rdkit outputs a molfile with correct isotope labels for me using just:
mol=Chem.MolFromSmiles("[3H]c1ccccc1[2H]")
Chem.MolToMolFile(mol,"test.mol")
or labelling the atoms post hoc:
mol=Chem.MolFromSmiles("c1ccccc1")
mol=Chem.AddHs(mol)
mol.GetAtomWithIdx(6).SetIsotope(3)
mol.GetAtomWithIdx(7).SetIsotope(2)
mol=Chem.RemoveHs(mol)
Chem.MolToMolFile(mol,"test2.mol")
I hope this helps
best wishes
wim
On Mon, Apr 10, 2023 at 4:43 PM Santiago Fraga <santi...@mestrelab.com>
wrote:
> Good afternoon!
>
> I am a relatively new user of RDKit, and mainly the C++ API.
>
> I am trying to save in a molfile the labels D and T for the hydrogen
> isotopes.
> Like in the following molfile:
>
> MJ230401
>
> 8 8 0 0 0 0 0 0 0 0999 V2000
> -0.3572 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0716 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0716 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.3572 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3572 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3572 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.3572 1.2375 0.0000 T 0 0 0 0 0 0 0 0 0 0 0 0
> 1.0717 0.4125 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0
> 3 4 2 0 0 0 0
> 4 5 1 0 0 0 0
> 5 6 2 0 0 0 0
> 6 1 1 0 0 0 0
> 1 2 2 0 0 0 0
> 2 3 1 0 0 0 0
> 6 8 1 0 0 0 0
> 1 7 1 0 0 0 0
> M END
>
> I am trying to set directly the labels in the hydrogen atoms:
>
> atom->setProp<string>("atomLabel", "D");
> or
> atom->setProp<string>("_displayLabel", "D");
>
> But when the molfile is generated the labels are not transferred.
> It seems also that when reading a mofile including the labels, they
> are discarded.
>
>
> Many thanks in advance
> Santiago Fraga
>
>
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