Re: [Rdkit-discuss] how to get indexes and atoms with H from smiles

[Francois B. <ml...@li...>]

Hello,

Maybe you can use this:
Chem.MolToSmiles(mol, allHsExplicit=True)

This will place each heavy atom between '[' and ']' and give you the 
number
of hydrogens for each.
It get easier to work with SMILES strings after this (you don't need 
anymore
a full blown SMILES parser).

Regards,
F.

On 09/05/2023 14:55, Haijun Feng wrote:
> [1]
> 
> Hi All,
> 
> I am trying to add atom numbers in smiles as belows,
> 
>     from rdkit import Chem
>     mol=Chem.MolFromSmiles('c1ccccc(C(N)=O)1')
>     for i, atom in enumerate(mol.GetAtoms()):
>       atom.SetProp('molAtomMapNumber',str(i))
>     smi=Chem.MolToSmiles(mol)
>     print(smi)
> 
> the output is: [cH:0]1[cH:1][cH:2][cH:3][cH:4][c:5]1C:6=[O:8]
> 
> then I want to split the smiles into atoms, I did it like this:
> 
>     from rdkit import Chem
>     mol=Chem.MolFromSmiles('c1ccccc(C(N)=O)1')
>     for i, atom in enumerate(mol.GetAtoms()):
>       atom.SetProp('molAtomMapNumber',str(i))
>       print(i,atom.GetSymbol())
> 
> the output is:
> 
> 0 C
> 1 C
> 2 C
> 3 C
> 4 C
> 5 C
> 6 C
> 7 N
> 8 O
> 
> But what I do want is something like this (with fragments instead of
> atoms):
> 
> 0 cH
> 1 CH
> ...
> 7 NH2
> 8 O
> 
> Can anyone help me figure out how to get each atom with H from the
> smiles as above. Thanks so much!
> 
> best,
> 
> Hal
> 
> Links:
> ------
> [1] https://stackoverflow.com/posts/76197437/timeline
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