Dear Ivan,
Many thanks for your reply.
Yes, when I give 3D hydrogen added molecule as input (molecule.pdb) the
result remains the same.
Say, if I give benzene molecule (C1=CC=CC=C1) as an input, or other complex
molecule, it prints the correct atom rank no matter whether hydrogen atoms
are there or not.
In [1]: from rdkit import Chem
In [2]: m = Chem.MolFromSmiles('C1=CC=CC=C1')
In [3]: ri = m.GetRingInfo()
In [4]: print(ri.AtomRings())
*((0, 5, 4, 3, 2, 1),)*
Thank and Best Regards,
Goutam
On Thu, Mar 11, 2021 at 5:49 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> 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
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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