Hi Goutam,
The ring atoms reported by RDKit in your example are correct; you just need
to consider that the atom indexes correspond to the position of each atom
in the SMILES string. How could RDKit guess the index that the atom might
have in a PDB file that's not even being read in your example?
I'm guessing maybe in your real use case you did read the PDB file. It is
possible that the atoms got renumbered, for example if the hydrogens were
deleted in the process.
Hope this helps,
Ivan
On Thu, Mar 11, 2021 at 11:35 AM Goutam Mukherjee <cyz078...@gmail.com>
wrote:
> 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
>
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