Thanks, Noel.
I had seen your method but I had decided to go with OBReaction + RXN, because
it would
make life much easier for users of the tool I'm writing. In this way, they
could import
their RXN files prepared elsewhere without having to craft SMARTS patterns
manually.
Then, when I got stuck with that, I went back to the transformations, but I was
able only
to change elements and bond orders, not adding extra atoms:
-----8<----8<---8<---8<----8<-----8<-----------
import pybel
ob = pybel.ob
start = '[O:1]=[C:2]-[C:3]=[C:4]'
# end = '[O:1]=[C:2]-[C:3]-[C:4]-[S][C]' # not working
end = '[O:1]=[C:2]-[C:3]-[C:4]-[S:5][C:6]' # not working
transformer = ob.OBChemTsfm()
transformer.Init(start, end)
org = 'C=CC(=O)Nc1ccccc1'
mol = pybel.readstring('can', org)
startPattern = pybel.Smarts(start)
endPattern = pybel.Smarts(end)
# check that the pattern is found
print "Find start matching: ", bool(len(startPattern.findall(mol)))
transformer.Apply(mol.OBMol)
print "Original :", org
print "Modified :", mol.write('can')
print "Check for modified pattern:", bool(len(endPattern.findall(mol)) )
-----8<----8<---8<---8<----8<-----8<-----------
Although, if there's a way to have OBChemTsfm() working also for in silico
reactions, how
hard would it be to parse a RXN reaction(*) and convert its elements into
SMARTS strings
to be used with the OBChemTsfm?
Stefano
(*) pairwise reactions only, at this point.
On 07/29/2014 05:09 AM, Noel O'Boyle wrote:
> Does this help?
> http://baoilleach.blogspot.co.uk/2012/08/transforming-molecules-intowellother.html
>
> Note that OBReaction was not involved at any point. Furthermore, we had some
> problems
> wrapping OBReaction in Python - not sure if these were ever resolved...
>
> - Noel
>
>
> On 29 July 2014 00:38, Stefano Forli <fo...@scripps.edu
> <mailto:fo...@scripps.edu>> wrote:
>
> Hi all,
>
> I'm trying to write a Python object to apply a RXN transformation to a
> series of
> molecules.
> In particular, I'm peeking at the RXN format source (rxnformat.cpp) to
> populate an
> OBReaction() object but then I don't know how to tie it to the OBChemTsfm
> class to perform
> the actual transformation.
> Unfortunately, I had not much luck in finding documentation on the
> matter, so any
> suggestions will be more than welcome.
>
> 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 <mailto: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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