[Rdkit-discuss] Error from qed

[Navid Shervani-T. <ns...@gm...>]

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