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Package: Nmr


    All data specific to NMR spectroscopy, including NMR experiments, analysis and assignments, constraint lists, shift lists, etc.
Classes
Data Types
Data Obj Types

Imported Packages:

NmrExpPrototype,   ccp.api.general.Citation,   ccp.api.general.DataLocation,   ccp.api.general.Instrument,   ccp.api.general.Method,   ccp.api.general.Template,   ccp.api.lims.Sample,   ccp.api.molecule.ChemComp,   ccp.api.molecule.ChemElement,   ccp.api.molecule.LabeledMolecule,   ccp.api.molecule.MolStructure,   ccp.api.molecule.MolSystem,   ccp.api.molecule.Molecule,   ccp.api.molecule.Validation,   memops.api.AccessControl,   memops.api.Implementation

Packages Importing ccp.api.nmr.Nmr:

NmrCalc,   NmrConstraint,   NmrEntry,   NmrScreen,   cambridge.api.Dangle,   ccpnmr.api.Analysis

Classes:

Class Description
AbstractDataDerivation Data Derivation that produces one or more derived data items in a single fitting.
AbstractDataDim Information about the individual dimensions in the data source. Each DataDim object corresponds to a single ExpDim object. Note that abstractDataDim.dim need not be equal to the corresponding expDim.dim.
AbstractMeasurement NMR parameter value (e.g. Chemical Shift, Coupling Constant, TROESY shift, MQ frequency, or in general any measured result associated with one or more Resonances (and through them with Atoms).
AbstractMeasurementList Abstract list of measurements. Different kinds of measurements belong to different kinsd of lists. All measurements belong to a list.

NB All MeasurementLists have the attribute 'unit' (mandatory, datatype Word) giving the unit of measurement. For each kind of MeasurementList the unit will default to the recommended value.
AbstractPeakDimContrib PeakDim assignment contribution, one of the multiple assignments of a PeakDim. This is a connection record, connecting a PeakDim and a PeakContrib to a Resonance or a set of Resonances. Note that two different AbstractPeakDimContribs may have both the same PeakDim and the same Resonance.

If there is only one peakContrib (or none) for the relevant PeakDim, the peakContribs link defaults to the only PeakContrib possible, creating it if necessary. This is the normal case. Note that this makes peakContribs an optional input parameter to the PeakDimContrib constructor, even though each AbstractPeakDimContrib must have at least one PeakContrib.
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.
ChainState One state of a molecule, belonging to a specific ChainStateSite. E.g. 'cis', 'protonated', 'bound-form', or 'loop-conformation-A'
ChainStateSet Defines a set of states that apply to a chain. The ChainStates in a ChainStateSet are mutually exclusive. Their exact nature is defined by the StateSiteType.

ChainStates serve to distinguish Resonances that arise from the same atom in different states of the chain, to describe the State of molecules used for a structure generation, and to define the state (including fast exchange) of a chain under the conditions of a given experiment.

A ChainState only describes the situation for one particular set of alternatives, and implies nothing about others. For example, a molecule with seven prolines in slow cis/trans equilibrium would have seven ChainStateSets. A given resonance could then be described (by linking it to ChainStates) as Pro-47 cis, Pro-112 trans, without implying anything about the state of the remaining five prolines.  

stateSetType and ChainState.name are freely changeable, reflecting the fact that the origin of sets of observed resonances is often unknown until a late stage of analysis. Once the precise situation is known, the following procedures should be used where applicable:

stateSetType: cis/trans
ChainState names: cis, trans
Links: to the two atoms that are cis or trans (in the case of peptide bonds to the two alpha carbons of the residues involved).

stateSetType: protonation
ChainState names: protonated, deprotonated
Links: To the proton that is removed on deprotonation.

stateSetType: isotopomer
ChainState names : isotope codes of the relevant isotopes (e.g. 12C, 13C)
Links: To the atom(s) that change isotope.
NB this mechanism only handles atoms of the same type that change in parallel. If the isotope substitution pattern is more complex, is may be necessary to define several ChainStateSets, possibly redefining the ChainStates when the situation has been analysed.

stateSetType: folding
ChainState names: folded, unfolded
Links : to the residues involved in the transition.

