Hi all,
I'm trying to draw two similar molecules with slightly different scaffolds
in the same orientation. I can't define a pattern to use
for GenerateDepictionMatching2DStructure, so I was instead trying to get
the MCS of the two molecules, get the coordinates of the MCS from the first
molecule, and use those to depict the second with coordMap, similarly as in
http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure.
This gives the required result most of the time, but in some cases the MCS
has a symmetry element and then the image ends up with distorted rings. Is
there a way to force rings to be drawn as they should be even when a
coordMap is used? Please find the code below. Thanks,
Márton
from rdkit import Chem
from rdkit import Geometry
from rdkit.Chem import AllChem
from rdkit.Chem import rdFMCS
from rdkit.Chem import Draw
mol1=Chem.MolFromSmiles("CC1=C2C=C(N)C=CC2=CC(Cl)=N1")
mol2=Chem.MolFromSmiles("CC1=C2C=C(N)C=CC2=NC(Cl)=C1")
mcs=Chem.MolFromSmarts(rdFMCS.FindMCS([mol1,mol2]).smartsString)
AllChem.Compute2DCoords(mol1)
match1=mol1.GetSubstructMatch(mcs)
match2=mol2.GetSubstructMatch(mcs)
coords=[mol1.GetConformer().GetAtomPosition(x) for x in match1]
coords2D = [Geometry.Point2D(pt.x,pt.y) for pt in coords]
coordDict={}
for i,coord in enumerate(coords2D):
coordDict[match2[i]] = coord
AllChem.Compute2DCoords(mol2,coordMap=coordDict)
Draw.MolsToGridImage([mol1,mol2],subImgSize=(250,250),molsPerRow=2)
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