Hi all,
I'm having an issue with SMARTS pattern matching and chirality.
I'm trying to recognize one specific chiral configuration, but I get unexpected
answers,
see the following example:
------------------------------
#!/usr/bin/env python
import pybel
ob = pybel.ob
patterns = [ ('p1' , '[$(*[C@@H])]'),
('p2' , 'F[C@@H](Br)Cl'),
('p3' , '[$(*[C@H])]'),
('p4' , 'F[C@H](Br)Cl'),
]
smi ='F[C@H](Br)Cl'
mol = pybel.readstring('smi', smi)
print "Molecule", mol
for pname, p in patterns:
print "PATTERN %s : %s => " % (pname, p),
smarts = pybel.Smarts(p)
print smarts.findall(mol)
------------------------------
$ python smartest.py
Molecule F[C@H](Br)Cl
PATTERN p1 : [$(*[C@@H])] => [(1,), (3,), (4,), (5,)]
PATTERN p2 : F[C@@H](Br)Cl => [(1, 2, 4, 5)]
PATTERN p3 : [$(*[C@H])] => [(1,), (3,), (4,), (5,)]
PATTERN p4 : F[C@H](Br)Cl => [(1, 2, 4, 5)]
I would expect patterns p1 and p2 to return no matches, and p3 and p4 to
succeed.
Although, even carbon chirality is clearly the opposite in the molecule and p1,
p2, the
script finds matches.
Am I missing something, maybe?
Advices will be much appreciated.
Thanks
S
--
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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