Source code for pdb4amber.pdb4amber_run

#!/usr/bin/env python3

"""Module containing the Pdb4amber class and the command line interface."""
import argparse
import shutil, re
from pathlib import Path, PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import  settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_amber.pdb4amber.common import *

[docs]class Pdb4amberRun(BiobbObject): """ | biobb_amber.pdb4amber.pdb4amber_run Pdb4amberRun | Wrapper of the `AmberTools (AMBER MD Package) pdb4amber tool <https://ambermd.org/AmberTools.php>`_ module. | Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package. Args: input_pdb_path (str): Input 3D structure PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/pdb4amber/1aki_fixed.pdb>`_. Accepted formats: pdb (edam:format_1476). output_pdb_path (str): Output 3D structure PDB file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pdb4amber/structure.pdb4amber.pdb>`_. Accepted formats: pdb (edam:format_1476). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **remove_hydrogens** (*bool*) - (False) Remove hydrogen atoms from the PDB file. * **remove_waters** (*bool*) - (False) Remove water molecules from the PDB file. * **constant_pH** (*bool*) - (False) Rename ionizable residues e.g. GLU,ASP,HIS for constant pH simulation. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. Examples: This is a use example of how to use the building block from Python:: from biobb_amber.pdb4amber.pdb4amber_run import pdb4amber_run prop = { 'remove_tmp': True } pdb4amber_run(input_pdb_path='/path/to/structure.pdb', output_pdb_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: AmberTools pdb4amber * version: >20.9 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_pdb_path: str, output_pdb_path: str, properties: dict, **kwargs): properties = properties or {} # Call parent class constructor super().__init__(properties) # Input/Output files self.io_dict = { 'in': { 'input_pdb_path': input_pdb_path }, 'out': { 'output_pdb_path': output_pdb_path } } # Properties specific for BB self.properties = properties self.remove_hydrogens = properties.get('remove_hydrogens', False) self.remove_waters = properties.get('remove_waters', False) self.constant_pH = properties.get('constant_pH', False) # Check the properties self.check_properties(properties)
[docs] def check_data_params(self, out_log, err_log): """ Checks input/output paths correctness """ # Check input(s) self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", False, out_log, self.__class__.__name__) # Check output(s) self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"],"output_pdb_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self): """Launches the execution of the Pdb4amberRun module.""" # check input/output paths and parameters self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Creating temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) # Command line # sander -O -i mdin/min.mdin -p $1.cpH.prmtop -c ph$i/$1.inpcrd -r ph$i/$1.min.rst7 -o ph$i/$1.min.o self.cmd = ['pdb4amber ', '-i', self.io_dict['in']['input_pdb_path'], '-o', self.io_dict['out']['output_pdb_path'] ] if self.remove_hydrogens: self.cmd.append("-y ") if self.remove_waters: self.cmd.append("-d ") if self.constant_pH: self.cmd.append("--constantph ") # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # remove temporary folder(s) if self.remove_tmp: self.tmp_files.append(self.tmp_folder) self.remove_tmp_files() return self.return_code
[docs]def pdb4amber_run(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`Pdb4amberRun <pdb4amber.pdb4amber_run.Pdb4amberRun>`pdb4amber.pdb4amber_run.Pdb4amberRun class and execute :meth:`launch() <pdb4amber.pdb4amber_run.Pdb4amberRun.launch>` method""" return Pdb4amberRun( input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.') required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file. Accepted formats: pdb.') args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call pdb4amber_run( input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)
if __name__ == '__main__': main()