Hi Puck,
I modified your previous example to use FragmentOnBonds():
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole, MolsToGridImage
smiles = "COC"
mol = Chem.MolFromSmiles("COC")
mol
Here there are no hydrogens (as expected from the SMILES)
mol = Chem.AddHs(mol)
mol
mol_f = Chem.FragmentOnBonds(mol, (2,))
mol_f
for a in mol_f.GetAtoms():
if (a.GetAtomicNum() == 0):
# convert the dummy into hydrogen a.SetAtomicNum(1)
# if you do not need the labels, you may clear them
a.SetIsotope(0)
mol_f
Cheers,
p.
On 18/02/2020 09:45, Puck van Gerwen wrote:
Dear Paolo
Thanks very much for your continuous help. I'm not sure I like the
idea of explicitly defining the valence, so I'll consider switching to
FragmentOnBonds(). From the example you gave previously though, it
quenched the fragments with dummy atoms rather than hydrogen. Is it
possible to quench with hydrogen using FragmentOnBonds()?
Kind regards
Puck
On Mon, 17 Feb 2020 at 13:42, Paolo Tosco <paolo.tosco.m...@gmail.com
<mailto:paolo.tosco.m...@gmail.com>> wrote:
Hi Puck,
sorry dor the delay in replying.
After removing the bond you will need to adjust the number of
explicit Hs on both ends with SetNumExplicitHs(), and then add
those Hs in the molecule graph as real atoms with Chem.AddHs():
rwmol = Chem.RWMol(mol)
bonds = rwmol.GetBonds()
b = rwmol.GetBondWithIdx(2)
a1 = b.GetBeginAtom()
a2 = b.GetEndAtom()
rwmol.RemoveBond(a1.GetIdx(), a2.GetIdx())
a1.SetNumExplicitHs(a1.GetNumExplicitHs() + 1)
a2.SetNumExplicitHs(a2.GetNumExplicitHs() + 1)
rwmol = Chem.AddHs(rwmol, explicitOnly=True)
The rdmolops.FragmentOnBonds() functions adjusts the valences for
you, but you will need to adjust them manually if you do the
fragmentation at a lower level with RemoveBond().
I have attached the modified notebook.
Cheers,
p.
On 12/02/2020 10:03, Puck van Gerwen wrote:
Dear all,
I am trying to read in SMILES to generate mol objects which I
then break into fragments using rwmol.RemoveBond(). Thereafter I
want to sanitize the fragments by saturating with hydrogen.
However, I am finding that rdkit often doesn't sanitize the
fragments consistently, leaving trivalent carbon atoms. I've
attached a jupyter notebook of an example. Could anyone help me
consistently generate sanitized fragments?
Best regards
--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/
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--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/
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