Can someone please explain the output of the pKa component when OutputPkaSiteInfo is set to true.
Specifically how and why does the "pKa" value differ from the "base_pka" value and which is the generally preferred value to use?
I've included an example below to facilitate the explanation/discussion
| Blank |
| Molecule | Atom Properties | smiles |
![]() | | AtomIndex | pKa | Site_Name | Base_pKa | Site_FP | Num_ClosestExamples | Distance_ClosestExamples | | 1 | | | | | | | | 2 | | | | | | | | 3 | | | | | | | | 4 | 4.78 | AmineTertiary | 8.2 | R1rC;R1rCrC;R1rCrCrN+;R1rCrCrN+rC;R1rCrCrN+C;R1rCrCrN+CC;R1C;R1CC;R1CCO;R1rC\$2;R1rCrC\$2;R1rCrCrN+\$2;R1rCrCrN+rC\$2;R1rCrCrN+C\$2;R1rCrCrN+CC\$2 | 1 | 0.266666666666667 | | 5 | | | | | | | | 6 | | | | | | | | 7 | 7.55 | AmineTertiary | 8.2 | R1rC;R1rCrC;R1rCrCrN;R1rCrCrNC;R1rCrCrNCC;R1rCrCrNrC;R1rC\$2;R1rCrC\$2;R1rCrCrN\$2;R1rCrCrNC\$2;R1rCrCrNCC\$2;R1rCrCrNrC\$2;R1C;R1CC;R1CCS;R1CCS=O;R1CCS=O\$2;R1CCSO- | 1 | 0 | | 8 | | | | | | | | 9 | | | | | | | | 10 | | | | | | | | 11 | | | | | | | | 12 | | | | | | | | 13 | | | | | | | | 14 | | | | | | | | 15 | 3 | Aliphatic_SOOH | 1.57 | R2C;R2CC;R2CCrN+;R2CCrN+rC;R2CCrN+rCrC;R2CCrN+rC\$2;R2CCrN+rCrC\$2 | 1 | 0 |
| OCCN1CCN(CC1)CCS(=O)(=O)O |
