Hi Pavel,
I believe you forgot to add hydrogen atoms to the molecule graph before
generating 3D conformers:
mol_h = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol_h, 50, Chem.rdDistGeom.ETKDGv2())
mol_h.GetNumConformers()
50
HTH, cheers
p.
On 21/02/2020 12:57, Pavel Polishchuk wrote:
Hello,
I want to generate conformers for a stereoisomeric sugar moiety. The
code below works (loads proccesor) but returns none of them.
But if I remove all stereoconfiguration info in input SMILES the
code generates conformers. Playing with this issue I noticed that
conformers are generated if only one stereocenter is defined. If I
define configuration of two centers the code stops working.
I'm puzzled. Is there a solution or workaround?
I use rdkit 2019.09.1
mol = Chem.MolFromSmiles('OC[C@H]1O[C@H](O)C[C@@H](O)[C@H]1O')
AllChem.EmbedMultipleConfs(mol, 50, Chem.rdDistGeom.ETKDGv2())
mol.GetConformers()
Kind regards,
Pavel.
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