[Open Babel] "complete protonation"

[<Pau...@me...>]

Dear OpenBabel community,

how do I enable a "complete protonation" of all atoms within PyBEL? A small
test of the OpenBabel Windows version revealed that COO- is converted COOH,
but R-NH2 is not converted to R-NH3+.
As data source, I work with MOL2 files, and this shall be the output as
well.
For the last group, the original atom type is set to N.3, and it is not
changed to N.4, although I chose a high pH of 14 to "protonate" the
molecule.

If you could provide any PyBEL snippet, I would very much appreciate this!


Best regards,

Paul

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