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

[Haijun F. <hai...@gm...>]

<https://stackoverflow.com/posts/76197437/timeline>

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 cH1 CH...7 NH28 O  *

Can anyone help me figure out how to get each atom with H from the smiles
as above. Thanks so much!


best,


Hal