ProtoCaller.Wrappers.pdb2pqrwrapper module

This module handles calls to a Python wrapped version of PDB2PQR. ProtoCaller makes sure all PDB information is retained after calling PDB2PQR, such as disulfide bond information, which is needed for subsequent parametrisation. If the user runs external protonation routines, they need to make sure to keep relevant PDB information afterwards.

ProtoCaller.Wrappers.pdb2pqrwrapper.pdb2pqrTransform(filename, pdb2pqr_executable='pdb2pqr30', **kwargs)

A thin wrapper around PDB2PQR which protonates an input PDB file.

Parameters

• filename (str) – Name of input file.

• pdb2pqr_executable (str) – Name or path to the pdb2pqr executable.

• kwargs – Keyword arguments to be passed on to PDB2PQR. All supported arguments can be found at e.g. pdb2pqr30 –help.

Returns

filename – Absolute path to the protonated file.

Return type

str