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? 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 > >> > > ------------------------------------------------------------------------------ Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
