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
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
>
>
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