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
>
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