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- analyzeShiftAssignments(pasdPot, refFilename='', completenessCutoff=4.0, methylCorrection=0.0, violCutoff=0.5, longRangeCutoff=5, minLikelihood=-1, maxLikelihood=2, description='initialMatch', verbose=False)
- Given a <pasdPot>.PASDPot term, generate statistics, and a set of
informational messages.
minLikelihood - perform analysis on peakAssignments whose likelihoods
maxLikelihood are between minLikelihood and maxLikelihood, and
disblae the others.
longRangeCutoff - difference in residue numner, a value greater than
which signifies a ``long range'' peakAssignment.
description - string descibing which stage of the PASD protocol is
calling this function.
refFilename - name of reference file (if available) used to annotate
whether peak assignments are good or bad.
completenessCutoff- distance cutoff for determining completeness (based
on reference structure).
methylCorrection - methyl distance cutoff for determining completeness
(based on reference structure).
violCutoff - violation threshold to determine if peak is good
(based on reference structure).
verbose - set to True for debugging messages.
Returns a string containing analysis results.
- cacheConnectedArray(crit, simulation=None)
- Return list of length simulation.numAtoms()
whose elements are are lists of indices of connected atoms.
- consolidateIdenticalStereopartners(pasdPot)
- Lots of shift tables have entries for an averaged stereopair that
look like two stereospecifically assigned protons that happen to have
the same chemical shift. After non-stereo processing, I won't be able
to tell them apart, and will end up with multiple to-from partners.
Eliminate these extra copies of shift assignments prior to non-stereo
processing
This is run directly after createShiftAssignments, before to-from
partners are set or non-stereo processing is done.
- createShiftAssignments(shifts, pot, fromProtonSel, toProtonSel, fromProtonSolventRange=None, toProtonSolventRange=None, flexibleRegionSel=None, fromHeavySel=None, toHeavySel=None, fromConnectedCriterion='one', toConnectedCriterion='one', namePrefix='', verbose=False)
- Given a list of chemical shifts (with each having the format of a tuple of
[val,selStrings,err]), and a pasdPot.PASDPot, generate shift
assignments from the from- and to- proton atom selections, excluding
shifts in the from- and to- solvent ranges, if specified.
The names of the ShiftAssignments are prefixed with the string namePrefix.
Shift assignments for experiments with greater than two dimensions are
handled by specifying nuclei of intermediate dimensions in either the
fromHeavySel or toHeavySel atom selections. To be considered in a chemical
shift assignment, a heavy atom must be contained in the corresponding atom
selection, and satisfy the specified criterion for being connected to its
related (to- or from-) proton. These critera can be specified as the
number of separating bonds using the strings "one", "two", "three",
"four", or "five", or as a number specifying a cutoff of distance from
the proton.
Returns informational string which is usually placed in the
shiftAssignments file.
- expandStereospecific(sas)
- Given a set of shiftAssignments,
Expand the selections of each shiftAssignment that
corresponds to half a stereopair to cover the entire
stereopair.
Note that this includes all functionality of
expandHalfStereopairShiftAssignments
- findStereopartner(sas, targetSA)
- Given sas, a list of shiftAssigns and a target shift assignment,
find a shiftAssign with the same from/to sense
that's the target's stereopartner.
If targetSA already covers an entire stereopair, return ""
If the target is either not part of a stereopair, return None
Returns partnerSA , message
- findToFromPartner(sas, targetSA)
- markMethyl(sas)
- recordStereoPartners(pasdPot)
- Fill in all shiftAssign's stereoPartnerNames.
- recordToFromPartners(pasdPot)
- removeSAsOutsideRange(pasdPot, dimension, shiftRange)
- Remove all shift assignments outside the specified shiftRange for the
specified dimension. Allowed dimensions are the strings
"fromProton", "fromHeavyatom", "toProton", "toHeavyatom".
Return a remarks string descibing removals performed.
- reportShiftAssignLikelihoods(pasdPot)
- Given a PASDPot term, return a string containing a histogram of
ShiftAssignment likelihoods.
- sasWithOverlappingSelections(sas, target)
- shiftAssignmentsWithOverlappingSelections
- selStringToAssignmentName(string)
- a quick way of converting (segid a and resid 4 and resn ala and name ca) to a_4_ala_ca
for use in shiftAssignment names
- selectionsAreConnected(sel1, sel2, connectedArray)
- Given two selections, see whether any atoms in the first
are bonded to any atoms in the second using the passed bonding info.
- shiftEntriesThatMatch(shiftList, targetSel)
- a way of caching chemical type selectivity for match*d, below.
shift errors are lost at this step
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