API Reference

The pdb2pqr30 command provides a command-line interface to PDB2PQR’s functionality. It is built on classes and functions in the pdb2pqr module. The API of pdb2pqr is documented here for developers who might want to directly use the PDB2PQR code.


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

Forcefield support

definitions XML handling for biomolecular residues.
forcefield Force fields are fun.

Molecular structures

aa Amino Acid Structures for PDB2PQR
hydrogens Hydrogen optimization for PDB2PQR
hydrogens.optimize Hydrogen bond optimization routines.
hydrogens.structures Topology-related classes for hydrogen optimization.
ligand Ligand support functions
ligand.mol2 Support molecules in Tripos MOL2 format.
ligand.peoe Implements the PEOE method described in:
ligand.topology Ligand topology classes.
na Nucleic Acid Structures for PDB2PQR
protein Routines for PDB2PQR
residue Biomolecular residue class.
structures Simple biomolecular structures
topology Parser for TOPOLOGY.xml

I/O support

cif CIF parsing methods
io Functions related to reading and writing data.
inputgen Create an APBS input file using psize data
pdb PDB parsing class

Other modules that need to be better organized

cells Cell list to facilitate neighbor searching.
debump Routines for PDB2PQR
main Perform functions related to _main_ execution of PDB2PQR.
psize psize
quatfit Quatfit routines for PDB2PQR
run Routines for running the code with a given set of options and PDB files.
utilities Utilities for PDB2PQR Suite