Hi Fredrik,
thanks a lot for the reply, it worked perfectly.
I'm pasting the script below, maybe it could be helpful to someone else.
Although, I believe the code "ob.OBTetrahedralStereo.Invert(config)" should be
supported
for sake of consistency (unless it's an issue with the 2.3.2 build in Ubuntu
13.10
repositories).
Cheers,
Stefano
-----------------
""" Invert chirality of atoms matching a given SMARTS pattern
NOTE: it doesn't work properly with SMARTS with more than
one chiral centers
"""
import pybel
ob = pybel.ob
smarts = 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:
canonical = pybel.readstring('smi', smi).write('can')
mol = pybel.readstring('can', canonical)
old = mol.__str__()
matches = smarts.findall(mol)
if matches:
firstmatch = matches[0]
print firstmatch
for matchingatom in firstmatch:
facade = ob.OBStereoFacade(mol.OBMol)
# NOTE GetTetrahedralStereo uses 0-based counting
# while pybel.smarts returns 1-based indices
ts = facade.GetTetrahedralStereo(matchingatom-1)
if ts:
config = ts.GetConfig()
if config.winding == 1:
config.winding = 2
else:
config.winding = 1
ts.SetConfig(config)
else:
print "\t\tNo match, passing on molecule:", mol
outputfile.write(mol)
new = mol.__str__()
check = (old == new)
print "STILL THE SAME?", check
if check:
print old
outputfile.close()
--------------------
On 06/18/2014 01:01 AM, Fredrik Wallner wrote:
> 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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>
--
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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