Dear Paolo Thank you for this illustrative example. I tried the same method on a few other molecules and didn't find consistent results. In the notebook attached, the first molecule is left with a bivalent carbon, and the second molecule is only sanitized after explicitly calling the SanitizeFrags option when getting individual fragments. Am I missing something?
Kind regards
Puck
On Tue, 18 Feb 2020 at 11:17, Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Hi Puck,
>
> I modified your previous example to use FragmentOnBonds():
>
> from rdkit import Chemfrom 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>
> 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/
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing
>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
> --
> *Puck van Gerwen*
> Doktorandin / PhD candidate
> Departement Chemie
> Klingelbergstrasse 80
> CH-4056 Basel
> https://chemspacelab.org/
>
>
--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://chemspacelab.org/
TestFragmentation.ipynb
Description: Binary data
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
