Hi Pablo, SMILES by definition has implicit hydrogens (enough to satisfy the typicial valence) for atoms that are not within brackets.
It doesn't matter if you write C, C[H], [H]C[H], or [H]C([H])([H])[H]; they are all methane. The number of hydrogens that are returned by GetNumImplicitHs() and GetNumExplicitHs() on the carbon atom do vary, though. But if you convert back to SMILES, you get "C" in all cases (with the default options). If you want an atom with no implicit hydrogens, you have to put it in brackets. [C] is a lone carbon atom. [CH3] or [H][C]([H])[H] is a methyl radical. But you still won't get sanitization errors for such species, because radicals are legitimate species after all, and I imagine RDKit doesn't want to guess whether you like radicals or not. So I suspect you'll have to write your own "sanity" function which uses whatever definition of sanity you need. For example, you could loop over the atoms and check the value of GetTotalValence() and compare it with the expected valence for that element. Or perhaps you could make use of GetNumRadicalElectrons(). Hope this helps, Ivan On Mon, May 11, 2020 at 9:37 AM Pablo Ramos <pablo.ra...@covestro.com> wrote: > Dear all, > > > > I am trying to catch an error every time that a smiles associated to a mol > object does not exist. To do this, I want to use sanitize function: if the > smiles is incorrect I will get my error. > > My smiles with *explicit hydrogens* is the next one: [H]C([H])O > > > > I want it to provide an error since valences do not match the ones > specified for Carbon and Oxygen beingHydrogens already explicit: C_val = 4 > ; O_val = 2 > > > > However, sanitizing this object creates automatically the missing Hydrogens > providing a valid smiles: [H]OC([H])([H])[H] and therefore it assumes the > smiles is correct. > > > > Is there any way to specify that my Hydrogens are already explicit during > sanitazion so I get my error message? > > > > Thank you so much J > > > > > > Best regards, > > > > *Pablo Ramos* > > Ph.D. at Covestro Deutschland AG > > > > > > covestro.com <http://www.covestro.com/> > > *Telephone* > > +49 214 6009 7356 > > > > Covestro Deutschland AG > > COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD > > B103, R164 > > 51365 Leverkusen, Germany > > *pablo.ra...@covestro.com <pablo.ra...@covestro.com>* > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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