Hi Folks Apologies if this is a silly question (I'm not a chemist), but could someone tell me how to consistently generate InChI/InChIKeys for a proton and protonated molecular hydrogen? Openbabel seems to assume removal of electrons rather than the addition of protons. Is there an (openbabel python bindings) option I can specify to force protonation? Feel free to point me to the FAQ - I haven't found it so far...
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) 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 Thanks in advance, Ken ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
