Thanks Greg, This was quite close to the way I already deal with these cases. What I was hoping for was a more general solution (via the MMFF94 implementation perhaps?), since things get more interesting when charges are missing from e.g. different species of sulfur...
-Juuso On Thu, Aug 10, 2017 at 9:17 AM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Juuso, > > A quick solution that seems like it would covert most cases would be to > construct a molecule from you input without doing sanitization, calculate > the atomic valences in non-strict mode, and then to identify all neutral N > atoms with a valence of 4 and add a positive charge to them > > Here's an example gist showing what I mean: > https://gist.github.com/greglandrum/7f546d1e35c2df537c68a64d887793b8 > > I hope this helps, > -greg > > > > On Wed, Aug 9, 2017 at 11:31 AM, Juuso Lehtivarjo > <juuso.lehtiva...@gmail.com> wrote: >> >> Hi All, >> >> and sorry if this has been previously answered. Found lots of threads >> close to this subject but not exactly what I'm looking for. >> >> I often encounter mol-files that have protonated atom species such as >> NH3+, with all protons explicitly present, but without charge lines. >> This leads to sanitation error (Explicit valence greater than >> permitted) unless I update the formal charge of the nitrogen to +1. Is >> there a way in RDKit to set default formal charges based on the >> molecular graph, given that it contains the correct amount of protons? >> >> Best, Juuso >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
