Guillaume- You may want to add hydrogens before embedding. Not sure *specifically* why it's required in this case - maybe the stereo center needs a hydrogen in order to pop it into 3d?
*dan nealschneider* | senior developer [image: Schrodinger Logo] <https://www.schrodinger.com/> On Wed, Sep 25, 2019 at 1:45 AM Guillaume GODIN < guillaume.go...@firmenich.com> wrote: > Dear All, > > > > One question why this is not working ? > > > > def mol3D(mol): > > tot = AllChem.EmbedMolecule(mol) > > try: > > X = AllChem.Get3DDistanceMatrix(mol) > > except: > > print('err') > > print(tot) > > n = mol.GetNumAtoms() > > X = np.zeros(n,n) > > return X > > > > mol = Chem.MolFromSmiles('CC[C@H](C)O') > > X = mol3D(mol) > > > > Result: > > > > err > > -1 > > --------------------------------------------------------------------------- > > ValueError Traceback (most recent call > last) > > <ipython-input-17-f18aabd854d2> in mol3D(mol) > > * 3* try: > > ----> 4 X = AllChem.Get3DDistanceMatrix(mol) > > * 5* except: > > > > ValueError: Bad Conformer Id > > > > During handling of the above exception, another exception occurred: > > > > Thanks in advance, > > > > Guillaume > > *********************************************************************************** > DISCLAIMER > This email and any files transmitted with it, including replies and > forwarded copies (which may contain alterations) subsequently transmitted > from Firmenich, are confidential and solely for the use of the intended > recipient. The contents do not represent the opinion of Firmenich except to > the extent that it relates to their official business. > > *********************************************************************************** > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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