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
[cid:image001.png@01D736A7.2701D9B0]
covestro.com<http://www.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<mailto:pablo.ra...@covestro.com>
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