[Rdkit-discuss] distance matrix for non-bonded atoms
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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Re: [Rdkit-discuss] distance matrix for non-bonded atoms
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('C')
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 distminimum:
minimum=dist
print(minimum)
On 3 December 2013 16:17, Nicholas Firth nicholas.fi...@icr.ac.uk 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('C')
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 nicholas.fi...@icr.ac.uk | 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 michal.kromp...@gmail.com 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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Re: [Rdkit-discuss] distance matrix for non-bonded atoms
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('C')
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
michal.kromp...@gmail.comwrote:
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('C')
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 distminimum:
minimum=dist
print(minimum)
On 3 December 2013 16:17, Nicholas Firth nicholas.fi...@icr.ac.uk 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('C')
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 nicholas.fi...@icr.ac.uk | 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 michal.kromp...@gmail.com
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
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into
your
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AppDynamics Pro!
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534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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Re: [Rdkit-discuss] distance matrix for non-bonded atoms
Dear all,
bugfixed version of my solution: (the previous one listed the shortest bond)
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('C')
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
conf = mol.GetConformer()
natom=mol.GetNumAtoms()
minimum=1e100
for i in range(0, natom-1):
for j in range(i+1,natom):
if mol.GetBondBetweenAtoms(i,j)==None:
dist=rdMolTransforms.GetBondLength(conf,i,j)
if distminimum:
minimum=dist
print(minimum)
On 3 December 2013 17:00, Michal Krompiec michal.kromp...@gmail.com 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('C')
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 distminimum:
minimum=dist
print(minimum)
On 3 December 2013 16:17, Nicholas Firth nicholas.fi...@icr.ac.uk 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('C')
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 nicholas.fi...@icr.ac.uk | 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 michal.kromp...@gmail.com 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
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics
Pro!
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with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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Re: [Rdkit-discuss] distance matrix for non-bonded atoms
Sorry for spamming the list. This is the correct version:
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles('')
mol=Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
conf = mol.GetConformer()
natom=mol.GetNumAtoms()
conf=mol.GetConformer()
minimum=1e100
for i in range(0, natom-1):
for j in range(i+1,natom):
if mol.GetBondBetweenAtoms(i,j)==None:
dist=rdMolTransforms.GetBondLength(conf,i,j)
if distminimum:
minimum=dist
print(minimum)
Best wishes,
Michal
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