In cheminformatics, the world of reactions is not as developed as single
molecules as databases of reactions are not widely available, and certainly
Open Babel's transformation code has limitations. If you are a C++
programmer, you may not find it too difficult to extend the functionality.
Otherwise, you're going to have to look elsewhere, to be honest. Indigo has
some code. RDKit has some code. But even the commercial toolkits may or may
not be able to do this. (Not that it's particularly difficult in this
instance - it's just that they don't have the functionality)
Regarding, "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?"
Again - this sounds reasonable, but is a more difficult problem, called
atom-mapping of reactions. This sometimes works, and sometimes doesn't. OB
has no code for this. I know that Indigo does. Whether you can then use the
atom-mapping to do a reaction, I'm not sure.
Sorry - not much help.
- Noel
On 30 July 2014 02:34, Stefano Forli <fo...@scripps.edu> wrote:
> 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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