On 19/07/2011 17:17, Igor Filippov wrote:
> Chris,
>
> Thank you. Simple approach - just pointers to OBMol's for reactans and
> products is just fine for now. I looked at OBReaction and it seems
> reasonably clear.
>
> At the moment I'm focusing on writing out reactions from assembled
> OBMols into a file or string and not on the reading of reactions or any
> fancy manipulation. How do I write out RSMI from OBReaction - do I use
> OBConversion the same way as I do for regular file formats? Perhaps you
> have a three line example?
Yes it is entirely analogous:
OBConversion conv;
conv.SetInAndOutFormats("rsmi","rsmi");
OBReaction react;
conv.ReadFile(&react, "example.rsmi");
conv.Write(&react, &cout);
Chris
> Best regards,
> Igor
>
> On Tue, 2011-07-19 at 12:01 -0400, Chris Morley wrote:
>> Igor
>>
>> OpenBabel supports formats like, CMLreact, RXN Reaction SMILES, ChemKin,
>> which specify reactions. The internal structure is OBReaction which for
>> reaction formats is handled in the conversion routines like OBMol is for
>> molecule formats. Reading a file containing
>> c1ccccc1>>Nc1ccccc1
>> with rmsi format will make an OBReaction. OBReaction is fairly simple
>> and is really just a container to hold shared_ptrs to the molecules
>> which are the reactants, products, etc. OB doesn't have much for
>> constructing or modifying reactions.
>>
>> I've written a version of chemdrawCDX.cpp which reads reactions as well
>> as molecules. The code contains the construction of an OBReaction and
>> its transfer to OB's conversion system. The email describing it that I
>> sent to Abe Heifets (who may be who Geoff is referring to) is below. The
>> files are at:
>> http://gaseq.co.uk/OB/benzene-to-aniline-reaction.cdx
>> http://gaseq.co.uk/OB/chemdrawcdx.h
>> http://gaseq.co.uk/OB/chemdrawcdx.cpp
>>
>> This is stalled at the moment because of the need to add code to parse a
>> geometric layout and derive which molecules are reactants, products,
>> etc. I guess this is what you are doing, so I would be interested if you
>> have a method already.
>>
>> Chris
>>
>>
>>
>>
>> Abe
>> You might be interested in this OpenBabel format for reading CDX files.
>> It reads reactions as well as molecules, but only if they are single
>> reactions and completely described. The attached example works but most
>> of the examples from patents you sent me don't. The code needs some
>> extra heuristics to find incompletely described reactions, but I haven't
>> yet managed to write it in the past six months.
>>
>> The format generates OBReaction objects when it can, which can be output
>> by rsmi, rxn, etc. Excess molecules are output as OBMol objects as
>> normal. The option -am generates only molecules. Actually most molecule
>> output formats will output the reactants and products if given an
>> OBReaction.
>>
>> The parsing is separated from the interpretation to a greater extent
>> than before, which should make it easier to do an XML version.
>>
>> It is also possible (-ad) to output the CDX tree, in a similar way to
>> CDXHexDumper, except that it contains human-readable names.
>>
>> The attached file should replace the existing one, and I hope will
>> compile ok. A copy of chemdrawcdx.h should be put in the /data directory
>> so it can be parsed for the names.
>>
>>
>>
>> On 18/07/2011 16:33, Geoffrey Hutchison wrote:
>>> Dear Igor,
>>>
>>> Open Babel supports CML (react) and MDL Rxn formats for reactions. I'm not
>>> sure if there's great support for polymers, but that would definitely be a
>>> nice addition. I know someone who's working on ChemDraw reaction support as
>>> well.
>>>
>>> Chris Morley should have an example of a reaction file example -- I'm not
>>> seeing anything at the moment in the OBReaction documentation. If Chris
>>> doesn't respond today, I'll dig around tomorrow.
>>>
>>> Thanks and best regards,
>>> -Geoff
>>>
>>> On Jul 18, 2011, at 11:25 AM, Igor Filippov [Contr] wrote:
>>>
>>>> Dear Geoff,
>>>>
>>>> Re: reaction recognition in OSRA -
>>>> Is there any format or formats which OpenBabel can write that have
>>>> support for reactions and/or polymers (brackets)? It doesn't have to be
>>>> the same format for both.
>>>> How would I go about creating a reaction file or a polymer in C++?
>>>>
>>>> Igor
>>>>
>>
>>
>
>
>
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