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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