Dear All,
I am trying to calculate MCS-based similarity for few enantiopure drugs. In
given example below, there is a difference in type of stereo-bonds about
chiral carbon (all 4 bonds are of non-hydrogen groups)
How do I distinguish between chiral bonds during MCS matching?
Any help would be appreciated.
Thanks
om
Om Prakash
Ph.D student
School of Computational and Integrative Sciences,
Jawaharlal Nehru University
New Delhi
India
################################
from rdkit.Chem import MCS
from rdkit import Chem
from rdkit.Chem import AllChem
import numpy as np
mol1 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@@]3(OCc2cc(C#N)ccc23)CCCN(C)C")
mol2 = Chem.MolFromSmiles("Fc1ccc(cc1)[C@]3(OCc2cc(C#N)ccc23)CCCN(C)C")
mol1.SetProp("_Name","S-Citalopram")
mol2.SetProp("_Name","R-Citalopram")
mols=[mol1,mol2]
###############
def mcssij(mols):
my_array = np.empty((len(mols), len(mols)))
for i in range(len(mols)):
iAtoms=mols[i].GetNumAtoms()
iBonds=mols[i].GetNumAtoms()
for j in range(len(mols)):
jAtoms=mols[j].GetNumAtoms()
jBonds=mols[j].GetNumAtoms()
# get mcs
out=MCS.FindMCS([mols[i],mols[j]])
natoms=out.numAtoms
nbonds=out.numBonds
#formula
simij=(natoms+nbonds)/((iAtoms+iBonds)+(jAtoms+jBonds)-(natoms+nbonds))
my_array[i,j]=simij
return my_array
############
sim=mcssij(mols)
sim
Out[984]:
array([[ 1., 1.],
[ 1., 1.]])
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