Hello Greg, Is UpdatePropertyCache "heavy"? If not, is it possible to fold it into SanitizeMol, so that users only need to remember the SanitizeMol function for refreshing a molecule?
Thank you. Ling On Mon, Aug 29, 2016 at 10:41 PM, Greg Landrum <[email protected]> wrote: > Hi Brian, > > On Tue, Aug 30, 2016 at 6:41 AM, Bennion, Brian <[email protected]> wrote: > >> >> I have seemed to hit a wall with what seems like a simple task. >> >> First, I have ~9800 compounds that have a primary amine for a reaction >> that I am completing in rdkit. >> About 250 of those compounds have a tertiary alkylamine that is most >> likely protonated at pH 7.4. >> >> The dataset is a set of smiles strings for which the tertiary amine is >> not protonated. I thought this would be easy enough to fix, just use a >> smarts substructure search, set the formal charge on any hits to one and >> then AddHs, sanitize, embed, and then minimize. >> >> Well, what I get is [N+] with all the other carbons with explicit atoms >> in the resulting smiles files, and if output to sdf I get a positively >> charged diradical positioned at the tertiary nitrogen. >> > > Yes, what's happening here is that AddHs() is using the implicit valence > on the N atoms to determine how many Hs to add. Since the implicit valence > is not recomputed when you set the formal charge, you end up with the wrong > number of Hs attached to the N. A call to UpdatePropertyCache() will fix > this: > > n [16]: m = Chem.MolFromSmiles('CN') > > In [17]: AllChem.CalcMolFormula(m) > Out[17]: 'CH5N' > > In [18]: m.GetAtomWithIdx(1).SetFormalCharge(1) > > In [19]: AllChem.CalcMolFormula(m) > Out[19]: 'CH5N+' > > In [20]: m.UpdatePropertyCache() > > In [21]: AllChem.CalcMolFormula(m) > Out[21]: 'CH6N+' > > In [22]: mh = Chem.AddHs(m) > > In [24]: mh.GetAtomWithIdx(1).GetDegree() > Out[24]: 4 > > Thank you for such a great tool >> > > You're welcome! Thanks for saying thanks. :-) > > Hope this helps, > -greg > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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