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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