hmm, I think this way is probably faster. And, once you grok the numpy
bits, it's arguably simpler:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('CCCCC')
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
dm=numpy.multiply(Chem.Get3DDistanceMatrix(mol),numpy.logical_not(Chem.GetAdjacencyMatrix(mol)))
dm[dm==0.0]=1000.0
minDist = numpy.min(dm)
# get the closest atoms:
mv=numpy.argmin(dm)
a1,a2 = mv // dm.shape[0],mv%dm.shape[0]
-greg
On Tue, Dec 3, 2013 at 6:00 PM, Michal Krompiec
<[email protected]>wrote:
> 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 @ICRnews
> >
> > Facebook www.facebook.com/theinstituteofcancerresearch
> >
> > 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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