I spotted a couple of bugs in the ambiguous constraint generation routines
in b18 which render it non-functional. Here are the fixes:
diff ConstraintBasic.py ConstraintBasic.py.dist
374,375c374,375
< shifts = findMatchingPeakDimShifts(peakDim, chemShiftRangesDict[dataDim], tolerance=tolerance, aliasing=doAliasing, findAssigned=1)
<
---
> shifts = findMatchingPeakDimShifts(peakDim, chemShiftRangesDict[dataDim],aliasing=doAliasing,findAssigned=1)
>
392c392
< shifts2 = findMatchingPeakDimShifts(peakDim2, chemShiftRangesDict[dataDim2], tolerance=tolerance2, aliasing=doAliasing, findAssigned=1)
---
> shifts = findMatchingPeakDimShifts(peakDim, chemShiftRangesDict[dataDim2],aliasing=doAliasing,findAssigned=1)
408c408
< shifts = findMatchingPeakDimShifts(peakDim, chemShiftRangesDict[dataDim], tolerance=tolerance, aliasing=doAliasing, findAssigned=1)
---
> shifts = findMatchingPeakDimShifts(peakDim, chemShiftRangesDict[dataDim],aliasing=doAliasing,findAssigned=1)
I also have some suggestions for other changes. Basically tidy up default
intensity -> distance values so they're sensible and get rid of the
superfluous line at 365.
diff ConstraintBasic.py ConstraintBasic.py.dist
130c130
< distanceClasses = [(3.5,2.5,2.5,0.0),(1.3,2.8,2.8,0.0),(0.3,4.0,4.0,0.0),(0.1,5.0,5.0,0.0),(0.0,6.0,6.0,0.0)]
---
> distanceClasses = [(3.5,2.8,2.8,0.0),(1.3,2.5,2.5,0.0),(0.3,4.0,4.0,0.0),(0.1,5.0,5.0,0.0),(0.0,6.0,6.0,0.0)]
136c136
< (targetValue, upperLimit, lowerLimit) = (6.0,6.0,0.0)
---
> (targetValue, upperLimit, lowerLimit) = (0.0,0.0,6.0)
365c365
< # dataDimRef = peakDim.dataDimRef
---
> dataDimRef = peakDim.dataDimRef
In CalcAmbigDistConstraintsPopup.py the default chemical shift ranges for
1H and 15N could do with extending. The water stripe removal default for
proton should either be made more inteligent (we know where the middle of
the 1H dim is?) or removed from the default (though it's good to have it
in there as an example of multiple ranges for a dimension)?
diff CalcAmbigDistConstraintsPopup.py CalcAmbigDistConstraintsPopup.py.dist
473c473
< self.chemShiftRanges.append( ['1H',-2.0,4.85] )
---
> self.chemShiftRanges.append( ['1H',-1.0,4.85] )
480c480
< (start,end) = (75.0,140.0)
---
> (start,end) = (95.0,135.0)
--
Dr. Brian O. Smith ---------------------- B.Smith at bio.gla.ac.uk
Division of Biochemistry & Molecular Biology,
Institute Biomedical & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459 Fax: 0141 330 8640
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