Dear Xplor-nih users,
I wish to include an extraTerm in the fixupCovalentGeom procedure. As far as I
can see one needs to add the extra potentials as tuples of (term, tolerance) as
in the below:
protocol.fixupCovalentGeom(maxIters=100,useVDW=1,maxViols=10,bondTol=0.025,angleTol=4.0,extraTerms=[(harmpot,100.0)])
However, this causes a crash as later it appears the items are only the term
and not the tol:
File "/home/jtn/xplor-nih-2.33-b/python/regularize.py", line 460, in
fixupCovalentGeom
fixupLoop_xplor(ivm,2*maxIters,verbose-1,0,minState)
File "/home/jtn/xplor-nih-2.33-b/python/regularize.py", line 317, in
fixupLoop_xplor
viols=covalentViols(lSim.fastCommand)
File "/home/jtn/xplor-nih-2.33-b/python/regularize.py", line 154, in
covalentViols
ret.append( term.violations() )
AttributeError: 'tuple' object has no attribute 'violations'
If I skip the tuple and try only with term I get another error:
protocol.fixupCovalentGeom(maxIters=100,useVDW=1,maxViols=10,bondTol=0.025,angleTol=4.0,extraTerms=[harmpot])
File "/home/jtn/xplor-nih-2.33-b/python/regularize.py", line 460, in
fixupCovalentGeom
fixupLoop_xplor(ivm,2*maxIters,verbose-1,0,minState)
File "/home/jtn/xplor-nih-2.33-b/python/regularize.py", line 342, in
fixupLoop_xplor
lXplorCommand("flags exclude * include %s end" % join(pots))
File
"/home/jtn/xplor-nih-2.33-b/python/bin.Linux_x86_64/lib/python2.7/string.py",
line 318, in join
return sep.join(words)
TypeError: sequence item 3: expected string, PotProxy(XplorPot) found
Am I doing something wrong, it appears to me there is a bug somewhere related
to the extraTerms. My extra term is a harmonic potential restraining some of
the coordinates. I am using version 2.33
Hope you can help me,
best wishes,
Jakob
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
