Hi Francois, Though there are various tables with electronegativity values in the code, they are all for particular purposes (i.e. the MMFF force field), not directly documented, and not really intended to be used elsewhere.
I think your idea of parsing the data from the BODR is the best approach -greg On Tue, Mar 8, 2022 at 9:42 AM Francois Berenger <mli...@ligand.eu> wrote: > On 08/03/2022 17:23, Francois Berenger wrote: > > Dear rdkit experts, > > > > I am looking to access the electronegativity value > > of a given atom in a molecule. > > > > Funnily, I don't know _at_ _all_ how to do this. > > > > I guess that there should be a way using the atomic number > > to get this value from a table inside of rdkit > > but my code searches on github where somewhat vain (we do have a > > constant table > > somewhere with the Allen scale values * 1000, but that > > doesn't look very practical to use). > > > > Before I do the horrible (hard-coding into my program > > the whole Allen scale copy-pasted from wikipedia, yes, nothing less), > > I prefer to ask rdkit experts. > > A less horrible option might be to extract the > bo:electronegativityPauling > values from the elements.xml file of the latest version of the Blue > Obelisk project. > > But, I would be quite surprised if rdkit doesn't hold this value already > somewhere... > > > If we have a choice between the Pauling scale or the Allen > > scale, I would be interested to know about that. > > If we can directly access the difference of ElNeg for two > > bonded atoms of a molecule, I might be happy living with that. > > > > Thanks a lot, > > F. > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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