On 03/03/2011 21:15, Noel O'Boyle wrote: > I've spent an hour on this and I'm still none the wiser. It definitely > appears to be commit r4403 (i.e. mine) but I can't see what the link > between mcdlutil.cpp and the inchi code is? > > The following converts successfully with 4402 but not 4403: > > obabel C:\Tools\openbabel\trunk\test\inchi\Samples.sdf -o inchi -f 1 > -l 1 # It fails with this first molecule, ferrocene I think... > > Chris, do you have any idea? Is the mcdlutil code used elsewhere?
The SDF file for ferrocene (part of the InChI documentation) uses aliases "CH" and "CH-" for the carbon atoms. (A very poor practice, in my view.) These are expanded in AliasData::FromNameLookup() which the uses the global function groupRedraw() from MCDL code to add atoms with coordinates to a 2D molecule. Builder is used for 3D molecules and also originally for 2D molecules, but MCDL gave better results. I don't know yet why calling this MCDL function should affect InChI but maybe some global or static data in the stereo code is affected? I'll keep looking. Chris Congratulations on getting the summer studentship funded! > - Noel > > On 3 March 2011 09:54, Noel O'Boyle<baoille...@gmail.com> wrote: >> Just to let everyone know that I'm aware I made the inchiSamples Test >> fail somehow with my commit to MCDL last night. I'll sort it out... >> >> - Noel >> >> ---------- Forwarded message ---------- >> From: CDash<ad...@www.cdash.org> >> Date: 3 March 2011 09:41 >> Subject: FAILED (t=1): Open Babel - Apple Mac OS X 10.6 GCC 4.0.1 - Nightly >> To: baoille...@gmail.com >> >> >> A submission to CDash for the project Open Babel has failing tests. >> You have been identified as one of the authors who have checked in >> changes that are part of this submission or you are listed in the >> default contact list. >> >> Details on the submission can be found at >> http://my.cdash.org/buildSummary.php?buildid=163484 >> >> Project: Open Babel >> Site: PLATINUM.geoffh >> Build Name: Apple Mac OS X 10.6 GCC 4.0.1 >> Build Time: 2011-03-03T04:35:28 EST >> Type: Nightly >> Tests failing: 1 >> >> >> *Tests failing* >> inchiSamples.sdf_Test >> (http://my.cdash.org/testDetails.php?test=5265363&build=163484) >> >> >> -CDash on my.cdash.org >> > ------------------------------------------------------------------------------ What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
