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 於 2021年3月11日週四 上午8:35寫道：
> Dear Members,
>
> I have found an error in
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
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?
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:*
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