Given that the tests pass on Windows, but not on Linux, are we running the same InChI version on Windows as on Linux (the Windows one uses a precompiled binary)?
- Noel On 15 April 2010 09:31, Chris Morley <[email protected]> wrote: > Geoffrey Hutchison wrote: >> Currently, the InChI test is failing on UNIX platforms for reasons I can't >> understand. Here's a run-down: >> http://my.cdash.org/testDetails.php?test=1930810&build=58657 >> >> So the main problem is that the molecule (ferrocene) shows an error: >> >> Not ok 1 # Mismatch in molecule #1. generated / correct >> # InChI=1S/2C5H5.2C5H.2Fe/c4*1-2-4-5-3-1;;/h2*1-5H;2*1H;;/q;;;;;+2 >> # InChI=1S/4C5H5.2Fe/c4*1-2-4-5-3-1;;/h4*1-5H;;/q;;2*-1;;+2 >> >> OK, so the second InChI is the correct one. But if you run "make install" >> and then run babel to generate the inchi from the SDF yourself, you get that >> *exact* InChI. So there's no problem with our code. >> >> I'm left trying to figure out the problem with the test environment. >> * Chris: what data files could mess up the test? >> * Marcus: how would CTest differ from a compiled babel? > > This may be clutching at straws, but the file samples.sdf has Windows > line endings. This should not matter with either inchiwrite.cpp or > babel, but possibly something has gone wrong. I've committed a version > with Unix line endings, so you can try it. > > It is just about possible that this would affect the parsing of the > sdf 'alias' data, which is where you suggest the problem is. > The InChI sdf samples use alias constructs like > > A 1 > CH > A 4 > CH- > > which is not good practice in my view; there are better ways of saying > that the C has an H and a maybe a negative charge. The code which > interprets this construct, AliasData::FormulaParse, was cobbled > together so that these InChI sample files could be read, and I would > have little confidence in its robustness. I was not inclined to write > a (much larger) complete parser for inline formulas, because I am not > aware of a specification for it, and anyway construct is obsolete and > IMO unnecessary. (Defined aliases like COOH are much more sensible and > are supported.) > > Chris > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > OpenBabel-Devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
