Thanks Aileen, This is very useful and may help spur improvement in CIF file format support. I didn't realise that CIF is yet another format that does not store the chemical structure; Open Babel has to guess what the chemist already knew (which always makes me shake my head).
Just to note though that the first two aren't bugs; it is possible to normalise nitro however you want (we can discuss this further if you are interested), and --unique works fine (it finds unique molecules in multimolecule file formats like SDF, not unique disconnected components in a single molecule like MOL). Regards, - Noel On 9 December 2013 16:44, daya <d...@rsc.org> wrote: > I’ve just supervised a student project in which we used OpenBabel to convert > over 44,000 Royal Society of Chemistry CIF structures to mol files, then a > student checked over 4,000 of these conversions so that we could upload the > successfully processed CIFs to ChemSpider for the corresponding ChemSpider > compounds. A summary of the results of that project are detailed here: > http://www.chemspider.com/blog/adding-rsc-cifs-to-chemspider.html > It seemed like a valuable opportunity to identify the most frequent > OpenBabel bugs when doing a CIF to Mol conversion so these are documented in > there, along with test cases to identify the problems and with a view to > fixing them and making OpenBabel more bulletproof. > We’re taking a bit of a break from this project for now, but in the next > phase of the project will see if we can fix at least some of the bugs > identified if they haven’t already been. > But we’re sharing these results here for now though since we thought you > would be interested in the project and the performance of OpenBabel when run > over such a large and varied test set, possibly even enough to look into > some of them yourselves… > Looking forward to working with you on some of them in the future… > Aileen Day (Informatics Analyst, RSC ChemSpider) > > > > -- > View this message in context: > http://forums.openbabel.org/Converting-CIFs-to-mols-using-OpenBabel-tp4657031.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Sponsored by Intel(R) XDK > Develop, test and display web and hybrid apps with a single code base. > Download it for free now! > http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
