Atom indexing

[kavi9030]

Hello. May I know how MolGpKa do the atom indexing? For example the molecule (CN(C)CCCN1C2=CC=CC=C2SC2=C1C=C(C=C2)C(C)=O) got 2 pKa for the N atoms and the base_dict = {9: 5.565207, 13: 9.476432}.

I tried to number my atoms using rdkit (https://stackoverflow.com/questions/53321453/rdkit-how-to-show-moleculars-atoms-number) but it doesn't match up with the indexes on MolGpKa. May I know how the atom indexing works? Is it generated based on the atom index of the ionizable atom in the SMARTS?

[xiaolinpan]

Hi, sorry for the delay in responding. Hydrogen atoms are necessary for MolGpKa predictions and must be included when labeling the atom index. Removing and then re-adding hydrogen atoms can lead to atom index changes, so the Mol object obtained from MolGpKa should be utilized for adding atom index.