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
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