Calculate the contour levels given baseLevel, numberLevels, levelChanger, changeMode
Nmr.DataSource, Float, Int, Float, Word (multiply or add)
The contour levels as a list
Change the number of contour levels of a spectrum by a given delta
Nmr.DataSource, Int
None
Give dimension numbers of a spectrum that pertain to a given Isotope
Nmr.DataSource, Word (Nmr.ExpDimRef.isotopeCode)
List of Ints
ExpDim that corresponds to acquisition dimension. NB uses heuristics
NmrExpPrototype.Experiment
NmrExpPrototype.ExpDim
RefExpDimRef that corresponds to acquisition dimension
NmrExpPrototype.RefExperiment
NmrExpPrototype.RefExpDimRef
Get the shift measurement isotopes for a spectrum data dim
Nmr.FreqDataDim
Set of Words (Nmr.ExpDimRef.isotopeCodes)
Get the full range of freq values for a data dimension reference taking into account spectral width and min/max unaliased freqs
ccp.nmr.Nmr.DataDimRef
2-List of Floats (min, max)
Get the 1D slice for the dataSource for a position which is fixed in all dimensions but sliceDim. Assumes that all dimenions are freqDataDim. position is of size dataSource.numDim. sliceDim is 1-based, not 0-based. The slice is returned as a Python list.
Nmr.DataSource, tuple/list of Float, Int
list of Float
Get tuples of spectrum data dimensions that have digaonal positions and are also in one bond connections
Nmr.DataSource
List of 2-List of Nmr.DataDims
Get pairs of spectrum data dimensions that are equivalent in terms of isotope type
Nmr.DataSource
List of 2-List of Nmr.DataDims
Get the first sampled data dimension for an experiment
ccp.nmr.Nmr.Experiment
List of ccp.nmr.Nmr.SampledDataDim
Gives the spectra for a given NMR experiment with a minimum number of dimensions .. describe:: Input
Nmr.Experiment, Integer
List of Nmr.DataSources
Get the possible reference NMR experiments for an experiment, given the prototypes available within its project, the category and external name settings and the nuclei on the axes. Optional argument to specify the category of possible experiments (‘use external’, ‘through-bond’, ‘through-space’, ‘quantification’,
‘other’).
Nmr.Experiment, NmrExpPrototype.NmrExpPrototype.ExpCategory
List of NmrExpPrototype.RefExperiments
Get the data dims of a spectrum that represent indirect (e.g. relayed NOESY) magnetisation transfers.
Nmr.DataSource
Set of 2-List of Nmr.FreqDataDims
For a given experiment find the pairs of isotopes present along onbond transfers connected via a relayed (indirect) through space transfer. Returns pairs of isotopes, direct and indirect, for each experimental dimension. An isotope may be None if one side of the through space transfer is observed in experiment, e.g. H_hC.NOESY.
Nmr.Experiment
Dict of Nmr.ExpDimRef:(ChemElement.Isotope, ChemElement.Isotope)
Get whether spectrum’s data file is big endian.
Spectrum
None if no dataStore or not BlockedBinaryMatrix, True if big endian, False if little endian
Get the min and max values of a dataSource. Not recommended unless 1D or 2D because slow.
Nmr.DataSource
(Float, Float)
Give all NMR spectra in a given project that have n dimensions
Project, Int
List of Nmr.DataSources
Get the NOE peak lists from a project. Option to include possible peak lists that are untyped
Implementation.MemopsRoot, Boolean
List of Nmr.Peaks
Estimate the noise level for a spectrum by choosing a random nsamples points and finding subsets with the lowest standars devation/
Nmr.DataSource, Int, Int, Float
Float
Get pairs of spectrum data dimensions that are connected by onebond transfers
Nmr.DataSource
List of 2-List of Nmr.DataDims
Get pairs of experiment dimensions that are connected by onebond transfers
Nmr.Experiment
List of 2-List of Nmr.ExpDimRefs
Get the possible reference NMR experiments for an experiment, given the prototypes available within its project, the category and external name settings. Optional argument to specify the category of possible experiments (‘use external’, ‘through-bond’, ‘through-space’, ‘quantification’,
‘other’).
