Add a peak to a peak list at a position in a specified GUI tile location
Nmr.Peak
Add a peak to the GUI current peak selection
Nmr.Peak, Tkinter.widget .. describe:: Output
None
Give the aliased points position of a given peak dimension
Nmr.PeakDim .. describe:: Output
Float (Nmr.PeakDim.position points)
Determine whether peaks carry the same resonance assignments. PeakDimContrib order unimportant. If one peak has a lower dimensionality than the other then the best overlapping mapping of dims is considered: e.g. 3D and 2D NOESY peaks have same asignment if common 1H dims carry same resonances. Reciprocal peaks; e.g. with resonances (r1, r2) and (r2, r1) respectively on their dims, are considered to be assigned the same.
Nmr.Peak, Nmr.Peak
Boolean
Ensure the contours of a peaks spectrum extend to cover the input peak’s position.
Nmr.Peak .. describe:: Output
None
Copies peaks from one peak list to another if appropriate, i.e dimension isotopes match Has the option to re-pick peaks, rather than doing a straight copy, NB this routine will not handle subpeaks correctly. Optional argument to copy only a subset of peaks from the source peak list.
Nmr.PeakList, Nmr.PeakList, ProgressBar, Boolean, List of Nmr.Peaks
None
Copies an entire peak list to another (or the same) DataSource) There are no appropriateness tests (so far) NB this routine will handle subpeaks correctly NB spectra must have same referencing otherwise peak points will not make sense
Nmr.PeakList, Nmr.DataSource, dictionary peakListParams is a dictionary of parameters that will be passed to the copy of the peaklist (for e.g. changing its name)
Nmr.PeakList (new peak list)
Delete given peaks with a warning
List of Nmr.Peaks .. describe:: Output
Boolean (success)
Nmr.Peak, Nmr.Peak .. describe:: Output
Boolean
Find peaks in a peak list within position tolerances of the input peak. Default tolerances are the assignment tolerances for each dimension The peak dimension distances are weighted according to the tolerances. Option to pick new peaks if no existing peaks are found. Option to look for peaks at aliased positions. Optional dict can be passed in to say how peak dims map together (list indices start at 0, key is for input peak). New peaks will not be picked below the noiseThreshold.
Nmr.Peak, Nmr.PeakList, List of Floats, Boolean, Boolean, Boolean
List of Nmr.Peaks
Define a region of a data dimension in terms of a given axis unit with extra thickness if required
Nmr.FreqDataDim, List of List of Floats (min,max poitions), Word (ShiftList.unit), List of Floats .. describe:: Output
List of Tuple of Floats min,max poitions), Float (min value), Float (max value)
Find peaks within a peak list that are within the data dim assignment tolerance
Nmr.PeakList, Nmr.PeakDim .. describe:: Output
List of Nmr.Peaks
Find the number if aliased spectral widths at a given point for a reference data dimension
Nmr.DataDimRef, Float .. describe:: Output
Int (number of aliasings)
Estimates the value of a peak’s box width
Nmr.Peak .. describe:: Output
List of List of Floats (min,max points positions for dim), List of Floats (Nmr.PeakDim.BoxWidth in points), List of Floats (centre position)
Finds the volume of a peak using the volume method passed in, or if not set then the one stored in application specific data.
Nmr.Peak .. describe:: Output
Float
Pick new peaks in a given region (units: ppm) of a peak list. Thickness (units: points) can be specified for orthogonal dimensions to include extra planes (must be of length ndim). ExcludedRegions (units: points) can be specified to exclude a list of regions. Each list is an ndim list of 2-tuples, with each 2-tuple the (min, max) of that dimension. Peaks are added to the GUI current selection.
Nmr.PeakList, List of List of Floats (min,max positions) in ppm, ‘w’idget, List of Floats, List of List of 2-tuples of Floats in points
List of Nmr.Peaks
Search the target peaklist or the peak lists of the input peaks for other groups of peaks which have matches to the positions of the input peaks in the given dimension. The search dimension is given but the input dictionary, keyed by peak list. Returns a ranked list of group positions in order of strength of match. Option to pass in a tolerance for the match dimension. Option to separate groups according to spinSystem assignment.
