> Then I take 8 different inputs allegedly describing the same molecule > and get 5 different outputs. According to David it's because the inputs > are broken -- that doesn't surprise me.
Look, we all want software to be deterministic. But bugs are inevitable in complex software, and there's a saying "garbage in, garbage out." It doesn't take a cheminformatics specialist to realize these strings are different: Stereo SMILES (CACTVS) CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)O[C@H](CCc2ccccc2)c3ccccc3 SMILES (CACTVS) CCC(C)(C)C(=O)C(=O)N1CCCC[CH]1C(=O)O[CH](CCc2ccccc2)c3ccccc3 Stereo SMILES (OpenEye) CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc2ccccc2)c3ccccc3 Clearly the CACTVS version completely erases stereo information. I'm giving credit to CACTVS for labeling both stereo centers. Now, if I take the 3D SDF version from the website, Open Babel gives a similar SMILES to CACTVS: C(=O)([C@@H]1CCCCN1C(=O)C(=O)C(CC)(C)C)O[C@H](CCc1ccccc1)c1ccccc1 And.. I get the same SMILES from the PDB file on that webpage. So I guess we're confused where the problem is in Open Babel? Heck, if I use that SMILES (or the CACTVS version) and generate new 3D coordinates using Open Babel, the result gives me the same SMILES back. -Geoff ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