Nmr.Experiment, NmrExpPrototype.NmrExpPrototype.ExpCategory
Iterator of NmrExpPrototype.RefExperiments
get dataDimRef child with lowest expDimRef.serial
freqDataDim
dataDimRef or None
get expDimRef child with lowest expDimRef.serial
expDim
expDimRef or None
Function used by getNoiseEstimate()
Get a set of categories (as strings) that a reference experiment belongs to
ccp.nmr.NmrExpPrototype.RefExperiment
Set of Lines
Wrapper to getFilteredRefExperiments - set category from 1) experiment.category (temporary) attribute (if present) 2) experiment.refExperiment category (if present) and pass call on to getFilteredRefExperiments
Nmr.Experiment
List of NmrExpPrototype.RefExperiments
Get a list of experiments in an NMR project that have sammpled data dims
ccp.nmr.Nmr.NmrProject
List of ccp.nmr.Nmr.Experiments
Get reference amide experiments which may be used for protein sequence assignment. Gives a set of amide experiment types and a subset of through CO specific experiment types.
Implementation.MemopsRoot
List of NmrExpPrototype.RefExperiments, List of NmrExpPrototype.RefExperiments
Give all processed spectra in a project with a minimum number of dimensions
Project, Int
List of Nmr.DataSources
Give NMR spectra of a given class in a project as identified by isotope-dimension mapping This funtion is just a temporary kludge prior to proper implementation on spectra types
Project, String
List of Nmr.DataSources
Give isotopes pertianing to the dimensions of a given NMR spectrum
Nmr.DataSource
List of Words (Nmr.ExpDimRef.IsotopeCodes)
Get the noise level for a spectrum. If the noise level is not already set it will be set at an estimated value.
Nmr.DataSource
Float
Get the data dims of a spectrum that represent through-space magnetisation transfers.
Nmr.DataSource
2-List of Nmr.FreqDataDims
Get the peak lists that have a through-space magnetisation ransfer, from a given project.
Implementation.MemopsRoot, Boolean
List of Nmr.Peaks
Refresh the covalently bound status for any resonances connected via peaks in a given experiment.
Nmr.Experiment
None
Set up the ExpTransfers for an experiment using available refExperiment information. Boolean option to remove any existing transfers.
Nmr.Experiment
List of Nmr.ExpTransfers
Determine (approximately) whether data file is big endian.
fileName and optionally numberType (‘float’ or ‘int’), fileHeaderSize, nbytes (bytes per word), nwords (number of words to check), threshold (above which value considered incorrect byte ordering), fraction (fraction of values checked which must have incorrect byte ordering, if considered swapped) fractionNonzero (fraction of values checked which must be nonzero to be considered ok)
True if big endian or if cannot determine, False if little endian
Check if referencing is consistent and/or fitw IUPAC referencing ratios
Determine if spectrum is a Shape spectrum, possibly during set-up
Spectrum
Boolean
Determines if a spectrum is valid for display, i.e. processed and has the min required number of dimensions
Nmr.DataSource, Int
Boolean
Determine (approximately) whether spectrum’s data file is big endian according to actual data.
Spectrum
None if cannot determine, True if big endian, False if little endian
Make a new ShiftList for a project with an optionally specified unit (default ppm).
Project, String (Nmr.ShiftList.unit)
Nmr.ShiftList
Truncate a region for a data dimension at its ppm bounds.
List of Floats (region), Nmr.DataDim
List of Floats (region)
Truncate a region for a data dimension at its data points bounds.
List of Floats (region), Nmr.DataDim
List of Floats (region)
set all ExpDimRef.isotopeCodes in experiment, from sf values Selects isotopes so that sf ratios match isotope gyromagmetic ratios Unknown and inconsistent isotopes efault to 1H
ccp/nmr.Nmr.Experiment
None
Set the shift list for a given experiment. Updates the shift values from the appropriate shift lists/
Nmr.NmrExperiment, Nmr.ShiftList
None
Set whether spectrum’s data file is big endian.
Spectrum, Boolean
None
Sets the reference experiment for an existing experiment and tries to map the ExpDims to RefExpDims appropriately.
Nmr.Experiment, NmrExpPrototype.RefExperiment
None