stateSetType : conformation
ChainState names: can be chosen freely
Links: to the residues changing conformation.
DataDerivation Member of a DataList.
DataDimRef Referencing information for a dimension of a DataSource ('spectrum'). A given dimension can have several alternative referencings.
DataList List of measurements, derived or not. Designed to accomodate measurements that do not fit any of the predefined categories.
DataSource This class describes the stored data matrix from an NMR spectrum.
It is a general class that may be used to describe data in the time domain, frequency domain a combination of the two, or axes that are neither time nor frequency
The actual data are kept in a location defined by the dataLocation link. The DataSource attributes contain the information required to extract the data from the source file, but the data model as such does not include the actual data matrix
DataSourceImage Locatino of Images to document DataSource
Datum Measurement, possibly derived, not fitting into a predefined type
DerivedData A measurement derived from peak data and/or other (non-derived) measurements. It is assigned to one or more Resonances, depending on its type.
DerivedDataList List of derived measurements. A derived measurement may be calculated from peak data and/or other (non-derived) measurements. Several measurement values may be calculated in a single derivation. Values are assigned to one or more Resonances depending on their type. A list may contain several values for the same (set of) resonance(s).
DimensionScaling Scaling factors used for various ExpDimRefs in this particular DataSource.
Note: If there is no DimensionScaling connecting a DataDim with an ExpDimRef (both belonging to the same ExpDim) this means that the ExpDimRef is not used. Note that a DimensionScaling with scalingFactors == (1.0,) is created automatically when a FreqDataDim or FidDataDim is created and 1) for each relevant ExpDimRef that has a refExpDimRef, 2) if nothing is created under 1) but there is only one relevant ExpDimRef, 3) if nothing is created above but there is ony one relevant ExpDimRef  with measurementType == 'Shift'
DipolarRelaxList List of dipole-dipole relaxation measurements.
DipolarRelaxation Dipole-dipole relaxation measurement
ExpChainState ChainStates describing the state of a molecule under the conditions of Experiment. If there is only one ChainState for each ChainStateSet this means that that was the state of the molecule (e.g. 'folded, 'loop 1 in conformation A'). If there is more than one ChainState for a given ChainStateSet, this means that the molecule was in fast exchange betnween those states, with relative probabilities given by the relative weights of the ExpChainStates.
ExpDim Dimension of Experiment
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
ExpDimRefMapping Mapping to other ExpDimRefs used in deriving this one.
ExpTransfer Describes transfer of magnetisation between two ExpDimRef belonging to different ExpDim of the same Experiment.
Experiment 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.
ExternalShiftReference Chemical Shift referencing. The reference actually used (not the one quoted against). Reference is external to the sample (e.g. in a coaxial capillary).
FidDataDim An FID dimension or any other dimension with a regular grid of values. A FidDataDim can contain any kind of regularly sampled data subjected to any kind of processing, except that data in the Fourier transformed domain relative to the originally acquired data must be put in a FreqDataDim.
FreqDataDim A frequency domain dimension in the data source file, i.e. a regularly sampled dimension that is in the Fourier transform domain relative to the original data.
HExchProtection Hydrogen exchange protection factor measurement. Strictly speaking this is simply a list of exchange rate as a ratio to a reference value (newValue/refValue).
HExchProtectionList List of hydrogen exchange protection factor measurements.
HExchRate Hydrogen exchange rate measurement.
HExchRateList List of hydrogen exchange rate measurements.
InternalShiftReference Chemical Shift referencing. The reference actually used (not the one quoted against). Used for references internal to (part of) the sample.
IsotropicS2 Order parameter (S2), calculated assuming isotropic motion.
IsotropicS2Derivation Data Derivation for a set of order parameters.
IsotropicS2List List of order parameters (S2), calculated assuming isotropic motion.
JCoupling J coupling measurement.
JCouplingList List of J coupling measurements
NmrExpSeries Series of Nmr experiments varying some variable. E.g. titration series, temperature series, T1 measurement.
NmrProject grouping of related NMR data
Noe NOE intensity measurement
NoeList List of NOE measurements, homonuclear or heteronuclear.
PKaDerivation Derivation for set of pKa(s) and associated parameters
Peak Crosspeak at a specific position in a specific spectrum.
PeakCluster Cluster of peaks that together make up a (nD) multiplet. The peaks may come from different PeakLists and Experiments.
PeakContrib Crosspeak contribution.  PeakContribs serve two slightly different purposes. They describe a Peak as a sum of different contributions (e.g. ovelapped peaks), whose relative values is determined by their relative weights. They also serve simply as a way of describing mutually exclusive sets of assignment possibilities, without any implication about the peak arising from multiple contributions. The two aspects are almost identical in practice. If all PeakContrib weights are 0.0, as is the default, it can be assumed that the Contribs are only describing assignment possibilities.

