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,
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
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