Dear Paolo That clears things up. Thanks very much!
Kind regards Puck On Tue, 18 Feb 2020 at 14:05, Paolo Tosco <paolo.tosco.m...@gmail.com> wrote: > Dear Puck, > > Here there is some confusion between the concept of implicit/explicit > hydrogens vs real hydrogen atoms. > > In your previous example you were fragmenting an acetone molecule with > real hydrogen atoms explicitly present in the molecule graph. Therefore, > after calling FragmentOnBonds() it was appropriate to convert the dummy > atoms into real hydrogens and leave them as such. > > In your latest example you are fragmenting a molecule with no real > hydrogen atoms, only implicit hydrogens, so after converting the dummy > atoms into real hydrogens you have a mixture of real and implicit hydrogens. > > Please refer to this gist for a (hopefully) cleare explanation: > > https://gist.github.com/ptosco/162b52b018dc95709bd43757c0078a28 > > You may also refer to the following threads on the mailing list: > > https://sourceforge.net/p/rdkit/mailman/message/29679834/ > https://sourceforge.net/p/rdkit/mailman/message/36696340/ > > and to this blog post by Roger Sayle: > > > https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/ > > for further clarifications on the various kinds of hydrogen in the RDKit. > Cheers, > p. > > On 18/02/2020 12:18, Puck van Gerwen wrote: > > 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/ > > -- *Puck van Gerwen* Doktorandin / PhD candidate Departement Chemie Klingelbergstrasse 80 CH-4056 Basel https://chemspacelab.org/
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