Module protkit.tools.pdb2pqr_adaptor
Implements class PDB2PQRAdaptor. The PDB2PQRAdaptor class provides an interface
to the pdb2pqr software, which is used to convert PDB files to PQR files.
The pdb2pqr software is a widely used tool for adding charges and radii to protein structures. It is used to prepare protein structures for molecular dynamics simulations, docking studies, and other computational analyses. pdb2pqr can add a limited number of missing heavy atoms to structures, as well as hydrogen atoms. It may change the coordinates of some atoms in the structure.
To use the PDB2PQRAdaptor class, you need to have the pdb2pqr software installed. The pdb2pqr software is automatically installed as a PyPi package when you install Protkit.
PDB2PQR was developed by the Baker Lab at the University of Washington. If you use pdb2pqr in your research, please cite the following papers:
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., & Baker, N. A. (2004). PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32, W665-W667. https://doi.org/10.1093/nar/gkh381
Dolinsky, T. J., Czodrowski, P., Li, H., Nielsen, J. E., Jensen, J. H., Klebe, G., & Baker, N. A. (2007). PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Research, 35, W522-W525. https://doi.org/10.1093/nar/gkm276
Unni, S., Huang, Y., Hanson, R. M., Tobias, M., Krishnan, S., Li, W. W., Nielsen, J. E., & Baker, N. A. (2011). Web servers and services for electrostatics calculations with APBS and PDB2PQR. Journal of Computational Chemistry, 32(7), 1488-1491. https://doi.org/10.1002/jcc.21720
Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L. E., Brookes, D. H., Wilson, L., Chen, J., Liles, K., Chun, M., Li, P., Gohara, D. W., Dolinsky, T., Konecny, R., Koes, D. R., Nielsen, J. E., Head-Gordon, T., Geng, W., Krasny, R., Wei, G. W., Holst, M. J., McCammon, J. A., & Baker, N. A. (2018). Improvements to the APBS biomolecular solvation software suite. Protein Science, 27(1), 112-128. https://doi.org/10.1002/pro.3280
Expand source code
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS), Claudio Jardim (CJ)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `PDB2PQRAdaptor`. The PDB2PQRAdaptor class provides an interface
to the pdb2pqr software, which is used to convert PDB files to PQR files.
The pdb2pqr software is a widely used tool for adding charges and radii to protein
structures. It is used to prepare protein structures for molecular dynamics
simulations, docking studies, and other computational analyses. pdb2pqr can add a
limited number of missing heavy atoms to structures, as well as
hydrogen atoms. It may change the coordinates of some atoms in the structure.
To use the PDB2PQRAdaptor class, you need to have the pdb2pqr software installed.
The pdb2pqr software is automatically installed as a PyPi package when you install
Protkit.
PDB2PQR was developed by the Baker Lab at the University of Washington. If you use
pdb2pqr in your research, please cite the following papers:
Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., & Baker, N. A. (2004).
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics
calculations. Nucleic Acids Research, 32, W665-W667.
https://doi.org/10.1093/nar/gkh381
Dolinsky, T. J., Czodrowski, P., Li, H., Nielsen, J. E., Jensen, J. H., Klebe, G., & Baker, N. A. (2007).
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Research, 35, W522-W525.
https://doi.org/10.1093/nar/gkm276
Unni, S., Huang, Y., Hanson, R. M., Tobias, M., Krishnan, S., Li, W. W., Nielsen, J. E., & Baker, N. A. (2011).
Web servers and services for electrostatics calculations with APBS and PDB2PQR.
Journal of Computational Chemistry, 32(7), 1488-1491.
https://doi.org/10.1002/jcc.21720
Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L. E., Brookes, D. H., Wilson, L., Chen, J., Liles, K., Chun, M., Li, P., Gohara, D. W., Dolinsky, T., Konecny, R., Koes, D. R., Nielsen, J. E., Head-Gordon, T., Geng, W., Krasny, R., Wei, G. W., Holst, M. J., McCammon, J. A., & Baker, N. A. (2018).
Improvements to the APBS biomolecular solvation software suite.
Protein Science, 27(1), 112-128.
https://doi.org/10.1002/pro.3280
"""
import subprocess
import tempfile
import os
from protkit.file_io import PDBIO
from protkit.file_io import PQRIO
from protkit.structure import Protein
class PDB2PQRAdaptorError(Exception):
pass
class PDB2PQRAdaptor():
"""
Adapter class for the pdb2pqr software.
