Dear Nick,
Thanks. I need it for the whole molecule. But indeed it seems to be
faster this way - loop over pairs of atoms:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('CCCCC')
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
conf=mol.GetConformer()
natom=mol.GetNumAtoms()
minimum=1e100
for i in range(0, natom):
for j in range(i+1,natom):
if mol.GetBondBetweenAtoms(i,j)!=None:
dist=rdMolTransforms.GetBondLength(conf,i,j)
if dist<minimum:
minimum=dist
print(minimum)
On 3 December 2013 16:17, Nicholas Firth <[email protected]> wrote:
>
> 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
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton |
> Surrey | SM2 5NG
>
> T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter
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>
> Making the discoveries that defeat cancer
>
>
>
> On 3 Dec 2013, at 15:56, Michal Krompiec <[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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