Hi,
I'm not sure I understand what you're looking for, but I think you want to
find an MCS subject to the additional constraint that matching atoms are
close to each other in space in 3D conformations? Here's a demo of how you
might do that:
https://gist.github.com/greglandrum/365b0b5f6cfedfe79b7686c1c261deb3
Note that this presumes that the molecules are already more or less aligned
to each other. If you don't have pre-aligned molecules (and need to find
that alignment) the problem is a bit more difficult. Let me know and I can
try to put something together there too.
Does that get close to what you're looking for?
On Fri, Jan 10, 2020 at 11:10 PM Luan Carvalho Martins <
luancarvalhomart...@gmail.com> wrote:
> 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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> Rdkit-discuss@lists.sourceforge.net
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>
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