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Package: NmrExpPrototype


    Package for describing NMR experment prototypes, which could also be described as template descriptions.
Classes
Data Types
Data Obj Types

Imported Packages:

ccp.api.molecule.ChemElement,   memops.api.AccessControl,   memops.api.Implementation

Packages Importing ccp.api.nmr.NmrExpPrototype:

Nmr,   ccpnmr.api.Analysis

Classes:

Class Description
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.
ExpGraph Set of Connected AtomSites, ExpTransfers, ExpSteps and ExpMeasurements that define the allowed magnetisation transfer paths and observables for an NMR experiment. Each ExpGraph, its ExpSteps and ExpTransfers, and the ExpMeasurements and AtomSites these are connected to, effectively define a self-contained NMR experiment. There may be several ExpGraphs that share some, but not all, AtomSites and ExpMeasurementsl, e.g. if you acquire CH and NH 2D HSQC experiments together, or if you have diferent molecule topologies giving rise to peaks of different sign.
ExpMeasurement Property being measured on a dimension of a multidimensional NMR experiment. Most common are shifts, but coupling constants, multi-quantum magnetisation, time (for relaxation time measurements) and others are possible.
ExpStep Defines the order in which Measurements are encountered within a (non-reversed) experiment, and, implicitly, which ExpMeasurements are involved in a given ExpGraph. The same measurement can appear several times, e.g. for out-and-back experiments.
ExpTransfer Magnetisation transfer between two AtomSites. The transfer does not say anything about direction, merely that e.g. an H and a C are connected by a one-bond coupling.

The ExpTransferPaths and the AtomSites they select describe the network of nuclei that must be present in order to get observable peaks from a ginve ExpGraph.
NmrExpPrototype Description of a reference NMR experiment as defined by its magnetisation transfer pathway. E.g. a 4D HCCH, 3D (H)CCH or HC(C)H, 2D H(C)(C)H and 2D (reduced dimensionality) HC(C)H are seen as the same experiment
RefExpDim Dimension of reference exeriment.
RefExpDimRef ExpDimRef for prototype experiment. Maps ExpDimRef on ExpStep, from which the information necessary for creating ExpDimRef can be found.

If there is more than one ExpGraph in the NmrExpPrototype, in general each RefExpDim will have an equivalent set of RefExpDimRef for every ExpGraph. Where this is not the case it may be assumed that the 'missing' RefExpDimRefs are 1) identical in content to those present and 2) correspond to the same ExpStep as those given. This convention is used to avoid having several identical RefExpDimRefs just because there are several ExpGraphs.

Note that the serial attribute is used to match Nmr.ExpDimRefs to RefExpDimRefs, so that objects with the same serial correspond to each other.
RefExperiment Reference Experiment. Selects experiment dimensions from the steps available in the NmrExpPrototype
SystematicName Systematic name for RefExperiment

Data Obj Types:

Type Description
None

Data Types:

Type Description
ConstantTimeType Constant time type for dimension. There are three alternatives, 'constant', 'variable', and 'partial'. The latter denotes a harmonica-type experiment.
ExpCategory Category of NmrExpPrototype.
'through-bond' are though-bond correlation experiments (TOCSY, HSQC, HNCOCA, ...)
'though-space' are through-space correlation experiments (NOESY, ROESY, HSQC-NOESY-HSQC,...)
'quantification' are experiments meant to measure parameters, such as relaxation, heteronuclear NOEs, dipolar and scalar couplings, quantitative exchange rates, ...)
'other' takes care of experiments that do not fit anything else.
ExpKeyword Proposed keywords (open enumeration) for NmrExpPrototype.keywords
ExpMeasurementType Type of Measurement that can appear (in the ExpDimRef) of an Nmr experiment. Equal to the Class name of the appropriate measurement class if one exists.
ExpTransferSubType Enumeration for subtype of ExpTransferType. E.g. 'ROESY' for main type 'NOESY', or 'HSQC' for main type 'onebond'
ExpTransferType Magnetisation transfer types for describing NMR experiments. Of the allowed values, NOESY includes ROESY, onebond is any transfer guaranteed to go along a single bond, Jmultibond is direct J coupling  excluding one-bond coupling, and Jcoupling is direct J coupling regardless of the number of intervening bonds.  Jnonlocal is a J coupling that may connect to any part of the molecule through space or noncovalent bonds. DipDip, SpinDiff, and CP are transfer types for solid state NMR. DipDip is dipole-dipoole transfer with an r-3 distance dependence, SpinDiff is spin diffusion possible mediated by another nucleus, with r-6 dependence, and CP is 'cross-polarization' which could be by a number of methods.
NamingSystem NamingSystems accepted for RefExperiments

Package guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:45_00019
  Data Model Version 2.0.5
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 26 16:58:08 2012    from data model package  ccp.api.nmr.NmrExpPrototype   revision 1.45  
  Work done by the CCPN team.
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