pestifer.tasks.pdb2pqr module

Definition of the PDB2PQRTask class for preparing PDB files for PQR generation using PDB2PQR. This class is a descendant of the PsfgenTask class and is used to prepare PDB files, generate PQR files with titration states, and apply necessary modifications to the molecular structure.

Usage is described in the pdb2pqr documentation.

The documentation of the pdb2pqr command is available at readthedocs.

class pestifer.tasks.pdb2pqr.PDB2PQRTask(specs: dict = None, **kwargs)

Bases: PsfgenTask

PDB2PQRTask class for preparing PDB files for PQR generation using PDB2PQR.

do() → int

Execute the PDB2PQR task.

prep_input()

Prepare the input PDB file for PDB2PQR processing. This method writes a hydrogen-free PDB file with histidine resnames reverted to HIS and water resnames changed to HOH. It uses the VMD scripter to create a script that performs these modifications. The resulting PDB file is saved with the basename followed by _pprep.pdb. It also updates the state variables with the new PDB file. The method returns the result of the VMD script execution.

Returns:

The result of the VMD script execution, typically 0 on success.

Return type:

int

prep_mods()

Prepare modifications based on the PKA table from the log parser. This method iterates through the PKA table and creates Patch objects for residues that require modifications. It handles different residue types such as histidines, acidic residues (ASP, GLU), basic residues (TYR, SER, LYS, ARG), and terminal residues (N+, C-). The patches are created based on the protonation state of the residues and their resnames. The patches are stored in the objmanager for later use.

run_pdb2pqr(pH=7.0)

Run PDB2PQR on the prepared PDB file to generate a PQR file with titration states. This method constructs a command to run PDB2PQR with the specified parameters, including the force field, output force field, pH, titration state method, and output file names. It uses the Command class to execute the PDB2PQR command and parse the results using the PDB2PQRLog parser. The method also updates the metadata with the protonation states of histidines based on the pKa values.

Parameters:

pH (float, optional) – The pH value to be used for titration state calculations. Default is 7.