Mirror conformation

[petrucci86]

Does RDkit provide a tool for inverting a molecule to its mirror image (e.g. right-handed to left-handed)? Thanks.

[wopozka]

Just copy molecule, iterate over all atoms, pick chiral ones and invert their configuration.

[petrucci86]

any code for sharing? if so, highly appreciated

[wopozka]

Well, lets create the simplest code possible:

from rdkit import Chem
chiral_mol = Chem.MolFromSmiles('C[C@@H](Cl)CC[C@@H](C)I')
invert_mol = Chem.MolFromSmiles('C[C@@H](Cl)CC[C@@H](C)I')
for atom in invert_mol.GetAtoms():
    atom.InvertChirality()
print(Chem.MolToSmiles(chiral_mol, invert_mol))

C[C@H](Cl)CC[C@H](C)I C[C@@H](Cl)CC[C@@H](C)I