I am trying to map atoms in one molecule to those of another using
GetSubstructMatch, but have a problem with molecule pairs like the two below
The problem is that GetSubstructMatch ignored the H on the n, so that the
protonated “n" in mol1 is mapped to the deprotonated “n”
in mol2, and vice ver
Dear Jan,
this gist shows a way to do what you need:
https://gist.github.com/ptosco/9b4a637a2814426846fe181f15aa8cdc
Basically, you'll need to convert explicit Hs into real atoms. Please
note that indices in the tuple obtained in the match with hydrogens
still apply to the original molecules
2 matches
Mail list logo