List of Nmr.Peaks, Dict of (NmrPeakList:Int) Int, Nmr.PeakLists, Float, Boolean
Tuple of (Float, List of Floats (positions), List of Nmr.Peaks)
Find a peak in a peak list (or all peak lists if none is specified) with the same assignment as the input peak, if it exists. Option to specifiy that the funtion only works for fully assigned peaks.
Nmr.Peak, Nmr.PeakList
List of Nmr.Peaks
List of 2-Lists [Float, Nmr.Peak] - (distance, peak)
List of Nmr.Peak .. describe:: Output
List of Nmr.Peaks
Fit peaks using the specified fitMethod. Input: peaks, all assumed to be from the same peakList.
fitMethod (String)
Output: None
Nmr.PeakDim, List of (Tuples of Floats (MinShift,MaxShift) ) .. describe:: Output
List of Floats (Nmr.PeakDim.positions)
Find the closest peak to the input peak from a list of peaks. The peak dimensions are weighted according to input tolerances. Optional dict can be passed in to say how peak dims map together (list indices start at 0).
Nmr.Peak, List of Nmr.Peaks, List of Floats, Dict of Int:Int
Nmr.Peak
Nmr.DataSource, Nmr.DataSource .. describe:: Output
Dict of Int:Int (DataDim.dim:DataDim.dim)
Nmr.DataSource, Nmr.DataSource .. describe:: Output
Dict of Nmr.DataDimRef:Nmr.DataDimRef
Get the diagonal exclusion for (dataDim1, dataDim2)
Nmr.AbstractDataDim, Nmr.AbstractDataDim .. describe:: Output
Get the diagonal exclusions for a given spectrum (used in C world).
Nmr.DataSource .. describe:: Output
Get the exclusion information for dataDim
Nmr.AbstractDataDim .. describe:: Output
Nmr.Peak, Float (tolerance), Dict of Resonance.isotopeCode:Float (isotope: scale factor) .. describe:: Output
List of Floats (tolerences), List of Floats (scale factors)
Get annotation text for the peak.
ccp.nmr.Nmr.Peak, String, String, String
String
Give the position of peak dimension in specified units
Nmr.PeakDim, Word (ShiftList.unit) .. describe:: Output
Float
Often depricated given peakDim.value Get the position of a peak dimension in PPM
Nmr.PeakDim .. describe:: Output
Float (ppm)
Gives a peak’s height
Nmr.Peak .. describe:: Output
Float (Nmr.PeakIntensity.value)
Gives a peak’s intensity value according to the input intensity type
Nmr.Peak .. describe:: Output
Float (Nmr.PeakIntensity.value)
Nmr.Peak, List of Floats (tolerances for each Nmr.PeakDim), Boolean .. describe:: Output
List of List of (Float, Float)
Gives a peak’s volume
Nmr.Peak .. describe:: Output
Float (Nmr.PeakIntensity.value)
Nmr.Peak, Nmr.Peak, List of Floats (tolerances for each Nmr.PeakDim), Boolean, Dict of Int:Int .. describe:: Output
Float
Makes a setring describing the spin system connectivities of a peak.
Nmr.Peak .. describe:: Output
Line
Determine whether a peak is within a given region optionally considering aliasing
Nmr.Peak, List of List of Floats (min,max poitions), Boolean .. describe:: Output
Boolean
List of Nmr.Peaks
Nmr.Peak
Nmr.Peak .. describe:: Output
None
Make an arteficial peak list using shift intersections from a shift list Boolean option to consider only shifts with atom assigned resonances. Option to filter on a specific molSystem. Option to limit through-space transfers to a limited number of bonds and a given residue range. Optional labelling scheme/mixture and threshold to filter according to isotopomers.
