Hi,
Newbie here. I have a list of SMARTS strings and a list of SMILES strings. For
each SMARTS string I would like to get the SMILES strings that are valid
instantiations of the SMARTS string. I am using the Python API. I have gotten
this far:
from rdkit import Chem
z3 =
Chem.MolFromSmarts("[C:1]-[C@@H;D3;+0:2](-[C;D1;H3:3])-[C@@H;D3;+0:4](-[C:5])-[O;H1;D1;+0]")
z2 =
Chem.MolFromSmiles("[C@:1]([C@@:17]([H:18])([C:14]1([CH3:16])[CH3:15])[C@:12]1([H:13])[CH2:11][CH2:10]2)([C@@:8]23[CH3:9])([C@@H:6]([CH3:7])[C@H:5](O)[CH2:4]4)[C@:2]34[H:3]")
if z3.HasSubstructMatch(z2):
# do something
This however would include cases where the SMILES matched only a sub-structure
of the SMARTS, whereas I am looking for complete matches. For example,
trivially, if the SMARTS represented several disjoint molecules separated by
'.' or a reaction with reactants and products separated by '>>' then I would
still get a match, which I don't want. As it happens, I know that neither of
these cases occur in my current dataset, but they might do in others; and I am
not a chemist, so I don't know whether it's possible for a proper substructure
to match without matching the whole SMARTS. I can't find anything in the RDKit
documentation or elsewhere online about this, but I am probably not using the
right terminology to search.
Also, my two datasets both have about 18 million records in them and for the
purposes of this question let's assume they are not canonical, so efficiency is
also an issue. I have 96 CPUs, 8 GPUs, and up to 376G RAM at my disposal.
Thanks in advance,
Robert
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