Hello,
I'm trying to find the Euclidean distance between two atoms in the molecule
with SMILES representation `O=CC1OC12CC1OC12` using the `rdkit` package.
Looking online, I have converged to the following code.
import numpy as np
from rdkit import Chem
mol = Chem.MolFromSmiles('O=CC1OC12CC1OC12')
conf = mol.GetConformer()
at1Coords = np.array(conf.GetAtomPosition(bond_i.GetBeginAtomIdx()))
at2Coords = np.array(conf.GetAtomPosition(bond_i.GetEndAtomIdx()))
print(np.linalg.norm(at2Coords - at1Coords))
But I get the error
conf = mol.GetConformer()
ValueError: Bad Conformer Id
I was wondering how to fix the issue.
Thanks!
Navid
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