I'm not sure whether you want to get these distances for the entire molecule or just certain atom pairs. But I guess the simplest way to get the distance between two atoms would be…
>>> from rdkit import Chem
>>> import numpy as np
>>> from rdkit.Chem import AllChem
>>> mol = Chem.MolFromSmiles('CCCCC')
>>> AllChem.EmbedMolecule(mol)
>>> AllChem.UFFOptimizeMolecule(mol)
>>> conf = mol.GetConformer()
>>> at1Coords = np.array(conf.GetAtomPosition(1))
>>> at2Coords = np.array(conf.GetAtomPosition(2))
>>> print np.linalg.norm(at1Coords-at2Coords)
1.52139356317
This can be optimised by not using numpy, I've not looked but there must be
some sort of euclidean distance using the Point3D class in RDKit.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
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On 3 Dec 2013, at 15:56, Michal Krompiec
<[email protected]<mailto:[email protected]>> wrote:
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
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