Hello everyone,
I will repeat the problem here:
Input: SMILES string of Chemical A ('c1ccccc1') an its calculated 3D
coordinates from rdkit and SMILES of Chemical B ('Oc1ccccc1')
Ouput: 3D coordinates of chem B that aligns with Chemical A
After looking at a few example, I came up with this code:
prbChem = Chem.MolToSmiles(Chem.MolFromSmiles('Oc1ccccc1'))
prbMol = Chem.MolFromSmiles(prbChem)
prbMolwithH = Chem.AddHs(prbMol)
##Molecule used as reference fr the alignment
refChem = Chem.MolToSmiles(Chem.MolFromSmiles('c1ccccc1'))
refMol = Chem.MolFromSmiles(refChem)
refMolwithH = Chem.AddHs(refMol)
MolChemwithHs = [prbMolwithH, refMolwithH]
for x in MolChemwithHs:
rdDistGeom.EmbedMolecule(x)
for x in MolChemwithHs:
AllChem.UFFOptimizeMolecule(x)
tform = rdMolAlign.GetAlignmentTransform(prbMolwithH, refMolwithH)
*Is it true that if I can find tform, I can convert the coordinates of
chemical B using AllChem.TransformMol(probMol, tform) ? *
*Also, with the code, I got the error of *
Traceback (most recent call last):
File "3DAlignment.py", line 27, in <module>
tform = rdMolAlign.GetAlignmentTransform(prbMolwithH, refMolwithH)
RuntimeError: std::exception
Would you please help me with this error?
Thank you so much for your help :)
--
Phuong Chau
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