Source code for utils.extract_residues

#!/usr/bin/env python3

"""Module containing the ExtractResidues class and the command line interface."""
import argparse
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from Bio.PDB.PDBParser import PDBParser
from biobb_structure_utils.utils.common import check_input_path, check_output_path, create_residues_list, create_biopython_residue, create_output_file


class ExtractResidues(BiobbObject):
    """
    | biobb_structure_utils ExtractResidues
    | Class to extract residues from a 3D structure using Biopython.

    Args:
        input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_heteroatom.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
        output_residues_path (str): Output residues file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_residues.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
        properties (dic - Python dictionary object containing the tool parameters, not input/output files):
            * **residues** (*list*) - (None) List of comma separated res_id (will extract all residues that match the res_id) or list of dictionaries with the name | res_id  | chain | model of the residues to be extracted. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}].
            * **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.extract_residues import extract_residues
            prop = {
                'residues': [
                    {
                        'name': 'HIS',
                        'res_id': '72',
                        'chain': 'A',
                        'model': '1'
                    }
                ]
            }
            extract_residues(input_structure_path='/path/to/myStructure.pdb',
                             output_residues_path='/path/to/newResidues.pdb',
                             properties=prop)

    Info:
        * wrapped_software:
            * name: In house using Biopython
            * version: >=1.79
            * license: other
        * ontology:
            * name: EDAM
            * schema: http://edamontology.org/EDAM.owl

    """

    def __init__(self, input_structure_path, output_residues_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_structure_path": input_structure_path},
            "out": {"output_residues_path": output_residues_path}
        }

        # Properties specific for BB
        self.residues = properties.get('residues', [])
        self.properties = properties

        # Check the properties
        self.check_properties(properties)
        self.check_arguments()

    @launchlogger
    def launch(self) -> int:
        """Execute the :class:`ExtractResidues <utils.extract_residues.ExtractResidues>` utils.extract_residues.ExtractResidues object."""

        self.io_dict['in']['input_structure_path'] = check_input_path(self.io_dict['in']['input_structure_path'],
                                                                      self.out_log, self.__class__.__name__)
        self.io_dict['out']['output_residues_path'] = check_output_path(self.io_dict['out']['output_residues_path'],
                                                                        self.out_log, self.__class__.__name__)

        # Setup Biobb
        if self.check_restart():
            return 0
        self.stage_files()

        # Business code
        # get list of Residues from properties
        list_residues = create_residues_list(self.residues, self.out_log)

        # load input into BioPython structure
        structure = PDBParser(QUIET=True).get_structure('structure', self.stage_io_dict['in']['input_structure_path'])

        new_structure = []
        # get desired residues
        for residue in structure.get_residues():
            r = create_biopython_residue(residue)
            if list_residues:
                for res in list_residues:
                    match = True
                    for code in res['code']:
                        if res[code].strip() != r[code].strip():
                            match = False
                            break
                    if match:
                        new_structure.append(r)
            else:
                new_structure.append(r)

        # if not residues found in structure, raise exit
        if not new_structure:
            fu.log(self.__class__.__name__ + ': The residues given by user were not found in input structure', self.out_log)
            raise SystemExit(self.__class__.__name__ + ': The residues given by user were not found in input structure')

        create_output_file(2, self.stage_io_dict['in']['input_structure_path'], new_structure, self.stage_io_dict['out']['output_residues_path'], self.out_log)

        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


def extract_residues(input_structure_path: str, output_residues_path: str, properties: dict = None, **kwargs) -> int:
    """Execute the :class:`ExtractResidues <utils.extract_residues.ExtractResidues>` class and
    execute the :meth:`launch() <utils.extract_residues.ExtractResidues.launch>` method."""

    return ExtractResidues(input_structure_path=input_structure_path,
                           output_residues_path=output_residues_path,
                           properties=properties, **kwargs).launch()


def main():
    """Command line execution of this building block. Please check the command line documentation."""
    parser = argparse.ArgumentParser(description="Extract a list of 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_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.")
    required_args.add_argument('-o', '--output_residues_path', required=True, help="Output residues file path. 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 of each building block
    extract_residues(input_structure_path=args.input_structure_path,
                     output_residues_path=args.output_residues_path,
                     properties=properties)


if __name__ == '__main__':
    main()