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
benzene-to-phenol-reaction.cdx
Description: Binary data
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