If the number of the ionizable groups in a molecule is less or equals with "8" then the default method called as "JCAcidicpKa" will be used for the pKa calculation.
In those other cases if the number of the ionizable groups is larger than "8" then the so called "JCAcidicpKaLargeMolecule" method can be used for calculating of the pKa values of a molecule.
The "JCAcidicpKaLargeMolecule" method usually more slower then the "JCAcidicpKa" method. It is a "safe" way to use this "JCAcidicpKaLargeMolecule" method for relatively large moleules (with molecular weight of 300-500 g/mol) just in case the number of the expected pKa values are above of "8".
Also, what are JCLogP and JCLogD?
The "JCLogP " is the "logP" value of the neutral form of a molecule.
Zwitterions are exceptions since their neutral form is not known in the "0-14 pH" range. For zwitterions the "JCLogD " is calculated automatically and will be returned.
The "JCLogD " is the "logP" value of a molecule at an optional pH in the "0-14" range.