On 05/09/2011 19:27, Ken Smith wrote: In response to this, I have made a few changes to the way OpenBabel calculates InChI.
> E.g. for a proton [H+], I get: > > InChI=1S/H/q+1 > (ASSFXGJQJOXDAB-UHFFFAOYSA-N) > > But I *think* I should be getting: > > InChI=1S/p+1 > (GPRLSGONYQIRFK-UHFFFAOYSA-N) OB now gives InChI=1S/p+1 which Dmitrii Tchekhovskoi on the InChI-discuss mailing list recommends as correct. > Likewise for protonated molecular hydrogen (whose SMILES notation I > assume is [H][H][H+]). I'm getting an InChI of: > > InChI=1S/H3/h1H2/q+1 > > whereas I'm fairly sure it should be something like: > > InChI=1S/H2/h1H/p+1 OB still gives InChI=1S/H3/h1H2/q+1, which is apparently correct for a linear structure. On the other list Dmitrii Tchekhovskoi and Geoff Hutchinson discussed calculating InChIKey directly from an input InChi, rather than going through an OBMol. This is now done by default on the commandline or in the GUI whenever InChI is the input format. There is an option to force a recalculation. (The inchi descriptor behaves as if it always reuses an input InChI.) Chris ------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
