Chris, Thank you for working on this! I do work on reaction recognition in OSRA - you can actually try for yourself the svn trunk release 905:
svn co -r 905 https://osra.svn.sourceforge.net/svnroot/osra/trunk I have a few additional questions about reactions in OB, if I may: 1) The only two formats that I got working for OBReaction output are RSMI and CMLR. It would be great to output others, such as RXN, but I'm getting a segfault on the exact same code when I try to generate RXN instead of RSMI. Would you be interested in looking at the problem with RXN output? 2) Neither SetComment() nor SetData seem to do anything for either RSMI or CMLR output. It's not a huge deal but it would be nice to be able to save some additional information about the reaction in a way which is independent of the output format. 3) SetReversible doesn't seem to do anything for RSMI. I haven't tested on CMLR because frankly I haven't found anything which can read CMLR format. I am also not sure it's possible to have a reversible reaction in RSMI - I don't know that much about the format. Best regards, Igor On Wed, 2012-06-20 at 07:28 -0400, Chris Morley wrote: > I've replaced the format chemdrawcdx.cpp with a new version that can > read *some* reactions as well as molecules. > > 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, although most OB > molecule output formats will output the reactants and products if given > an OBReaction. > > The parsing of the cdx file is separated from the interpretation to a > greater extent than before, which should make it easier to do an XML > version (but cdxmlformat.cpp has not been changed yet). The CDX tree can > be displayed (-ad), in a similar way to Cambridgesoft's CDXHexDumper, > except that it contains human-readable names, obtained by parsing the > enums in the header file. > > The reaction parsing works only for cdx files which have single > reactions which are completely described in the file's data tree, as in > the attached file. This sadly is not the case for most cdx files where > additional heuristics based on the position of the arrow in the image is > necessary. I have been holding off committing these changes pending this > improvement, but have got round to it. Parsing an ordinary image would > be very similar, and I know Igor Filippov is working on this for OSRA, > so maybe this could be applied in cdx parsing. Rich Apodaca also seems > to have renewed interest, > http://depth-first.com/articles/2012/06/01/reading-and-rendering-chemdraw-cdx-files-in-javascript/ > > . > > Chris > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