"""
AMBER = "AMBER"
CHARMM = "CHARMM"
PARSE = "PARSE"
TYL06 = "TYL06"
PEOEPB = "PEOEPB"
SWANSON = "SWANSON"
def __init__(self,
pdb2pqr_bin_path: str = None,
force_field: str = PARSE):
"""
Initialize the PDB2PQR adaptor.
Args:
pdb2pqr_bin_path (str): The path to the pdb2pqr binary. If
None, the adaptor will use the pdb2pqr binary in the PATH.
force_field (str): The force field to use for the PQR file.
Options: AMBER, CHARMM, PARSE, TYL06, PEOEPB, SWANSON
Returns:
None
"""
super().__init__()
self._pdb2pqr_bin_path = pdb2pqr_bin_path
self._force_field = force_field
def run(self,
protein: Protein,
output_pqr_file_path: str=None,
output_pdb_file_path: str=None) -> Protein:
"""
Run pdb2pqr on the specified PDB file.
Args:
protein (Protein): The protein to be converted to a PQR file.
output_pqr_file_path (str): If set, the PQR file will be written to this file.
output_pdb_file_path (str): If set, the PDB file that is used as input
to pdb2pqr will be written to this file.
Returns:
Protein: The protein with the PQR file information.
"""
# Save PDB file to serve as input to PDB2PQR
if output_pdb_file_path is None:
temp_file_pdb = tempfile.NamedTemporaryFile(delete=True)
output_pdb_file_path = temp_file_pdb.name
PDBIO.save(protein, output_pdb_file_path)
# Allocate a temporary file for the PQR file
if output_pqr_file_path is None:
temp_file_pqr = tempfile.NamedTemporaryFile(delete=True)
temp_file_pqr.close()
output_pqr_file_path = temp_file_pqr.name
# Ensure the directory for the log file exists
log_directory = os.path.dirname(output_pqr_file_path)
if not os.path.exists(log_directory):
os.makedirs(log_directory)
# Setup PDB2PQR
if self._pdb2pqr_bin_path is None:
args = ["pdb2pqr", output_pdb_file_path, output_pqr_file_path, "--ff=" + self._force_field, "--keep-chain"]
else:
args = [self._pdb2pqr_bin_path, output_pdb_file_path, output_pqr_file_path, "--ff=" + self._force_field, "--keep-chain"]
pdb2pqr_process = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
# Run PDB2PQR
stdout, stderr = pdb2pqr_process.communicate()
exit_code = pdb2pqr_process.returncode
if exit_code != 0:
raise PDB2PQRAdaptorError(
"Error while running pdb2pqr." + stderr.decode("utf8")
)
# Load PQR file
protein = PQRIO.load(output_pqr_file_path)[0]
return proteinClasses
class PDB2PQRAdaptor (pdb2pqr_bin_path: str = None, force_field: str = 'PARSE')-
Adapter class for the pdb2pqr software.
Initialize the PDB2PQR adaptor.
Args
pdb2pqr_bin_path:str- The path to the pdb2pqr binary. If None, the adaptor will use the pdb2pqr binary in the PATH.
