I've encountered a strange behavior while parsing the CDX file representing this reaction http://www.google.com/patents?id=bZ7WAAAAEBAJ&zoom=4&pg=PA14#v=onepage&q&f=false
When I read a CDX file and produce smiles output, it looks like OpenBabel reads three molecules. When I run it to produce rxn output, it looks like only two are read. I thought the logic for input and output were separated in OpenBabel. Specifically rxnformat's WriteChemObject calls OBConversion's GetChemObject once, so I thought the data would have to be fully loaded in by writing time. Is this behavior correct? Did I miss something? Do output formats tell the input readers how many molecules to expect? Am I running something incorrectly? I'm running OpenBabel 2.3.0 on a Mac. This behavior doesn't change when using the SVN build. Cheers, Abe The log from producing RXN output. It produces two 'Reading/Done reading' pairs, which I'm interpreting as two molecules. $ ./build/bin/babel -icdx ~/data/Patent/cdx_examples/US07804087-20100928-C00031.CDX -orxn Reading 0x100319860 Done reading 0x100319860 Reading 0x10032f470 Done reading 0x10032f470 0 reactions converted 9 audit log messages 367 debugging messages The log from producing Smiles output. It produces three 'Reading/Done reading' pairs, which I'm interpreting as two molecules. $ ./build/bin/babel -icdx ~/data/Patent/cdx_examples/US07804087-20100928-C00031.CDX -osmiles Reading 0x100319860 Done reading 0x100319860 Reading 0x10032f470 Done reading 0x10032f470 ============================== *** Open Babel Warning in Init Cannot open atomtyp.txt defaulting to compiled data. ============================== *** Open Babel Warning in Init Cannot open aromatic.txt defaulting to compiled data. ============================== *** Open Babel Warning in Init Cannot open phmodel.txt defaulting to compiled data. ============================== *** Open Babel Warning in Init Cannot open element.txt defaulting to compiled data. c1cc2c3c4c1C(=O)OC(=O)c4ccc3c(=O)n(c2=O)C1CCCCC1 00027001.cdx Reading 0x100319860 Done reading 0x100319860 C1[C@H](CC[C@@H](C1)C)N /home/data/Patent/cdx_examples/US07804087-20100928-C00031.CDX c1cc2c3c4c1c(=O)n(c(=O)c4ccc3c(=O)n(c2=O)C1CCCCC1)[C@@H]1CC[C@@H](CC1)C /home/data/Patent/cdx_examples/US07804087-20100928-C00031.CDX 3 molecules converted 4 warnings 112 audit log messages 750 debugging messages -- A. Heifets http://www.cs.toronto.edu/~aheifets/ ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
