Data Model version 2.1.2
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Class: Experiment

The Experiment constructor includes non-standard actions.
    A description of an NMR experiment. This corresponds to a single collection of data and so is roughly equivalent to a single Bruker expName/n or a Varian .. directory. The data model contains no description of either a generic experiment or a combination of pulse sequence, sample, conditions and so on that may be recorded several times.

    Creating an Experiment autiomatically creates the
    correct number of ExpDims as well.
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: name, numDim
Known Subclasses: None
Children:
link dataSources to class DataSource
link expChainStates to class ExpChainState
link expDims to class ExpDim
link expTransfers to class ExpTransfer
Constructor: newObj = Experiment( nmrProject,name=value, numDim=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
date DateTime 0..1 Date experiment was acquired (starting date).  
details String 0..1 Free text, for notes, explanatory comments, etc.  
name Line 1..1 name of Experiment, freely chosen and modifiable.  
nmrTubeType Line 0..1 text field describing NMR tube type. E.g. "Shigemi 10mm"  
numDim Int 1..1 number of dimensions.  
numScans Int 0..1 Number of transients averaged per data point. A single scan for a complex point counts as numScans 1, not 2.  
sampleState ExpSampleState 0..1 State of sample during experiment.  
sampleVolume Float 0..1 Sample volume  
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  
spinningAngle Float 0..1 NMR tube spinning angle (in degrees) relative to the magnet bore axis.  
spinningRate Float 0..1 NMR tube spinning rate (in Hz)  
userExpCode Line 0..1 User experiment code; typically referes to external data organisation. E.g. lab book page or lab book ID.  
volumeUnit Word 0..1 Unit for sample volume.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
citations ccp.api.general.Citation.Citation 0..* Citation for NMR experiment pulse sequence.  
dataLists DataList 0..* measurement lists valid for Experiment. There can be several, seeing that there may be measurements of different types.  
dataSources DataSource 0..* (Child link). child link  
derivationMethod ccp.api.general.Method.Method 0..1 Method used to derive Experiment - only meaningful for Experiments where derivedFrom is not empty  
derivedFrom Experiment 0..* Experiments from which the current Experiment is derived  
derivedTo Experiment 0..* Experiments that are derived from the data in this one.  
dipolarRelaxList DipolarRelaxList 0..1 Dipole-diploe relaxation list valid for Experiment  
entries ccp.api.nmr.NmrEntry.Entry 0..* Bmrb Entries for Nmr Experiment  
expChainStates ExpChainState 0..* (Child link). child link to class ExpChainState  
expDims ExpDim 0..* (Child link). child link  
expTransfers ExpTransfer 0..* (Child link). child link to class ExpTransfer  
hExchProtectionList HExchProtectionList 0..1 Hydrogen exchange protection factor list valid for experiment  
hExchRateList HExchRateList 0..1 Hydrogen exchange rate list valid for experiment  
isotropicS2List IsotropicS2List 0..1 isotroisc order parameter list valid for Experiment  
jCouplingList JCouplingList 0..1 JcouplingList valid for Experiment  
labeledMixtures ccp.api.molecule.LabeledMolecule.LabeledMixture 0..* LabeledMixtures that describe molecules for Experiment. There should be only one LabeledMixture for every Molecule, but the constraint is not currently enforced.  
molSystems ccp.api.molecule.MolSystem.MolSystem 0..* MolSystems involved in Experiment  
nmrExpSeries NmrExpSeries 0..* Experiment series that involve experiment  
nmrProject NmrProject 1..1 (Parent link). parent link  
noeList NoeList 0..1 List of homonuclear NOEs for experiment  
parent NmrProject 1..1 link to parent object - synonym for nmrProject  
pkaList PkaList 0..1 pKa list valid for Experiment  
probe ccp.api.general.Instrument.NmrProbe 0..1 Probe used for acquiring experiment  
rawData DataSource 0..1 DataSource containing raw unprocessed data for experiment.  
rdcList RdcList 0..1 List of Reduced Dipolar Couplings for Experiment  
refExperiment ccp.api.nmr.NmrExpPrototype.RefExperiment 0..1 Reference experiment corresponding to Experiment.  
sample ccp.api.lims.Sample.Sample 0..1 Sample on which experiment is carried out.  
sampleConditionSet SampleConditionSet 0..1 Set of sample conditions that apply to an experiment  
shiftAnisotropyList ShiftAnisotropyList 0..1 ShiftAnisotropyList valid for Experiment  
shiftDifferenceList ShiftDifferenceList 0..1 Chemical shift difference list relevant for Experiment  
shiftList ShiftList 0..1 Chemical shift list relevant for Experiment  
shiftReferences ShiftReference 0..* Shift references used for Experiment  
spectralDensityList SpectralDensityList 0..1 List of spectral densities valid for Experiment  
spectrometer ccp.api.general.Instrument.NmrSpectrometer 0..1 Spectrometer used for Experiment  
t1List T1List 0..1 T1 measurement list valid for Experiment.  
t1RhoList T1RhoList 0..1 List of T1rho relaxation valid for Experiment  
t2List T2List 0..1 T2 list valid for Experiment  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
date
getDate DateTime -
setDate - DateTime
details
getDetails String -
setDetails - String
name
getName Line -
setName - Line
nmrTubeType
getNmrTubeType Line -
setNmrTubeType - Line
numDim
getNumDim Int -
setNumDim - Int
numScans
getNumScans Int -
setNumScans - Int
sampleState
getSampleState ExpSampleState -
setSampleState - ExpSampleState
sampleVolume
getSampleVolume Float -
setSampleVolume - Float
serial
getSerial Int -
setSerial - Int
spinningAngle
getSpinningAngle Float -
setSpinningAngle - Float
spinningRate
getSpinningRate Float -
setSpinningRate - Float
userExpCode
getUserExpCode Line -
setUserExpCode - Line
volumeUnit
getVolumeUnit Word -
setVolumeUnit - Word

