I tested your code on several structures and noticed that it failed on
molecules with only one element (NH3, OH2...).
Then I checked
https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html and saw
that the default ignores hydrogens. So try
Chem.rdMolTransforms.ComputeCanonicalTransform(conf, ignoreHs=False) in the
last line and see if it fixes your problem.
Regards
Em qua., 21 de abr. de 2021 às 07:21, Pablo Ramos
escreveu:
> Dear community,
>
>
>
> I want to pick a fragment from a molecule, and canonicalize its conformer
> in order to align its principal moments of inertia. However, this does not
> seem to work. Any idea why this could be happening?
>
>
>
> mol1 = Chem.MolFromSmiles('[H]C([H])=O.[H]N([H])[H]')
>
> mol1 = Chem.AddHs(mol1)
>
> for fragment in Chem.GetMolFrags(mol1, asMols=True):
>
> AllChem.EmbedMolecule(fragment, useRandomCoords=False)
>
> conf = fragment.GetConformer()
>
> Chem.rdMolTransforms.ComputeCanonicalTransform(conf)
>
>
>
> RuntimeError: Invariant Violation
>
>
>
> Violation occurred on line 298 in file
> Code/GraphMol/MolTransforms/MolTransforms.cpp
>
> Failed Expression: dim >= 1
>
> RDKIT: 2021.03.1
>
> BOOST: 1_74
>
>
>
>
>
> Best regards,
>
>
>
> *Pablo Ramos*
> Ph.D. at Covestro Deutschland AG
>
>
>
>
>
> covestro.com
>
> *Telephone*
>
> +49 214 6009 7356
>
>
>
> Covestro Deutschland AG
>
> COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD
>
> B103, R164
>
> 51365 Leverkusen, Germany
>
> *pablo.ra...@covestro.com *
>
>
>
>
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--
Rafael da Fonseca Lameiro
[image: orcid logo 16px] https://orcid.org/-0003-4466-2682
PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED)
São Carlos Institute of Chemistry - University of São Paulo - Brazil
Av. Trabalhador Sancarlense, 400 - ZIP code: 13566-590 - São Carlos/SP
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