Dear all,
I'm facing issues applying FindMCS to chiral molecules. What I'm trying to
obtain is a 3D-like MCS (i.e.: an MCS containing the chiral carbons, but
not the substituents which differ). This is not what matchChiralFlag
does (*include
atom chirality in the match*). Is there a way of obtaining such MCS from
FindMCS?
A simple example:
m1 = rdkit.Chem.AddHs(rdkit.Chem.MolFromSmiles('CC(C)[C@H](C)O'))
m2 = rdkit.Chem.AddHs(rdkit.Chem.MolFromSmiles('CC(C)[C@@H](C)O'))
rdkit.Chem.rdFMCS.FindMCS([m1, m2], **magicalOptions).smartsString
Out: [H]C([H])([H])C([H])(CO)C([H])([H])[H]
If there is no simple option set to do that, is there another way to
achieve such? I'm thinking about using a flexible molecular alignment
(maybe first using an MCS core constraint to get more good conformers),
then compare atoms close to each other given a small tolerance. Then maybe
checking for ring membership and completeRingsOnly somehow.
Thank you very much
Sincerely,
Luan Carvalho Martins
luancarvalhomart...@gmail.com
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