Each PeakContrib may have any number (including zero) peakDimContrib for every dim. The set of possible complete assignments for a PeakContrib is found as follows:
For each dimension all PeakDimContribs belonging to the dimension are potential assignments. If there are say 3, 2, and 5 possibilities in the three dimensions (of a 3D peak) there will be a total of 3*2*5=30 possible assignment states belonging to the PeakContrib. If there are no possibilities for one dimension (say 3, 0, and 5 for the three dimensions), there will be 3*5=15 alternative (partial) assignment states.
PeakDim Crosspeak dimension
Note: There is no attribute 'linewidth', as the term is too ambiguous in practical use to allow a clear definition. Various aspects of line widths are covered by positionError, boxWidth, and decayRate.
PeakDimComponent Additional assignment component of peak. In many cases (TROSY, reduced-dimensionality experiments, multiplet components), the position of a peak reflects the sum of more than one NMR parameter. In those cases the additional NMR parameters are assigned through PeakDimComponents. E.g. a DQF-COSY multiplet component would have a main contribution from the shift, and one or more PeakDimComponents for the various couplings that contribute to the peak position.

NOTE: To calculate the value corresponding to the PeakDimComponent, you yourself must calculate xPoints, the (signed) number of points that are due to the PeakDimComponent. The desired value is then self.scalingFactor*self.dataDimRef.pointToValue(xPoints)
PeakDimContrib PeakDimContrib for parameters assigned to a single Resonance (the normal case).
PeakDimContribN PeakDimContrib for cases where assignments are made to two or more Resonances (e.g. J couplings, multiple quantum coherences).
PeakIntensity Peak Intensity covers both volume and height, determined with various methods.
PeakList List of Peaks, all belonging to a specific DataSource.
Pka Derived pKa and associated parameters
PkaList List of derived pKa measurements
Rdc Reduced dipolar coupling measurement.
RdcList List of reduced dipolar coupling measurements.
ResidueProb Connecting record, expressing the probability that a SpinSystem corresponds to specific Residue in a chain
ResidueTypeProb Connecting record, expressing the probability that a SpinSystem corresponds to a ChemComp
Resonance A connection record for assignment. 'Stands for' a single Atom or group of atoms in fast exchange.

The Resonance holds a central place in the Nmr package, as almost all assignment, of Chemical shifts, Atoms, Constraints, Peaks etc. is done through the intermediary of a Resonance. This allows the relationship between Shifts, Peaks, Constraints, (...) to be described precisely without first assigning the Nmr spectrum, provides a simple mechanism for handling prochiral groups, and in general permits greater flexibility.
ResonanceGroup Group of Resonances belonging within the same Residue. Serves to organise Resonances that have not yet been assigned, and to set Residue types, (sequential) neighbours, Residues and their probabilities for an entire group without necesarily assigning the individual Resonances. Coherence between ResonanceGroup (probable) assignments and assignments of Resonances to Atoms are not checked by the API software. In case of conflicts the assignment of the Resonance should take precedence over any information carried by the ResonanceGroup, in accordance with the status of the ResonanceGroup as a vehicle for tentative assignments.
ResonanceGroupProb Link class for ResonanceGroup-to-ResonanceGroup link. Holds information about the kind of link and its probability. To calculate probabilities, weights are summed over all ResonanceGroupProbs belonging to the same resonance with the same linktype and the same sequenceOffset. sequenceOffset and the linktype are cooperative, so that e.g. linkType == 'basepaired', sequenceOffset == -1 means the base that is basepaired to the preceding base of the sequence. For non-polymers sequenceOffsets are strictly speaking meaningless, but as a special convention the sequenceOffset '1' is interpreted as 'directly bonded to current ResonanceGroup'.
ResonanceProb Probability for a Resonance to belong to a given Reasonance group. For cases where precise belonging can not be established, e.g. with a HNCA experiment where the CA could be from either the i or the i-1 ResonanceGroup
ResonanceSet Connection between Resonance and AtomSet. Connects to several Resonances and several AtomSets. The semantics are that one object on one side is connected to exactly one object on the other side, with excess objects not belonging, but that it is not known which object maps to which. The typical example is a prochiral group (e.g. a methylene) and the two resonances that corresponds to the two atoms. Linking these into a ResonanceSet reflects the information that each of the resonances corresponds to one (and only one) of the AtomSets, but it is not known which. If there is only one object on each side (and only then), can the Resonance be inferred from the AtomSet and vice versa.
SampleCondition Individual sample condition that applies to a sample during a specific experiment. Because of the many possible conditions, type and unit can be set freely.
SampleConditionSet Conditions under which an experiment is carried out.
SampledDataDim A data dimension where points are not regularly spaced. The point values are given as an explicit list (pointValues). Intended for non-linear sampling, T1 or titration series, ...
Shift Chemical shift measurement.
ShiftAnisotropy Chemical shift anisotropy measurement.
ShiftAnisotropyList List of chemical shift anisotropy measurements
ShiftDifference Chemical shift difference measurement
ShiftDifferenceList List of Chemical Shift differences (e.g. isotope shifts, ligand binding shifts). The values given are :
modifiedShift - shift_in_referenceShiftList
ShiftList List of chemical shifts.
ShiftReference Chemical Shift referencing. The reference actually used (not the one quoted against).
SparseSampling Describes the sparse sampling schedule. For every dim that is sparsely sampled, there will be a SparseSampling object. The nth value in SparseSampling.pointNumbers gives the timestep number for this dimension that was used in the nth sparsely sampled hypercomplex point..
SpectralDensity Spectral density for a pair of resonances at a given frequency.
SpectralDensityDerivation Derivation for set of spectral densities.
SpectralDensityList List of spectral density sets.
StructureAnalysis A sstructure analysis with associated structures and constraint lists
StructureGeneration One cycle of Nmr Structure generation, with associated constraints, protocol, parameters, etc., producing one family of structures. NB protocol etc. information still not modeled.
T1 T1 measurement
T1List List of T1 measurements.

