On 2013-11-17 12:34, Geoffrey Hutchison wrote: > It doesn't take a cheminformatics specialist to realize these strings are > different:
Well, as I understand it, one of the problems with smiles is you can start your graph at any atom. Which gives you any number of different smiles string for the same molecule. For all I know they're all different descriptions of the exact same graph. ... > 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 Well, sorry, it does take a cheminformatics specialist to know that is "more similar" to "CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)O[C@H](CCc2ccccc2)c3ccccc3" than "CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc2ccccc2)c3ccccc3" > 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? I don't think the problem is in OpenBabel, but I can't tell. RCSB says they're all describing the same molecule. OpenBabel says they aren't. Who should I trust and why? So I asked. Dima ------------------------------------------------------------------------------ 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
