Hi all,
for a while, now, I'm banging my head on how to perform simple modifications on
molecules
(I wouldn't dare to call them reactions), but I'm having a hard time getting
anything
done. I'm using v2.3.2 with Python, and the core of my code is basically this:
reactor = ob.OBChemTsfm()
reactor.Init(start_pattern, end_pattern)
reactor.Apply(mol)
Since I couldn't get it to work with my molecules, I've tested one simple
reaction example
from here [1]:
[CH2:1]=[CH:2][CH:3]=[CH:4][CH2:5][H:6]>>
[H:6][CH2:1][CH:2]=[CH:3][CH:4]=[CH2:5]
and I found that it doesn't seem to work on a simple test molecule such
"C/C=C\C=C".
I think the problem is that the first part of the reaction is not recognized
using it as
SMARTS pattern, even without indexes (i.e. "[CH2]=[CH][CH]=[CH][CH2][H]").
The documentation suggests that OBChemTsfm is indeed the one to use to perform
chemical
transformations, while OBReaction holds only the information about it.
I suspect I'm doing something wrong, but I can't figure out what it is.
Any advice on the matter?
Thanks!
S
[1] http://www.daylight.com/meetings/summerschool01/course/basics/smirks.html
--
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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