Re: [Rdkit-discuss] transformation of an atom or group of atoms by atom indices
Jason, Exactly what I need to do. Thank you for your example code. Much appreciated. Regards, Jim Metz -Original Message- From: Jason Biggs To: James T. Metz Cc: RDKit Discuss Sent: Thu, Nov 9, 2017 3:28 pm Subject: Re: [Rdkit-discuss] transformation of an atom or group of atoms by atom indices Something along these lines? mol = Chem.MolFromSmiles('') 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 wrote: RDKit Discussion Group, Suppose I have a molecule smiles1 = '' 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
Re: [Rdkit-discuss] transformation of an atom or group of atoms by atom indices
Something along these lines? mol = Chem.MolFromSmiles('')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 = '' > > 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
[Rdkit-discuss] transformation of an atom or group of atoms by atom indices
RDKit Discussion Group, Suppose I have a molecule smiles1 = '' 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