That's a pretty bad regression, and I will investigate the two examples you sent.
Certainly if you can prepare a test set (in whatever format) that would be extremely helpful, since it could be added as a unit test. Not only would this ensure all such examples will be fixed, but future versions will need to ensure they pass. I'd actually be very interested in such a set for other reasons, since the gen3d builder and other parts of he code (UFF) need similar testing on inorganic compounds. You can either send the CIFs to me personally, or provide entries into the COD, since I can script the downloads. As I said before, I really want to know of these types of bugs (inorganics, but also any type of changes from one release to another). Thanks, Geoff > On Dec 14, 2013, at 1:26 AM, mquiros <mqui...@ugr.es> wrote > 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