Nmr.DataSource, Boolean, memops.gui.ProgressBar, Nmr.ShiftList MolSystem.MolSystem, Int, 2-Tuple of Ints, ChemComLabel.LabelingScheme or True (automatic from experiment MolLabel), Float
None
ccp.nmr.Nmr.PeakList .. describe:: Output
ccp.nmr.Nmr.PeakList
Merge two peaks together. * Function needs work/checking * Not really used in Analysis currently
List of Nmr.Peaks .. describe:: Output
Nmr.Peak
Move a peak to a given position. Automatically calculates any peak aliasing
Nmr.Peak, List of Floats (Nmr.PeakDim.postion in points) .. describe:: Output
None
Pick a peak at a given position in given units in a peak list.
Nmr.PeakList, List of Floats (Nmr.PeakDim.positions), Word (Nmr.ShiftList.unit), Boolean .. describe:: Output
Nmr.Peak
Nmr.Peak, List of Nmr.Peaks .. describe:: Output
None
Refreshes all of the peak and peakDim annotations for all peaks in a project
Project .. describe:: Output
None
Remove a peak to the GUI current peak selection
Nmr.Peak, Tkinter.widget .. describe:: Output
None
Clear all peak dimension contribs for a list of peaks
List of Nmr.Peaks .. describe:: Output
None
Find existing peaks within a given region of a peak list. Add peaks to the current GUI selection. Thickness (units: points) can be specified for orthogonal dimensions to include extra planes (must be of length ndim or is ignored for a given peakList).
Nmr.PeakList, List of List of Floats (min,max positions), ‘w’idget, List of Floats
List of Nmr.Peaks
Manually define a peaks volume/height
Nmr.Peak, Float (Nmr.PeakIntensity.value), String (Nmr.PeakIntensity.intensityType) .. describe:: Output
None
Nmr.PeakDim, Integer (peakDim.numAliasing) .. describe:: Output
None
Define the position of a peak and its aliasing tile
Nmr.Peak, List of Floats (Nmr.PeakDim.position), List of Ints (Nmr.PeakDim.numAliasing) .. describe:: Output
None
Initialise reference data dimensions, peak position and intensities for a new peak.
Nmr.Peak (new) .. describe:: Output
None
Setup the underlying real peakDim positional values for MQ spectra etc.
Nmr.Peak
None
Gives a peak a default data dim reference if it has none
Nmr.Peak .. describe:: Output
None
Fit a newly created Nmr.Peak to a position in the spectral data specified by its dataSource
Nmr.Peak (new) Optionally String describing the fitMethod
None
Determine a peaks height from the spectral data specified by its dataSource
Nmr.Peak .. describe:: Output
None
Fit linewidth of Nmr.Peak
Nmr.Peak .. describe:: Output
None
Determine a peaks volume from the spectral data specified by its dataSource
Nmr.Peak .. describe:: Output
None
List of Nmr.Peaks, Boolean .. describe:: Output
None
List of Nmr.Peaks, Boolean .. describe:: Output
None
Predict the positions of NOESY peaks given a shift list and a structure ensemble. Produces a peak list which peaks that would represent distances less than a given threshold. Optional labelling scheme/mixture to filter according to isotopomers. Optional structure model to use in ensemble, otherwise all models are used - in this case the average distance must be bwlow threshold. Option to specify a minumum hight value so that peaks are not picked below a threshold.
MolStructure.StructureEnsemble, Nmr.DataSource, Float, ProgressBar (Tk widget), ChemCompLabel.LabelingScheme or rue (automatic from experiment MolLabel), Float, MolStructure.Model, Float
Nmr.PeakList
ccp.nmr.Nmr.Peak, ccp.nmr.Nmr.Peak, dict: int->int .. describe:: Output
None
Coordinate all peaks in the peak list of the input peak so that all peak dimensions that are assigned to the same resonances as the input peak have the same peak dimension position.
ccp.nmr.Nmr.Peak .. describe:: Output
ccp.nmr.Nmr.Peaks