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