Hi,
I'm wondering what is the reason that the 'Match' method in the
'OBSmartsPattern' class automatically adds hydrogens to a molecule if the
SMARTS pattern has a hydrogen in it.
It seems to me that this hidden addition of hydrogens has a couple
limitations:
First, the indices that the 'GetUMapList' method reruns may be wrong with
respect to the query molecule. This is particularly problematic if one wants
to map the indices back to the atoms in the query molecule.
Second, it modifies the input molecule such that for example checking for
patterns under different PH conditions is hard.
Cheers,
Izhar
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