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Pydoc: module pasd.protocol
 
pasd.protocol		 index


 

 
Classes
       
builtins.tuple(builtins.object)
FileDatum

 
class FileDatum(builtins.tuple)
    FileDatum(name, atomPosArr)
 
FileDatum(name, atomPosArr)
 
 
Method resolution order:
FileDatum
builtins.tuple
builtins.object
Methods defined here:
__getnewargs__(self)
Return self as a plain tuple.  Used by copy and pickle.
__repr__(self)
Return a nicely formatted representation string
_asdict(self)
Return a new dict which maps field names to their values.
_replace(self, /, **kwds)
Return a new FileDatum object replacing specified fields with new values
Class methods defined here:
_make(iterable) from builtins.type
Make a new FileDatum object from a sequence or iterable
Static methods defined here:
__new__(_cls, name, atomPosArr)
Create new instance of FileDatum(name, atomPosArr)
Data descriptors defined here:
name

 
Alias for field number 0
atomPosArr

 
Alias for field number 1
Data and other attributes defined here:
__match_args__ = ('name', 'atomPosArr')
_field_defaults = {}
_fields = ('name', 'atomPosArr')
Methods inherited from builtins.tuple:
__add__(self, value, /)
Return self+value.
__contains__(self, key, /)
Return key in self.
__eq__(self, value, /)
Return self==value.
__ge__(self, value, /)
Return self>=value.
__getattribute__(self, name, /)
Return getattr(self, name).
__getitem__(self, key, /)
Return self[key].
__gt__(self, value, /)
Return self>value.
__hash__(self, /)
Return hash(self).
__iter__(self, /)
Implement iter(self).
__le__(self, value, /)
Return self<=value.
__len__(self, /)
Return len(self).
__lt__(self, value, /)
Return self<value.
__mul__(self, value, /)
Return self*value.
__ne__(self, value, /)
Return self!=value.
__rmul__(self, value, /)
Return value*self.
count(self, value, /)
Return number of occurrences of value.
index(self, value, start=0, stop=9223372036854775807, /)
Return first index of value.
 
Raises ValueError if the value is not present.
Class methods inherited from builtins.tuple:
__class_getitem__(...) from builtins.type
See PEP 585

 
Functions
       
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='inPass', outPassName='outPass', 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*)', longRangeCutoff=5, 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.
 
If the default value of filenames is used, the inPassName argument is
used to build a glob of structure filenames to process.
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, assignmentThreshold=None, 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).
                   
  basePhase -       -1 or +1 to specify peak sign in non-folded region
 
  fromProtonSolventRange - create exceptions for assignments which have
                          shifts in this range.
  toProtonSolventRange   -
 
  assignmentThreshold - if set, delete all peaks which have more peak
                        assignments than this value.
 
  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)

 
Data
        fileSectionHeader = '!PASD section --- '