T1 values are referred to a single Resonance. Where more than one resonance is involved (coherence type 'zz'), it is assumed that the other one is obvious from context, and/or that identifying information is presented in the 'details' record.
T1Rho T1 rho measurement.
T1rhoList T1 rho measurement list
T2 T2 relaxation measurement
T2List List of T2 relaxation measurements.

T2 values are referred to a single Resonance. Where more than one resonance is involved (coherence types other than 'SQ'), it is assumed that the other one is obvious from context, and/or that identifying information is presented in the 'details' record.

Data Obj Types:

Type Description
None

Data Types:

Type Description
ChainStateSetType Values for ChainStateSet.stateSetType.
DataSourceDataType DataSource.dataType data
ExpSampleState State of Sample for Experiment
HExchProtectionType Data Type for ShiftDifference types, describing the origin of the chemical shift difference. 'intrinsic' means the hydrogen exchange protection factor relative to a calculated intrinsic exchange rate.
IntensityType PeakIntensity intensityType
LinkType DataType for ResonanceGroupProb.linkType. 'identity means that two ResoanceGroups correspond to the same Residue, 'sequential' that they are in the same chain, one or more residues apart.
NoeValueType Intensity type for NOE measurements
PeakClusterType Type of PeakCluster. Alternatives are:

'multiplet': peaks in cluster are subcomponents of the same multiplet. They share the same mainPeakDimContribs and hence the same central assignment.

'static': peaks in cluster represent the same peak in different experiments, where the experiments share the same shift list. The peakDimContribs, and hence the assignment, are the same for all peaks. A typical example would be peaks in a T1 experiment series.

'shift': peaks in cluster represent the same peak in different experiments, where the experiments belong to different shift lists. The peakDimContribs, and hence the assignment, is the same for all peaks. A typical esample would be peaks in a titration or temperature series.

'symmetry': peaks are symmetry equivalent. They may belong to the same or different experiments. Examples are peaks on opposite sides of the diagonal in a 2D NOESY or 4D HCCH  experiments. Also possible would be a H-CH and a HN-H peak from different experiments that represented the same H-H NOE. Their assignments are correlated, but exactly how would depend on the context.
SampleConditionType Type for SampleCondition.condition
ShiftDifferenceType Data Type for ShiftDifference types, describing the origin of the chemical shift difference.
ShiftRefType Allowed values for ccp.Nmr.ShiftReference.referenceType
ShiftReferenceMolecule Molecules used for ShiftReference
StructureGenerationType Data Type for StructureGeneration generationType
T1CoherenceType Coherence type measured for lists of T1 relaxation times. Values are 'z': z-magnetisation, 'zz': zz longitudinal spin order
T2CoherenceType Coherence type for T2 and T1rho transverse relaxation time lists. 'SQ', 'DQ', and 'ZQ' refer to single, double, and zero quantum magnetisation, 'antiphase' to antiphase magnetisation, and 'crosscorrelation' to DD/CSA crosscorrelation.
TempCalibMethod Temperature calibration method enumeration
TempControlMethod Temperature control method enumeration

Package guid:

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  Data Model Version 2.0.5
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