Hi, Maybe someone with more insight into the specifics can give a more stable answer, but what I’ve found is that you can invert a center with the following code: config.winding = 2 if config.winding == 1 else 1 ts.SetConfig(config) So replacing config.Invert() with these two lines will make your example work at least…
Kind regards,
Fredrik
18 jun 2014 kl. 03:45 skrev Stefano Forli <fo...@scripps.edu>:
> 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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