[Rdkit-discuss] Euclidean distance between atoms using RDKit

[Navid Shervani-Tabar]

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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