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
citations
getCitations ccp.api.general.Citation.Citation Set -
setCitations - ccp.api.general.Citation.Citation Set
sortedCitations ccp.api.general.Citation.Citation List -
findFirstCitation ccp.api.general.Citation.Citation keyword=value pairs
findAllCitations ccp.api.general.Citation.Citation Set keyword=value pairs
dataLists
getDataLists DataList Set -
setDataLists - DataList Set
sortedDataLists DataList List -
addDataList - DataList
removeDataList - DataList
findFirstDataList DataList keyword=value pairs
findAllDataLists DataList Set keyword=value pairs
dataSources
getDataSources DataSource Set -
sortedDataSources DataSource List -
findFirstDataSource DataSource keyword=value pairs
findAllDataSources DataSource Set keyword=value pairs
derivationMethod
getDerivationMethod ccp.api.general.Method.Method -
setDerivationMethod - ccp.api.general.Method.Method
derivedFrom
getDerivedFrom Experiment Set -
setDerivedFrom - Experiment Set
sortedDerivedFrom Experiment List -
addDerivedFrom - Experiment
removeDerivedFrom - Experiment
findFirstDerivedFrom Experiment keyword=value pairs
findAllDerivedFrom Experiment Set keyword=value pairs
derivedTo
getDerivedTo Experiment Set -
setDerivedTo - Experiment Set
sortedDerivedTo Experiment List -
addDerivedTo - Experiment
removeDerivedTo - Experiment
findFirstDerivedTo Experiment keyword=value pairs
findAllDerivedTo Experiment Set keyword=value pairs
dipolarRelaxList
getDipolarRelaxList DipolarRelaxList -
setDipolarRelaxList - DipolarRelaxList
entries
getEntries ccp.api.nmr.NmrEntry.Entry Set -
setEntries - ccp.api.nmr.NmrEntry.Entry Set
sortedEntries ccp.api.nmr.NmrEntry.Entry List -
addEntry - ccp.api.nmr.NmrEntry.Entry
removeEntry - ccp.api.nmr.NmrEntry.Entry
findFirstEntry ccp.api.nmr.NmrEntry.Entry keyword=value pairs
findAllEntries ccp.api.nmr.NmrEntry.Entry Set keyword=value pairs
expChainStates
getExpChainStates ExpChainState Set -
sortedExpChainStates ExpChainState List -
findFirstExpChainState ExpChainState keyword=value pairs
findAllExpChainStates ExpChainState Set keyword=value pairs
expDims
getExpDims ExpDim Set -
sortedExpDims ExpDim List -
findFirstExpDim ExpDim keyword=value pairs
findAllExpDims ExpDim Set keyword=value pairs
expTransfers
getExpTransfers ExpTransfer Set -
sortedExpTransfers ExpTransfer List -
findFirstExpTransfer ExpTransfer keyword=value pairs
findAllExpTransfers ExpTransfer Set keyword=value pairs
hExchProtectionList
getHExchProtectionList HExchProtectionList -
setHExchProtectionList - HExchProtectionList
hExchRateList
getHExchRateList HExchRateList -
setHExchRateList - HExchRateList
isotropicS2List
getIsotropicS2List IsotropicS2List -
setIsotropicS2List - IsotropicS2List
jCouplingList
getJCouplingList JCouplingList -
setJCouplingList - JCouplingList
labeledMixtures
getLabeledMixtures ccp.api.molecule.LabeledMolecule.LabeledMixture Set -
setLabeledMixtures - ccp.api.molecule.LabeledMolecule.LabeledMixture Set
sortedLabeledMixtures ccp.api.molecule.LabeledMolecule.LabeledMixture List -
addLabeledMixture - ccp.api.molecule.LabeledMolecule.LabeledMixture
removeLabeledMixture - ccp.api.molecule.LabeledMolecule.LabeledMixture
findFirstLabeledMixture ccp.api.molecule.LabeledMolecule.LabeledMixture keyword=value pairs
findAllLabeledMixtures ccp.api.molecule.LabeledMolecule.LabeledMixture Set keyword=value pairs
