El 13/12/2013 22:16, Geoffrey Hutchison escribió: >> I need to review and, in most cases, fix the SMILES chains coming >> out >> from OpenBabel for inorganic compounds (either manually or >> semiautomatically). I am also stuck to version 2.2.3 because >> versions >> newer than this perform worse for inorganic compounds. > > If you can give some bug reports or somewhat more detailed > descriptions of the problems we'd obviously really appreciate it. I > suspect many of these issues can be resolved, but if we're operating > in a vacuum, it's hard to know what bugs exist. For example, we're > firming up plans for v2.4, and obviously, I'd prefer to have improved > inorganic / organometallic support. > > As you say, some issues are inevitable, since there is a mismatch > between inorganic / organometallic bonding and the valence bond > model, > but that doesn't mean we can't aim to represent things well. For > example, the latest development code has improved support for "zero > order" bonds, including an extension to the SD file format. > > All of these discussions are quite productive, thanks! > -Geoff
Hello. Thanks a lot for your interest. I think I have already provided examples in previous posts, but if you want just a couple of quick examples, ferrocene and a pyridine complex (tetrakispyridine copper(II) chloride) with just SMILES -> SMILES conversion (the "inorganic problems" are not a CIF format problem but a more general one). I have prepared the following files with a single line: cupyrcl.smi: [Cu]([n]1ccccc1)([n]1ccccc1)([n]1ccccc1)[n]1ccccc1.[Cl-].[Cl-] Cupyr4Cl2 ferrocene.smi: [Fe]12345678([cH]9[cH]1[cH]2[cH]3[cH]49)[cH]1[cH]5[cH]6[cH]7[cH]18 ferrocene If I perform "babel cupyrcl.smi -osmi" and "babel ferrocene.smi -osmi", I expect the output to be equal to the input (or perhaps just changing the order of atoms). In the first example, I got it right with babel 2.2.3 but with babel 2.3.2, the output is very wrong: [Cu](N1CCCCC1)(N1CCCCC1)(N1CCCCC1)N1CCCCC1.[Cl-].[Cl-] Cupyr4Cl2 Full conversion of pyridine into piperidinato, all CH changed to CH2. Babel 2.3.2 wants to keep valence 3 for nitrogen even at the cost of completely corrupting the whole heterocycle. For ferrocene, with any of the two versions, the output is: [Fe]12345678(C9C1C2C3C49)C1C5C6C7C81 ferrocene Again dearomatization, the hydrogen count is however correct in this case. But I want the conversions to perform substructure search and any inorganic chemist looking for ferrocene derivatives will regard ferrocene as an aromatic compound and the search will fail. I can provide thousands of examples: metalocenes, metal carbonyls, phosphane complexes, imino complexes, boranes and carboranes, acetylacetonato complexes and a long etcetera that include the vast majority of metal-organic and organometallic compounds. Perhaps I can prepare a bunch of CIF files including at least one belonging to each of the most oustanding inorganic families to use as a test bench. Thanks again. Best wishes, Miguel Quirós ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
