Dear All,
Thanks to find a solution. But, that’s true, it’s clearly a “bug” in the processus of embegging. I observe this issue only few of those “@” or “@@” cases. Examples: C[C@H]1CCCC[C@H]1C works CC[C@H](C)O failed Thanks for helping, Guillaume De : Greg Landrum <greg.land...@gmail.com> Date : samedi, 28 septembre 2019 à 07:22 À : RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Cc : Guillaume GODIN <guillaume.go...@firmenich.com> Objet : Re: [Rdkit-discuss] Issue with Chirality As Dan said: you should be adding Hs to the molecule before generating conformations. That clears up the problem: In [17]: AllChem.EmbedMolecule(Chem.MolFromSmiles('CC[C@H](C)O')) Out[17]: -1 In [18]: AllChem.EmbedMolecule(Chem.AddHs(Chem.MolFromSmiles('CC[C@H](C)O'))) Out[18]: 0 I would have actually expected that you could get a conformer with the Hs and think there's likely a bug connected to the way chiral centers are handed in the conformer generation code (embedding the non-chiral SMILES CCC(C)O works just fine) that's causing this failure, but that doesn't change the fact that it's always better to add Hs before generating conformations. -greg On Fri, Sep 27, 2019 at 10:12 PM Dan Nealschneider <dan.nealschnei...@schrodinger.com<mailto:dan.nealschnei...@schrodinger.com>> wrote: 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 Erreur ! Nom du fichier non spécifié.<https://www.schrodinger.com/> On Wed, Sep 25, 2019 at 1:45 AM Guillaume GODIN <guillaume.go...@firmenich.com<mailto: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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss *********************************************************************************** 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. ***********************************************************************************
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