Source code for utils.closest_residues

#!/usr/bin/env python3

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

[docs]class ClosestResidues(BiobbObject): """ | biobb_structure_utils ClosestResidues | Class to search closest residues from a 3D structure using Biopython. | Return all residues that have at least one atom within radius of center from a list of given residues. Args: input_structure_path (str): Input structure file path. File type: input. `Sample file <>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476). output_residues_path (str): Output molcules file path. File type: output. `Sample file <>`_. 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 or list of dictionaries with the name | res_id | chain | model of the residues to find the closest neighbours. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}]. * **radius** (*float*) - (5) Distance in Ångströms to neighbours of the given list of residues. * **preserve_target** (*bool*) - (True) Whether or not to preserve the target residues in the output structure. * **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.closest_residues import closest_residues prop = { 'residues': [ { 'name': 'HIS', 'res_id': '72', 'chain': 'A', 'model': '1' } ], 'radius': 5, 'preserve_target': False } closest_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: """ 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.radius = properties.get('radius', 5) self.preserve_target = properties.get('preserve_target', True) = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`ClosestResidues <utils.closest_residues.ClosestResidues>` utils.closest_residues.ClosestResidues 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 = Bio.PDB.PDBParser(QUIET=True).get_structure('structure', self.stage_io_dict['in']['input_structure_path']) str_residues = [] # format selected 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: str_residues.append(r) else: str_residues.append(r) # get target residues in BioPython format target_residues = [] for sr in str_residues: # try for residues, if exception, try as HETATM try: target_residues.append(structure[int(sr['model']) - 1][sr['chain']][int(sr['res_id'])]) except KeyError: target_residues.append(structure[int(sr['model']) - 1][sr['chain']]['H_' + sr['name'], int(sr['res_id']), ' ']) except Exception: fu.log(self.__class__.__name__ + ': Unable to find residue %s', sr['res_id'], self.out_log) # get all atoms from target_residues target_atoms = Bio.PDB.Selection.unfold_entities(target_residues, 'A') # get all atoms of input structure all_atoms = Bio.PDB.Selection.unfold_entities(structure, 'A') # generate NeighborSearch object ns = Bio.PDB.NeighborSearch(all_atoms) # set comprehension list nearby_residues = {res for center_atom in target_atoms for res in, self.radius, 'R')} # format nearby residues to pure python objects neighbor_residues = [] for residue in nearby_residues: r = create_biopython_residue(residue) neighbor_residues.append(r) # if preserve_target == False, don't add the residues of self.residues to the final structure if not self.preserve_target: neighbor_residues = [x for x in neighbor_residues if x not in str_residues] fu.log('Found %d nearby residues' % len(neighbor_residues), self.out_log) if len(neighbor_residues) == 0: fu.log(self.__class__.__name__ + ': No neighbour residues found, exiting', self.out_log) raise SystemExit(self.__class__.__name__ + ': No neighbour residues found, exiting') create_output_file(0, self.stage_io_dict['in']['input_structure_path'], neighbor_residues, 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
[docs]def closest_residues(input_structure_path: str, output_residues_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`ClosestResidues <utils.closest_residues.ClosestResidues>` class and execute the :meth:`launch() <utils.closest_residues.ClosestResidues.launch>` method.""" return ClosestResidues(input_structure_path=input_structure_path, output_residues_path=output_residues_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="Search closest residues to a list of given residues.", 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 closest_residues(input_structure_path=args.input_structure_path, output_residues_path=args.output_residues_path, properties=properties)
if __name__ == '__main__': main()