Yeah, to reinforce what Paolo said: we're not going to be able to help unless you show us the code that you're using that's producing the error.
-greg On Thu, Jul 4, 2019 at 11:00 AM Paolo Tosco <[email protected]> wrote: > Hi Navid, > > based on the adjacency matrix that you reported the first molecule has the > following topology: > > i.e., it features an oxygen atom with 3 valences, plus a disconnected > oxygen (the last one in the node). That molecule makes little chemical > sense to me - it looks like some sort of slightly broken sydnonimine. > However, unless you set a +1 formal charge on the oxygen wth index 6 in > your node the RDKit will fail to sanitize that molecule. > > The second compound is nitromethane followed by a bunch of disconnected > atoms: > > Again, as that nitrogen has a valence of 4, RDKit will fail to sanitize > the molecule unless you set a formal charge of +1 on that nitrogen (and > most likely a formal charge of -1 on the single-bonded oxygen). However, > all those disconnected atoms (C, N, H) in the rest of your node seem > suspicious to me - I wonder if something has gone wrong somewhere in your > workflow. > > I hope the above helps, cheers > p. > On 03/07/2019 22:10, Navid Shervani-Tabar wrote: > > Hello, > > I was trying to find quantitative estimation of drug-likeness (QED) for > qm9 dataset. qm9 dataset provides a graph representation of the molecule, > these are translated into mol objects and then qed is estimated. > > ``` > from rdkit.Chem.QED import qed > . > . > . > mol = Graphs2Mol(node, adj_mat) > my_qed = qed(mol) > ``` > > I was trying to find qed for molecule with node and adjacency matrix > > ``` > node = ['C', 'C', 'C', 'C', 'C', 'N', 'O', 'N', 'O'] > > adj_mat = > [[0 1 0 0 0 0 0 0 0] > [1 0 2 1 0 0 0 0 0] > [0 2 0 0 0 0 0 0 0] > [0 1 0 0 1 0 0 0 0] > [0 0 0 1 0 1 2 0 0] > [0 0 0 0 1 0 0 0 0] > [0 0 0 0 2 0 0 1 0] > [0 0 0 0 0 0 1 0 0] > [0 0 0 0 0 0 0 0 0]] > ``` > > and I received following error > > `ValueError: Sanitization error: Explicit valence for atom # 6 O, 3, is > greater than permitted > ` > Same happened with > ``` > node = ['O', 'N', 'O', 'C', 'C', 'C', 'C', 'N', 'H'] > > adj_mat = > [[0 2 0 0 0 0 0 0 0] > [2 0 1 1 0 0 0 0 0] > [0 1 0 0 0 0 0 0 0] > [0 1 0 0 0 0 0 0 0] > [0 0 0 0 0 0 0 0 0] > [0 0 0 0 0 0 0 0 0] > [0 0 0 0 0 0 0 0 0] > [0 0 0 0 0 0 0 0 0] > [0 0 0 0 0 0 0 0 0]] > ``` > > and I received > > `ValueError: Sanitization error: Explicit valence for atom # 1 N, 4, is > greater than permitted > ` > Any suggestions on what might be incorrect? Thanks. > > Navid > > > _______________________________________________ > Rdkit-discuss mailing > [email protected]https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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