pasd.protocol
index
/home/schwitrs/xplor/python/pasd/protocol.py


 

 
Functions
       
activateLikelyPAs(pot, threshold=0.9)
#@trace.notrace_decorate
initLikelihoods(pot, maxFiltersFailed=0)
set previous likelihoods to 0 or 1 based on numFilteredFailed relative
to maxFiltersFailed.
jointFilter(pots, minPeakScore=-1, minExpectedScore=0.08, primarySeqFilter=False, refPDB=None, writeFiles=False, assignmentThreshold=None, activePAThreshold=None, inactiveAssignmentThreshold=None, deleteNonIntraPAs=False, 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.
 
These additional arguments are passed through to netfilter.netFilter:
   knownContacts, printResiduePairScores, passFrac, numIters,
   initScoresFrom
 
The above filters are run after the network filter.
markGoodPeakAssigns(peaks, cutoff=0.5)
set as good all peak assignments which satisfy distance restraints
to within cutoff.
writePASDFiles(pot, shifts, peaks, exceptions, refPDB='', minLikelihood=0.8, maxLikelihood=1.0)
pot is a PASDPot term