force_field:str- The force field to use for the PQR file. Options: AMBER, CHARMM, PARSE, TYL06, PEOEPB, SWANSON
Returns
None
Expand source code
class PDB2PQRAdaptor(): """ Adapter class for the pdb2pqr software. """ AMBER = "AMBER" CHARMM = "CHARMM" PARSE = "PARSE" TYL06 = "TYL06" PEOEPB = "PEOEPB" SWANSON = "SWANSON" def __init__(self, pdb2pqr_bin_path: str = None, force_field: str = PARSE): """ Initialize the PDB2PQR adaptor. Args: pdb2pqr_bin_path (str): The path to the pdb2pqr binary. If None, the adaptor will use the pdb2pqr binary in the PATH. force_field (str): The force field to use for the PQR file. Options: AMBER, CHARMM, PARSE, TYL06, PEOEPB, SWANSON Returns: None """ super().__init__() self._pdb2pqr_bin_path = pdb2pqr_bin_path self._force_field = force_field def run(self, protein: Protein, output_pqr_file_path: str=None, output_pdb_file_path: str=None) -> Protein: """ Run pdb2pqr on the specified PDB file. Args: protein (Protein): The protein to be converted to a PQR file. output_pqr_file_path (str): If set, the PQR file will be written to this file. output_pdb_file_path (str): If set, the PDB file that is used as input to pdb2pqr will be written to this file. Returns: Protein: The protein with the PQR file information. """ # Save PDB file to serve as input to PDB2PQR if output_pdb_file_path is None: temp_file_pdb = tempfile.NamedTemporaryFile(delete=True) output_pdb_file_path = temp_file_pdb.name PDBIO.save(protein, output_pdb_file_path) # Allocate a temporary file for the PQR file if output_pqr_file_path is None: temp_file_pqr = tempfile.NamedTemporaryFile(delete=True) temp_file_pqr.close() output_pqr_file_path = temp_file_pqr.name # Ensure the directory for the log file exists log_directory = os.path.dirname(output_pqr_file_path) if not os.path.exists(log_directory): os.makedirs(log_directory) # Setup PDB2PQR if self._pdb2pqr_bin_path is None: args = ["pdb2pqr", output_pdb_file_path, output_pqr_file_path, "--ff=" + self._force_field, "--keep-chain"] else: args = [self._pdb2pqr_bin_path, output_pdb_file_path, output_pqr_file_path, "--ff=" + self._force_field, "--keep-chain"] pdb2pqr_process = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) # Run PDB2PQR stdout, stderr = pdb2pqr_process.communicate() exit_code = pdb2pqr_process.returncode if exit_code != 0: raise PDB2PQRAdaptorError( "Error while running pdb2pqr." + stderr.decode("utf8") ) # Load PQR file protein = PQRIO.load(output_pqr_file_path)[0] return proteinClass variables
var AMBERvar CHARMMvar PARSEvar PEOEPBvar SWANSONvar TYL06
Methods
def run(self, protein: Protein, output_pqr_file_path: str = None, output_pdb_file_path: str = None) ‑> Protein-
Run pdb2pqr on the specified PDB file.
Args
protein:Protein- The protein to be converted to a PQR file.
output_pqr_file_path:str- If set, the PQR file will be written to this file.
output_pdb_file_path:str- If set, the PDB file that is used as input to pdb2pqr will be written to this file.
Returns
Protein- The protein with the PQR file information.
Expand source code
def run(self, protein: Protein, output_pqr_file_path: str=None, output_pdb_file_path: str=None) -> Protein: """ Run pdb2pqr on the specified PDB file. Args: protein (Protein): The protein to be converted to a PQR file. output_pqr_file_path (str): If set, the PQR file will be written to this file. output_pdb_file_path (str): If set, the PDB file that is used as input to pdb2pqr will be written to this file. Returns: Protein: The protein with the PQR file information. """ # Save PDB file to serve as input to PDB2PQR if output_pdb_file_path is None: temp_file_pdb = tempfile.NamedTemporaryFile(delete=True) output_pdb_file_path = temp_file_pdb.name PDBIO.save(protein, output_pdb_file_path) # Allocate a temporary file for the PQR file if output_pqr_file_path is None: temp_file_pqr = tempfile.NamedTemporaryFile(delete=True) temp_file_pqr.close() output_pqr_file_path = temp_file_pqr.name # Ensure the directory for the log file exists log_directory = os.path.dirname(output_pqr_file_path) if not os.path.exists(log_directory): os.makedirs(log_directory) # Setup PDB2PQR if self._pdb2pqr_bin_path is None: args = ["pdb2pqr", output_pdb_file_path, output_pqr_file_path, "--ff=" + self._force_field, "--keep-chain"] else: args = [self._pdb2pqr_bin_path, output_pdb_file_path, output_pqr_file_path, "--ff=" + self._force_field, "--keep-chain"] pdb2pqr_process = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) # Run PDB2PQR stdout, stderr = pdb2pqr_process.communicate() exit_code = pdb2pqr_process.returncode if exit_code != 0: raise PDB2PQRAdaptorError( "Error while running pdb2pqr." + stderr.decode("utf8") ) # Load PQR file protein = PQRIO.load(output_pqr_file_path)[0] return protein
class PDB2PQRAdaptorError (*args, **kwargs)-
Common base class for all non-exit exceptions.
Expand source code
class PDB2PQRAdaptorError(Exception): passAncestors
- builtins.Exception
- builtins.BaseException