Hi all, Quick question: I have noticed that when I read a compound from an SDF/Mol file where all coordinates are already defined, the embedding process changes the conformation of the RDKit mol object, hence coordinates are not preserved:
import rdkit cdk2_path = os.path.join(data_path, "cdk2_validation") rdkit_mol = rdkit.Chem.MolFromMolFile(os.path.join(cdk2_path, "26Z.sdf")) rdkit_mol = rdkit.Chem.AddHs(rdkit_mol) rdkit.Chem.AllChem.EmbedMolecule(rdkit_mol) What is the best practice for reading a molecule with coordinates without shuffling them? (e.g. for a ligand from the PDB). Thanks, -- *Gianmarco*
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