Hello Goutam,
There are not even 30 atoms in your smiles string. This is because, for
example, [C@H] denotes one carbon atom. The H is there to describe the C.
It is not an atom in the smiles string.
Ling
Goutam Mukherjee <cyz078...@gmail.com> 於 2021年3月11日週四 上午8:35寫道：
> 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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