The (de)protonation rules are stored as a list of transformation using SMARTS format in a file called /phmodel.txt/inside the /data/ directory. Such file is editable but as Geoff suggested is not trivial to carefully enumerate all the potential transformations for many functional groups and substructures at different pH. As far as I know currently there is no open source software that do that properly, so any advance in this sense will be appreciated by the community. Gio
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