Re: [Rdkit-discuss] Euclidean distance between atoms using RDKit

[Navid Shervani-T. <ns...@gm...>]

Thanks Omar, That indeed fix the problem.

Navid

On Wed, Sep 4, 2019 at 7:15 PM Omar H94 <oma...@gm...> wrote:

> Dear Navid,
> You need to embed your molecule to have a 3D conformation.
> Try:
>
> from rdkit.Chem import AllChem
> mol = Chem.MolFromSmiles('O=CC1OC12CC1OC12')
> AllChem.EmbedMolecule(mol)
> conf = mol.GetConformer()
> at1Coords = np.array(conf.GetAtomPosition(1))
> at2Coords = np.array(conf.GetAtomPosition(2))
> print(np.linalg.norm(at2Coords - at1Coords))
>
> I hope this works for you.
> Best regards,
> Omar
>
> On Thu, Sep 5, 2019 at 1:59 AM Navid Shervani-Tabar <ns...@gm...>
> wrote:
>
>> 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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