Dear Members, I have found an error in RDKit output. I am not sure whether it is my mistake. I have a SMILES code of a molecule: C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N
the 3D coordinates of the molecule is attached here with.
*I ran the following command:*
*In [1]: from rdkit import ChemIn [2]: m =
Chem.MolFromSmiles('C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N')In
[3]: ri = m.GetRingInfo()In [4]: print(ri.AtomRings())((10, 11, 12, 13,
15), (18, 17, 21, 20, 19), (22, 23, 24, 25, 20, 21))*
Here the atom rank does not correspond to the ring atom ranks.
This molecule contains two five members and one six member ring
The true atom rank would be
*{(11, 13, 14, 16, 19), (22, 23, 24, 25, 26), (25, 26, 27, 28, 29, 30)}*
Could anyone please give me a solution how I get a corect atom ranks which
are part of a ring.
Thanks and Best Regards,
Goutam
molecule.pdb
Description: Binary data
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