NMR spectra but may be irrelevant in other cases.  
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  
sf Float 1..1 Absolute frequency at carrier frequency (or at measured frequency 0.0 for splittings) of the spectrum in MHz (or dimensionless - see below). Used for conversion between Hz and ppm, and for scaling with the magnetic field. By definition DataDimRef.valuePerPoint = FreqDataDim.valuePerPoint/ExpDimRef.sf. This is also the case for e.g. coupling constant dimensions, where sf then becomes a dimensionless scaling factor.  
unit Word 0..1 Unit used for value in DataDimRefs (if any). As DataDimRefs are defined only for FreqDataDims this attribute is only relevant for dimensions eventually transformed into FreqDataDims, essentially dimensions that are eventually Fourier Transformed or similar. Unit will be 'ppm' for most standard NMR experiments.  
variableIncrFraction FloatRatio 0..1 Describes the fraction of the incrementation done by actually incrementing delays rather than by constant time. Defined as (actual time increment)/(total increment). Is 0.0 for a pure constant-time experiment and 1.0 for a pure variable-time experiment. This parameter serves for normal NMR experiments but may be irrelevant in some other cases.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
dataDimRefs DataDimRef 0..* DatDimRefs corresponding to ExpDimRef  
derivedTo ExpDimRefMapping 0..* ExpDimRefMappings for ExpDimRefs derived from current ExpDimRef  
dimensionScalings DimensionScaling 0..* ScalingFactors that apply to ExpDimRef  
expDim ExpDim 1..1 (Parent link). parent link  
expDimRefMappings ExpDimRefMapping 0..* (Child link). child link to class ExpDimRefMapping  
expTransfers ExpTransfer 0..* Magentisation transfers involving ExpDimRef  
isotopes ccp.api.molecule.ChemElement.Isotope 0..* Derived. Isotopes corresponding to the ExpDimRef. In the most common case there will be only one Isotope - multiple Isotopes can appear where the ExpDimRef describes e.g. coupling constants or multiple quantum coherence.  
parent ExpDim 1..1 link to parent object - synonym for expDim  
refExpDimRef ccp.api.nmr.NmrExpPrototype.RefExpDimRef 0..1 Corresponding ExpDimRef for RefExperiment  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
baseFrequency
getBaseFrequency Float -
setBaseFrequency - Float
constantTimePeriod
getConstantTimePeriod Float -
setConstantTimePeriod - Float
displayName
getDisplayName Word -
setDisplayName - Word
groupingNumber
getGroupingNumber PositiveInt -
setGroupingNumber - PositiveInt
hasAliasedFreq
getHasAliasedFreq Boolean - non-std.
isAxisReversed
getIsAxisReversed Boolean -
setIsAxisReversed - Boolean
isFolded
getIsFolded Boolean -
setIsFolded - Boolean
isotopeCodes
getIsotopeCodes Word Tuple -
setIsotopeCodes - Word List
addIsotopeCode - Word
removeIsotopeCode - Word
maxAliasedFreq
getMaxAliasedFreq Float -
setMaxAliasedFreq - Float
measurementType
getMeasurementType ccp.api.nmr.NmrExpPrototype.ExpMeasurementType -
setMeasurementType - ccp.api.nmr.NmrExpPrototype.ExpMeasurementType
minAliasedFreq
getMinAliasedFreq Float -
setMinAliasedFreq - Float
name
getName Word -
setName - Word
nominalRefValue
getNominalRefValue Float -
setNominalRefValue - Float
serial
getSerial Int -
setSerial - Int
sf
getSf Float -
setSf - Float
unit
getUnit Word -
setUnit - Word
variableIncrFraction
getVariableIncrFraction FloatRatio -
setVariableIncrFraction - FloatRatio

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
dataDimRefs
getDataDimRefs DataDimRef Set -
setDataDimRefs - DataDimRef Set
sortedDataDimRefs DataDimRef List -
findFirstDataDimRef DataDimRef keyword=value pairs
findAllDataDimRefs DataDimRef Set keyword=value pairs
derivedTo
getDerivedTo ExpDimRefMapping Set -
setDerivedTo - ExpDimRefMapping Set
sortedDerivedTo ExpDimRefMapping List -
findFirstDerivedTo ExpDimRefMapping keyword=value pairs
findAllDerivedTo ExpDimRefMapping Set keyword=value pairs
dimensionScalings
getDimensionScalings DimensionScaling Set -
setDimensionScalings - DimensionScaling Set
sortedDimensionScalings DimensionScaling List -
findFirstDimensionScaling DimensionScaling keyword=value pairs
findAllDimensionScalings DimensionScaling Set keyword=value pairs
expDim
getExpDim ExpDim -
expDimRefMappings
getExpDimRefMappings ExpDimRefMapping Set -
sortedExpDimRefMappings ExpDimRefMapping List -
findFirstExpDimRefMapping ExpDimRefMapping keyword=value pairs
findAllExpDimRefMappings ExpDimRefMapping 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
isotopes
getIsotopes ccp.api.molecule.ChemElement.Isotope Tuple - non-std.
findFirstIsotope ccp.api.molecule.ChemElement.Isotope keyword=value pairs
findAllIsotopes ccp.api.molecule.ChemElement.Isotope List keyword=value pairs
parent
getParent ExpDim -
refExpDimRef
getRefExpDimRef ccp.api.nmr.NmrExpPrototype.RefExpDimRef -
setRefExpDimRef - ccp.api.nmr.NmrExpPrototype.RefExpDimRef

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey ExpDimRef 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
newExpDimRefMapping ExpDimRefMapping derivedFrom, ...

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_00027

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  Fri Mar 28 11:18:25 2014    from data model package  ccp.api.nmr.Nmr.ExpDimRef   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk