Right now the user specifies SMIRKS indices and atom indices on input.
I think this puts undo stress on the user to understand how SMIRKS indices are used. There is no reason way we can't create SMIRKS indices based on the order of atoms in a tuple. For example, a bond just needs two atom indices (1,2) not a dictionary with SMIRKS indices {1:1, 2:2}.
This will make input into the smirksifier easier to work with since it won't need to lists of dictionaries for every molecule it can just be an ordered list by type.
bannanc
commented
5 years ago
Right now the user specifies SMIRKS indices and atom indices on input.
I think this puts undo stress on the user to understand how SMIRKS indices are used. There is no reason way we can't create SMIRKS indices based on the order of atoms in a tuple. For example, a bond just needs two atom indices
(1,2)not a dictionary with SMIRKS indices{1:1, 2:2}.This will make input into the
smirksifiereasier to work with since it won't need to lists of dictionaries for every molecule it can just be an ordered list by type.This may also make issue #36 easier.