[Rdkit-discuss] distance matrix for non-bonded atoms

[Michal K. <mic...@gm...>]

Hello,
Is there any simpler (=faster) way of calculating the shortest
distance between non-bonded atoms in a molecule?

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolTransforms
import numpy
mol=Chem.MolFromSmiles("Cc2ccsc2c1sccc1C")
mol=Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.MMFFOptimizeMolecule(mol)
dm=numpy.multiply(Chem.Get3DDistanceMatrix(mol),numpy.logical_not(Chem.GetAdjacencyMatrix(mol)))
print("minimum non-bonded atom-atom distance:
{}".format(numpy.min(dm[numpy.nonzero(dm)])))

Best wishes,

Michal