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Pydoc: module pasd.match

pasd.match

index

Functions to match shift assignments to peaks.

Functions

foldedOrAliasedPosition(rawShift, shiftRange, signChangeFlag, isFolded): determine folded positions of shiftAssignments for
the diagonal check in creating explicit inverse exceptions

match4d(pot, unfoldedSign, fromProtonTol, fromProtonRange, toProtonTol, toProtonRange, fromHeavyTol=None, fromHeavyRange=[], toHeavyTol=None, toHeavyRange=[], peakList=[], saList=[], minSALikelihood=-1, verboseOutsideSpectrum=False, useIndividualTols=False, fromProtonSignChanges=False, fromHeavySignChanges=False, toProtonSignChanges=False, toHeavySignChanges=False, foldedAlongFromProton=False, foldedAlongFromHeavy=False, foldedAlongToProton=False, foldedAlongToHeavy=False, ignoreSign=False, aveExp=None): Dimensionality is determined by which heavy atom spectral ranges are
specified.

matchOnePeak(peak, pot, unfoldedSign, fromProtonTol, fromProtonRange, toProtonTol, toProtonRange, fromHeavyTol, fromHeavyRange, toHeavyTol, toHeavyRange, useIndividualTols, fromProtonSignChanges, fromHeavySignChanges, toProtonSignChanges, toHeavySignChanges, foldedAlongFromProton, foldedAlongFromHeavy, foldedAlongToProton, foldedAlongToHeavy, ignoreSign, fromSAs, toSAs, expectFromHeavy, expectToHeavy): Process a single peak to find matching shift assignments.

Return a list identifying peaks outside of the spectrum.

peakOutsideSpectrum(peakPosn, shiftRange): sanity check that each peak's position is within the range
specified by the top and bottom

recordUnfoldedPositions(pot=None, saList=None, fromProtonRange=(0, 1), fromHeavyRange=(0, 1), toProtonRange=[], toHeavyRange=[], fromProtonSignChanges=0, fromHeavySignChanges=0, toProtonSignChanges=0, toHeavySignChanges=0, foldedAlongFromProton=0, foldedAlongFromHeavy=0, foldedAlongToProton=0, foldedAlongToHeavy=0)

unfoldPeakPosnToMatch(peakPosn, targetPosn, isFolded, shiftRange, signChangesUponFolding): Given a raw peak position, a raw shift assignment, and the range
of the spectrum (all in PPM),
a folded/aliased flag, and a sign changes flag,

Return the un-folded/aliased peak positions closest to the shiftAssignment and their expected signs
as [unfoldedPeakPos, expectedSign] pairs

unfoldedPeakPosnMatches(unfoldedPeakPosn, targetPosn, tolerance): Given an unfolded peak position from unfoldPeakPosnToMatch, a raw
shiftAssignment, and a tolerance (all in PPM), return whether the
unfolded position is within tolerance of the shiftAssignment.

Note that this assumes that tolerance < spectralWidth