[Rdkit-discuss] Is there any function that can calculate the 2D distance between two atoms?

[杨弘宾 <yan...@16...>]

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?