Something along these lines?
mol = Chem.MolFromSmiles('CCCC')emol =
Chem.EditableMol(mol)emol.ReplaceAtom(3, Chem.Atom(1))mol =
emol.GetMol()
In [12]:
Chem.MolToSmiles(mol)
Out[12]:
'[H]CCC'
In [13]:
Chem.MolToSmiles(Chem.RemoveHs(mol))
Out[13]:
'CCC'
Jason Biggs
On Thu, Nov 9, 2017 at 3:12 PM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> RDKit Discussion Group,
>
> Suppose I have a molecule
>
> smiles1 = 'CCCC'
>
> The carbon atoms will be assigned indices 0, 1, 2, and 3.
>
> Suppose I want to specifically change carbon 3 to a hydrogen.
> Is this possible using RDkit?
>
> I am aware of using SMARTS to match a pattern and then change
> that group of atoms. In my example, I would like to be able to
> change an atom or group of atoms based on the atom indices, not
> a SMARTS pattern which might be problematic for molecules with
> local symmetry.
>
> Regards,
> Jim Metz
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
