I would like to know whether you have a possibility to screen automatically a large molecular database for weak acids or bases molecules?
I used to work with Marvin Chemsketch and look for molecule pKa and ionization to decide manually if a molecule is a weak acid or base. Do you have an automatic tool for this purpose?
Examples how acidic pKa can be calculated and how molecules can be filtered using the Chemical Terms Evaluator command line application.
Calculate strongest acidic pKa:
$ evaluate -e 'apka("1")' acids_and_bases.smiles
Filter weak acids (acidic pKa > 3):
$ evaluate -e 'apka("1") > 3' -x smiles acids_and_bases.smiles
Test file is attached.
I hope this helps.