4. API Reference

The propka3 command provides a command-line interface to PROPKA 3’s functionality. It is built on classes and functions in the propka module. The API of propka is documented here for developers who might want to directly use the PROPKA 3 code.

Note

The API is still changing and there is currently no guarantee that it will remain stable between minor releases.

4.1. Data structures

atom	Atom
bonds	Bonds
group	Data structures for groups
conformation_container	Molecular data structures
molecular_container	PDB molecular container

4.2. I/O

input	Input handling
lib	Set-up of a PROPKA calculation
output	Output
parameters	Configuration file parameters
hybrid36	Hybrid36 PDB-like file format
ligand_pka_values	Ligand pKa values from Marvin
run	Script functionality
version	Version-based configuration

4.3. Structure processing

protonate	Protonate a structure
hydrogens	Hydrogens
ligand	Ligand atom typing

4.4. Calculations

calculations	Calculations
coupled_groups	Coupling between groups
determinant	Determinant
determinants	Working with Determinants
energy	Energy calculations
iterative	Working with Determinants
vector_algebra	Vector calculations