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- analyze(potList)
- perform analysis of PASDPot terms and return nicely formatted summary
- cooling_updateTerms(terms, fractionDone, totSteps, numNOEshuffles=64, numMCsteps=10, distViolWeight=(1, 1), prevLikeliWeight=(1, 0), noeCompleteWeight=(1, 1), charDistViol=(10.0, 2.0), charNoeComplete=(0.05, 0.05), charScatter=(1, 1), charDeltaDV=(0.01, 0.01), charDeltaNoeComplete=(0.01, 0.01), charDeltaScatter=(0.001, 0.001))
- create_PASDPot(name, shifts=None, peaks=None, exceptions=None, pasdFilename=None, asTuple=False, verbose=True)
- Create a pasdPot.PASDPot object with specified instanceName.
Results from previous PASD passes can be read in by specifying the
optional pasdFilename argument, or alternatively using separate shifts,
peaks and exceptions arguments. For each of these arguments, a filename
or string including file contents can be passed.
If asTuple=True, the return value is a tuple of forward and inverse PASD
energy terms, otherwise the combination is returned.
- highTemp1_updateTerms(terms, fractionDone, totSteps, numNOEshuffles=64, numMCsteps=10, charDistViol=10.0, charDeltaDV=0.01, prevLikeliWeight=1)
- highTemp2_updateTerms(terms, fractionDone, totSteps, numNOEshuffles=64, numMCsteps=10, charDistViol=10.0, charDeltaDV=0.1, prevLikeliWeight=1)
- linearInterp(frac, minMax)
- Return interpolated value between start and stop at fraction step/steps
step takes values between 0 and steps-1
- maybeShuffleAssignments(pasdTerms, fracDone, reshuffleProb, potProperties, numMCsteps=1, charDeltaFac=1, verbose=False)
- numActivePeaks(pot)
- numViolatedPeaks(pot, violCutoff=0.5)
- Count the number of violated peaks in the given pasdPot.
Uses the lowestViolation method, which ignores issues of
activation or peakAssignment choice. It tries all peakAssignments
and reports the minimum. Unassigned peaks return
a bestViolation value of -1, which doesn't hurt this
calculation.
FIX: maybe this should be pot.violations(), with violCutoff being
threshold...
- updateActivation(pot, numMCsteps=1, charDeltaFac=1.0, verbose=False)
- Update which assignments are active using a Monte Carlo algorithm.
- writeNEF(noe, name, removeIntersected=True)
- Given an pasdPot.NOEPot term,
write a NEF record with the specified saveframe name.
If removeIntersected==True eliminate peakAssignments that have
non-disjoint from and to proton selections.
Return the a tuple of the string associated with the generated NEF object,
and a list of peak linkage information.
- writeOneNEFAssignment(cat, peak, removeIntersected, id, index)
- Internal routine to be called by writeNEFAssignments. Returns the comments
associated with the particular peak
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