Looks like a bug in the code that builds an OBMol from the return value of the InChI code. There is some special handling of hydrogens which must have gone astray.
Regards, - Noel On 24 October 2014 17:15, vamin <victor.a...@gmail.com> wrote: > I am having trouble parsing InChIs for hydrogen-only molecules: > > InChI=1S/H/q-1 Hydrogen atom anion 12385136 > InChI=1/H Hydrogen atom 12385136 > InChI=1S/p+1 Hydrogen atom cation 12385136 > InChI=1S/H/q-1/i1+1 Deuterium atom anion 16873179 > InChI=1/H/i1+1 Deuterium atom 16873179 > InChI=1S/p+1/i1+1 Deuterium atom cation 16873179 > InChI=1/H2/h1H/i1+1 Deuterium hydride 13983205 > InChI=1/H2/h1H/i1+1D Deuterium diatomic 7782390 > InChI=1S/H2/h1H/q-1 hydrogen diatomic anion 1333740 > InChI=1/H2/h1H Hydrogen diatomic 1333740 > InChI=1S/H2/h1H/q+1 Hydrogen cation 1333740 > InChI=1S/H3/c1-2-3-1/q+1 hydrogen trimer cation 28132481 > (these examples are from http://cccbdb.nist.gov/inchi.asp) > > e.g.: >>>> mol = pybel.readstring('inchi', 'InChI=1S/H/q-1') >>>> mol.write('can') > '\t\n' > > and: >>>> mol = pybel.readstring('inchi', 'InChI=1S/H2/h1H/q-1') >>>> mol.write('can') > '\t\n' > > but: >>>> mol = pybel.readstring('inchi', 'InChI=1S/He/q-1') >>>> mol.write('can') > '[He-]\t\n' > > I am using Python 2.7 and OpenBabel 2.3.2: >>>> pybel.ob.OBReleaseVersion() > '2.3.2' > > If I am doing something wrong, I would appreciate pointers. Otherwise I > would like to report this as a bug. If this is not the right place to do > that, I'd be happy to file a bug report in whatever manner works best for > you. > > Best, > > Victor > > > > -- > View this message in context: > http://forums.openbabel.org/Hydrogen-only-InChIs-tp4657800.html > Sent from the openbabel-devel mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