molSystems
getMolSystems ccp.api.molecule.MolSystem.MolSystem Set -
setMolSystems - ccp.api.molecule.MolSystem.MolSystem Set
sortedMolSystems ccp.api.molecule.MolSystem.MolSystem List -
addMolSystem - ccp.api.molecule.MolSystem.MolSystem
removeMolSystem - ccp.api.molecule.MolSystem.MolSystem
findFirstMolSystem ccp.api.molecule.MolSystem.MolSystem keyword=value pairs
findAllMolSystems ccp.api.molecule.MolSystem.MolSystem Set keyword=value pairs
nmrExpSeries
getNmrExpSeries NmrExpSeries Set -
setNmrExpSeries - NmrExpSeries Set
sortedNmrExpSeries NmrExpSeries List -
addNmrExpSeries - NmrExpSeries
removeNmrExpSeries - NmrExpSeries
findFirstNmrExpSeries NmrExpSeries keyword=value pairs
findAllNmrExpSeries NmrExpSeries Set keyword=value pairs
nmrProject
getNmrProject NmrProject -
noeList
getNoeList NoeList -
setNoeList - NoeList
parent
getParent NmrProject -
pkaList
getPkaList PkaList -
setPkaList - PkaList
probe
getProbe ccp.api.general.Instrument.NmrProbe -
setProbe - ccp.api.general.Instrument.NmrProbe
rawData
getRawData DataSource -
setRawData - DataSource
rdcList
getRdcList RdcList -
setRdcList - RdcList
refExperiment
getRefExperiment ccp.api.nmr.NmrExpPrototype.RefExperiment -
setRefExperiment - ccp.api.nmr.NmrExpPrototype.RefExperiment
sample
getSample ccp.api.lims.Sample.Sample -
setSample - ccp.api.lims.Sample.Sample
sampleConditionSet
getSampleConditionSet SampleConditionSet -
setSampleConditionSet - SampleConditionSet
shiftAnisotropyList
getShiftAnisotropyList ShiftAnisotropyList -
setShiftAnisotropyList - ShiftAnisotropyList
shiftDifferenceList
getShiftDifferenceList ShiftDifferenceList -
setShiftDifferenceList - ShiftDifferenceList
shiftList
getShiftList ShiftList -
setShiftList - ShiftList
shiftReferences
getShiftReferences ShiftReference Set -
setShiftReferences - ShiftReference Set
sortedShiftReferences ShiftReference List -
addShiftReference - ShiftReference
removeShiftReference - ShiftReference
findFirstShiftReference ShiftReference keyword=value pairs
findAllShiftReferences ShiftReference Set keyword=value pairs
spectralDensityList
getSpectralDensityList SpectralDensityList -
setSpectralDensityList - SpectralDensityList
spectrometer
getSpectrometer ccp.api.general.Instrument.NmrSpectrometer -
setSpectrometer - ccp.api.general.Instrument.NmrSpectrometer
t1List
getT1List T1List -
setT1List - T1List
t1RhoList
getT1RhoList T1RhoList -
setT1RhoList - T1RhoList
t2List
getT2List T2List -
setT2List - T2List

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Experiment 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
newDataSource DataSource dataType, name, numDim, ...
newExpChainState ExpChainState chainState, ...
newExpDim ExpDim dim, ...
newExpTransfer ExpTransfer expDimRefs, ...

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_00028

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

for i in range(self.numDim or 0):
  self.newExpDim(dim=i+1)

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

number_of_expDims_eq_numDim
Constraint code: self.numDim == len(self.expDims)
Known inward one-way links: ccp.api.nmr.NmrConstraint.AbstractConstraintList.experiments
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:55 2015    from data model package  ccp.api.nmr.Nmr.Experiment   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk