Hi, guys.? ? I wanted to calculate the topological distance between two
substructures. For example, the distance between carboxyl and acetyl in aspirin
is 3 (or 4 if consider bond numbers) which are carbon, carbon and oxygen.? ? My
idea is to compare all the matched atoms between the two substructures.?
>>> m = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')>>> carboxyl =
>>> Chem.MolFromSmarts('C(=O)[OH]')>>> m.GetSubstructMatch(carboxyl)(10, 11,
>>> 12)>>> acetyl = Chem.MolFromSmarts('[CH3]C(=O)O')>>>
>>> m.GetSubstructMatch(acetyl)
(0, 1, 2, 3)
So, What I want is :a = [10,11,12]b = [0,1,2,3]def distrance(id1,id2):? ? m =
Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')? ? ...? ? return d>>> min (
map(distance, [(x,y) for x in a for y in b] ) )3 ( or 4)
Unnecessary to consider that using m as a parameter is better.
Is it possible to define the distrance function with rdkit python API ? ?I
tried to use atom pair but found that it seemed helpless.
Hongbin Yang?
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