Hello all,
I tried to extend this method to whole QM9 database. For few molecules
including 'CC12CCC1CC2' and 'CC12CC3C1OC32', however, GetNumConformers() shows
zero conformations on the molecule. Is there a way to generalize computing
bond length to include such molecules?
Thanks!
Navid
On Wed, Sep 4, 2019 at 7:28 PM Navid Shervani-Tabar <nshe...@gmail.com>
wrote:
> Thanks Omar, That indeed fix the problem.
>
> Navid
>
> On Wed, Sep 4, 2019 at 7:15 PM Omar H94 <omar8...@gmail.com> 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 <nshe...@gmail.com>
>> 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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>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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>
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