Hi everyone,
I'm trying to invert the chirality of a chemical group using Python. I had
searched quite
a while before finding something that I could use (despite the fact the
question showed up
a few times in the mailing list).
My starting points were a discussion on Blueobelisk[1] and a guide file[2] that
Noel
linked in an old mailing list thread but I couldn't find in the current release.
The example in [2] didn't work in my case, and it seems to use deprecated
.Set*ClockwiseStereo() functions, therefore, I tried the other one that's
following the
blessed way (correct me if I'm wrong) with OBStereoFacade.
Here is the code, that works up to a certain point:
-----
import pybel
ob = pybel.ob
smarts = pybel.Smarts("c[C@H](C(=O)O)")
inverse = pybel.Smarts("c[C@@H](C(=O)O)")
outputfile = pybel.Outputfile('smi', 'converted.smi', overwrite=1)
inmol = [ '[O]C(=O)[C@H](c1cccnc1)C' ]
for smi in inmol:
mol = pybel.readstring('smi', smi)
old = mol.__str__
matches = smarts.findall(mol)
firstmatch = matches[0]
if matches:
print "MATCH"
facade = ob.OBStereoFacade(mol.OBMol)
for matchingatom in firstmatch:
ts = facade.GetTetrahedralStereo(matchingatom)
if ts:
print "TS\t", ts
config = ts.GetConfig()
print "CONFIG\t", config
# these commands will raise an error
# ob.OBTetrahedralStereo.Invert(config)
# ob.OBTetrahedralStereo_invert(config)
config.Invert()
ts.SetConfig(config)
assert inverse.findall(mol), "Hasn't been inverted!"
outputfile.write(mol)
new = mol.__str__
print "STILL THE SAME?", old == new
outputfile.close()
-----
When attempting to invert the chirality, it fails with the following error:
Traceback (most recent call last):
File "invertChiralityFacade.py", line 24, in <module>
config.Invert()
AttributeError: 'OBTetrahedralConfig' object has no attribute 'Invert'
I've tried all combinations mentioned here [3] and none of them worked.
Besides, it seems
here is no mention of the Invert function in openbabel.py.
I would really appreciate any input on the matter.
Thanks!
Stefano
[1]
http://blueobelisk.shapado.com/questions/which-openbabel-dev-version-methods-should-be-used-for-altering-stereochemistry
[2]
http://www.filewatcher.com/p/openbabel-2.3.0.tar.gz.14321281/openbabel-2.3.0/doc/guide/_sources/UseTheLibrary/PythonExamples.txt.html
[3] https://code.google.com/p/pythonocc/issues/detail?id=20
--
Stefano Forli, PhD
Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: (858) 784-2055
fax: (858) 784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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