Jason,
Exactly what I need to do. Thank you for your example code. Much
appreciated.
Regards,
Jim Metz
-----Original Message-----
From: Jason Biggs <jasondbi...@gmail.com>
To: James T. Metz <jamestm...@aol.com>
Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
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('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
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