Re: [Rdkit-discuss] Issue with Chirality

septembre 2019 à 07:22 À : RDKit Discuss Cc : Guillaume GODIN 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'

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

Re: [Rdkit-discuss] Issue with Chirality

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] On Wed, Sep 25,

[Rdkit-discuss] Issue with Chirality

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.MolFromS