Source code for utils.sort_gro_residues

#!/usr/bin/env python3

"""Module containing the SortGroResidues 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
from biobb_structure_utils.gro_lib.gro import Gro

[docs]class SortGroResidues(BiobbObject): """ | biobb_structure_utils SortGroResidues | Class to sort the selected residues from a GRO 3D structure. Args: input_gro_path (str): Input GRO file path. File type: input. `Sample file <>`_. Accepted formats: gro (edam:format_2033). output_gro_path (str): Output sorted GRO file path. File type: output. `Sample file <>`_. Accepted formats: gro (edam:format_2033). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **residue_name_list** (*list*) - (["NA", "CL", "SOL"]) Ordered residue name list. * **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.sort_gro_residues import sort_gro_residues prop = { 'residue_name_list': ['NA', 'CL', 'SOL'] } sort_gro_residues(input_gro_path='/path/to/myInputStr.gro', output_gro_path='/path/to/newStructure.gro', properties=prop) Info: * wrapped_software: * name: In house * license: Apache-2.0 * ontology: * name: EDAM * schema: """ def __init__(self, input_gro_path, output_gro_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_gro_path": input_gro_path}, "out": {"output_gro_path": output_gro_path} } # Properties specific for BB self.residue_name_list = properties.get('residue_name_list', ["NA", "CL", "SOL"]) # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` utils.sort_gro_residues.SortGroResidues object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Business code in_gro = Gro() in_gro.read_gro_file(self.stage_io_dict['in']['input_gro_path']) in_gro.sort_residues2(self.residue_name_list) in_gro.write_gro_file(self.stage_io_dict['out']['output_gro_path']) self.return_code = 0 ########## # 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 sort_gro_residues(input_gro_path: str, output_gro_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`SortGroResidues <utils.sort_gro_residues.SortGroResidues>` class and execute the :meth:`launch() <utils.sort_gro_residues.SortGroResidues.launch>` method.""" return SortGroResidues(input_gro_path=input_gro_path, output_gro_path=output_gro_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="Renumber atoms and residues from a 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_gro_path', required=True, help="Input GRO file name") required_args.add_argument('-o', '--output_gro_path', required=True, help="Output sorted GRO 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 sort_gro_residues(input_gro_path=args.input_gro_path, output_gro_path=args.output_gro_path, properties=properties)
if __name__ == '__main__': main()