On 4 March 2011 10:43, Chris Morley <c.mor...@gaseq.co.uk> wrote: > > 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.
Thank goodness you found the link. I was going nutty. I look into it some more over the weekend if you haven't figured it out. At least I have somewhere to start now... > Chris > > Congratulations on getting the summer studentship funded!. ------------------------------------------------------------------------------ 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
