Dear Masgils,
Try:
AllChem.GetBestRMS(mols[0],mols[1],map=[list(zip(a,b))])
I hope this works.
Regards,
Omar
On Fri, Jul 26, 2019 at 4:52 AM Masgils wrote:
> Dear Paolo,
> Thank you very much. It was very helpful.
> I get atom idx of the corresponding structure in each molecule successful!
Dear Paolo,
Thank you very much. It was very helpful.
I get atom idx of the corresponding structure in each molecule successful!
But there is another problem.
When I used:
a = mols[0].GetSubstructMatch(generic)
b = mols[1].GetSubstructMatch(generic)
Dear Masgils,
you may try something along these lines, i.e. make atoms and/or bonds
generic on one of the molecules withrdmolops.AdjustQueryProperties() in
order to get subtructures to match, and then use rdMolAlign.GetBestRMS():
piperidine = Chem.AddHs(Chem.MolFromSmiles("C1CC(C)CCN1"))
Hi, all
Is it possible use GetSubstructMatches() to match a substructure with one or
two atom different from ref_mol? (eg. a Piperidine ring and a Piperazing ring)
And how to get the RMSD between corresponding atoms of two substructures?
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