Source code for utils.remove_pdb_water

#!/usr/bin/env python3

"""Module containing the RemovePdbWater class and the command line interface."""
import argparse
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from import launchlogger

[docs]class RemovePdbWater(BiobbObject): """ | biobb_structure_utils RemovePdbWater | This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures. | Wrapper for the `Structure Checking <>`_ tool to remove water molecules from PDB 3D structures. Args: input_pdb_path (str): Input PDB file path. File type: input. `Sample file <>`_. Accepted formats: pdb (edam:format_1476). output_pdb_path (str): Output PDB file path. File type: output. `Sample file <>`_. Accepted formats: pdb (edam:format_1476). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **binary_path** (*string*) - ("check_structure") path to the check_structure application * **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_structure_utils.utils.remove_pdb_water import remove_pdb_water prop = { } remove_pdb_water(input_pdb_path='/path/to/myStructure.pdb', output_pdb_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: Structure Checking from MDWeb * version: >=3.0.3 * license: Apache-2.0 * ontology: * name: EDAM * schema: """ def __init__(self, input_pdb_path, output_pdb_path, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # 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.binary_path = properties.get('binary_path', 'check_structure') # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` utils.remove_pdb_water.RemovePdbWater object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() self.cmd = [self.binary_path, '-i', self.stage_io_dict['in']['input_pdb_path'], '-o', self.stage_io_dict['out']['output_pdb_path'], '--force_save', 'water', '--remove', 'yes'] # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # Remove temporal files self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def remove_pdb_water(input_pdb_path: str, output_pdb_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`RemovePdbWater <utils.remove_pdb_water.RemovePdbWater>` class and execute the :meth:`launch() <utils.remove_pdb_water.RemovePdbWater.launch>` method.""" return RemovePdbWater(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path, properties=properties, **kwargs).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Remove the water molecules from a PDB 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-i', '--input_pdb_path', required=True, help="Input pdb file name") required_args.add_argument('-o', '--output_pdb_path', required=True, help="Output pdb file name") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block remove_pdb_water(input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path, properties=properties)
if __name__ == '__main__': main()