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- activateLikelyPAs(pot, minLikelihood=0.9, maxLikelihood=100)
- activateNonviolatedPeakAssigns(pot, violCutoff=0.5)
- Given a distance violation cutoff,
activate all peakAssigns that are not currently violated
and deactivate all peakAssigns that are
- binCenter(minVal, maxVal, nBins, whichBin)
- Given a range minVal .. maxVal,
divided into nBins bins
which are numbered 0 .. nBins - 1,
Return the value of the center of bin #whichBin
defend against maxVal == minVal
- chooseBestFraction(fileData, peaks, completenessPots=[], frac=0.1, violCutoff=0.5, inverseBound=4.0, inverseMethylCorrection=0, completenessWeight=0, useNonviolatedCount=False, verbose=False)
- Given a list of FileDatum, check each one's violations of a given set of
peaks and return a list of FileDatum corresponding to the top frac.
- correctShiftOffset(pasdPot, correctTo=True, correctFrom=False, verbose=False, binWidth=0.001, minNumSymmetricPeaks=100, minOffsetToApply=0.015)
- For correcting proton shifts.
Find all the symmetric, intraresidue peak pairs.
Determine the most common difference between the peak position
on the from proton dimension and the peak position
of the same SA on the to dimension.
If the offset is larger than a cutoff and the number of peaks
used in determining it is larger than a cutoff, apply it to all the
peak locations along the indicated dimension and throw an exception
(to let the calling proc know that peak locations have changed)
If the correction is smaller than the cutoff, do nothing.
- correctUpBoundsForMethyls(peaks)
- This isn't necessary. Could just use the methyl flag on each
shiftAssignment and the methyl correction defined for the inverse
restraints in MarvinNOEPotential
- createExplicitInverseExceptions(pasdPot, fromProtonSolventRange=[], toProtonSolventRange=[], failedFiltersCutoff=9999, diagTol=0.001)
- initLikelihoods(pot, maxFiltersFailed=0)
- set previous likelihoods to 0 or 1 based on numFilteredFailed relative
to maxFiltersFailed.
- jointFilter(pots, selection='[protein]', minPeakScore=-1, minExpectedScore=0.08, primarySeqFilter=False, minLikelihood=0.9, maxLikelihood=2.0, writeFiles=False, assignmentThreshold=None, activePAThreshold=None, inactiveAssignmentThreshold=None, deleteNonIntraPAs=False, refStructFilename='', refPDB=None, filenamePrefix='NAME_pass2', **kwargs)
- Filenames are generated from filenamePrefix by substituting the PASDPot
instanceName for the 'NAME' literal, and then appending .exceptions,
.peaks or .shiftAssignments for the respective filenames.
assignmentThreshold - if set, delete all peaks which have more peak
assignments than this value.
inactiveAssignmentThreshold - if set, delete peaks with no active peaks,
but with more assignments than this value.
activePAThreshold - if set, delete peaks with more active peak
assignments than this value.
deleteNonIntraPAs - if True, delete all non-intramolecular peak
assignments if there is an intramolecular peak
assignment.
minLikelihood - passed through to saTools.analyzeShiftAssignments
maxLikelihood and peakTools.analyzePeaks.
These additional arguments are passed through to netfilter.netFilter:
knownContacts, printResiduePairScores, passFrac, numIters,
initScoresFrom, minExpectedScore
The above filters are run after the network filter.
- likelihoodsFromStructs(fileData, peaks, violCutoff=0.5)
- Given a list of <filename, atomPosArray> pairs of converged structures
and a list of peaks,
use the coords to determine the likelihood of each peakAssignment
Could be replaced with something that would calculate previous likelihood
of any pair of ShiftAssignments, whether they're used in a PeakAssignment
or not.
- markGoodPeakAssigns(peaks, cutoff=0.5)
- set as good all peak assignments which satisfy distance restraints
to within cutoff.
- processStructurePass(pots, inPassName, outPassName, filenames='INPASS_[0-9]*.pdb', combinedFiles=True, aveFilename='INPASS_ave.pdb', refStructFilename=None, violCutoff=0.5, fracConverged=0.1, highLikelihoodCutoff=0.9, noeCompletenessCutoff=0.0, scatterCutoff=999.9, completenessWeight=0.0, useSingleAssignmentBehavior=False, backboneSelStr='name CA C N', heavyatomSelStr='not (PSEUDO or name H*)', outPeakFilenames=None, outSAfilenames=None, outExceptionsFilename=None, verbose=False)
- Given a list of input pasdPot.PASDPot terms and a list (or glob string)
of structure filenames, generate new PeakAssignment likelihoods.
- saLikelihoodsFromStructs(fileData, pasdPot, violCutoff, noeCompletenessCutoff, scatterCutoff, inverseBound, inverseMethylCorrection)
- standardInitMatch(pasdPot, fromProtonRange, toProtonRange, fromHeavyatomRange=[], toHeavyatomRange=[], basePhase=1, refStructFilename='', filenamePrefix='NAME_pass1', peakFilename=None, saFilename=None, exceptionFilename=None, writeFiles=True, writeEachStage=False, allWeakPeaks=False, fromProtonSolventRange=[], toProtonSolventRange=[], fromProtonBroadTol=0.075, toProtonBroadTol=0.075, fromHeavyBroadTol=0.75, toHeavyBroadTol=0.75, fromProtonTightTol=0.02, toProtonTightTol=0.02, fromHeavyTightTol=0.2, toHeavyTightTol=0.2, doStripeCorrection=True, useIndividualTols=False, doCorrectShiftOffset=True, saRemarks='', peakRemarks='')
- This will process 2D, 3D and 4D spectra. In order to process spectra
with more than two dimensions, the appropriate from/toHeavyRange
argument must be specified.
filenamePrefix - is used to create file names for peaks, shift
assignments and inverse exceptions with the extensions
.peaks, .shiftAssignments, and .exceptions,
respectively. If present, the literal NAME is replaced
with pasdPot.instanceName(). The values can also be
specified on an individual basis using the
peakFilename, saFilename, or exceptionFilename
arguments. Setting any of these to the value False
will disable writing the corresponding file.
allWeakPeaks - if set, treat all peaks as weak - i.e. the associated
distance range will from smallest possible (minimum
value in pasd.distanceBins) to largest possible
(maximum value in pasd.distanceBins).
Returns tuple of (peakRemarks, saRemarks), strings containing info and
analysis of ShiftAssignments, and Peaks, respectively.
Output is written to filenamePrefix+".pasd" if writeFiles="combined".
For backwards compatibility, individual file names can be specified
using the peakFilename, saFilename exceptionFilename
arguments.
- writeExceptions(exceptionsFilename, pasdPot, fileAccess='w', tcl=None)
- writePeaks(peakFilename, pasdPot=None, remarks='', fileAccess='w', tcl=None)
- writeShiftAssignments(saFilename, pasdPot=None, sas=[], remarks='', fileAccess='w', tcl=None)
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