I'm trying to set the configuration of a molecule with a double bond, but
it doesn't seem to be working. Here's my code:
===============
from rdkit.Chem import AllChem
from rdkit import Chem
from rdkit.Chem.rdchem import BondStereo
# Make a molecule with a double bond, no stereo specified (cis or trans)
smi = "NC(O)=C(C)S"
mol = Chem.MolFromSmiles(smi)
# Get that double bond
double_bonds = [b.GetIdx() for b in mol.GetBonds() if
b.GetBondTypeAsDouble() == 2 and b.GetStereo() is BondStereo.STEREONONE]
double_bond_index = double_bonds[0]
double_bond = mol.GetBondWithIdx(double_bond_index)
# It's stereo is STEREONONE at this point
print double_bond.GetStereo()
# Get the bonds connected to the first and second atoms
first_atom = double_bond.GetBeginAtom()
bonds_connected_to_first_atom = first_atom.GetBonds()
second_atom = double_bond.GetEndAtom()
bonds_connected_to_second_atom = second_atom.GetBonds()
# Get the indecies of those bonds, removing the central double bond.
bonds_connected_to_first_atom_indecies = [b.GetIdx() for b in
first_atom.GetBonds()]
bonds_connected_to_first_atom_indecies.remove(double_bond_index)
bonds_connected_to_second_atom_indecies = [b.GetIdx() for b in
second_atom.GetBonds()]
bonds_connected_to_second_atom_indecies.remove(double_bond_index)
# Set the directions of the for bonds connected to this double bond.
mol.GetBondWithIdx(bonds_connected_to_first_atom_indecies[0]).SetBondDir(Chem.BondDir.ENDUPRIGHT)
mol.GetBondWithIdx(bonds_connected_to_first_atom_indecies[1]).SetBondDir(Chem.BondDir.ENDDOWNRIGHT)
mol.GetBondWithIdx(bonds_connected_to_second_atom_indecies[0]).SetBondDir(Chem.BondDir.ENDUPRIGHT)
mol.GetBondWithIdx(bonds_connected_to_second_atom_indecies[1]).SetBondDir(Chem.BondDir.ENDDOWNRIGHT)
# I assume this should set the stereochemistry. But it doesn't appear to.
# It's stereo is STEREONONE at this point
print double_bond.GetStereo()
Chem.AssignStereochemistry(mol)
# Still STEREONONE
print double_bond.GetStereo()
# And when I print out the smiles, no stereochemistry is given.
print Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
# CC(S)=C(N)O
===============
Any suggestions? Thanks!
~Jacob
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