Source code for utils.extract_heteroatoms

#!/usr/bin/env python3

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

[docs]class ExtractHeteroAtoms(BiobbObject): """ | biobb_structure_utils ExtractHeteroAtoms | Class to extract hetero-atoms from a 3D structure using Biopython. 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_heteroatom_path (str): Output heteroatom 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): * **heteroatoms** (*list*) - (None) List of dictionaries with the name | res_id | chain | model of the heteroatoms to be extracted. Format: [{"name": "ZZ7", "res_id": "302", "chain": "B", "model": "1"}]. If empty, all the heteroatoms of the structure will be returned. * **water** (*bool*) - (False) Add or not waters. * **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_heteroatoms import extract_heteroatoms prop = { 'heteroatoms': [ { 'name': 'ZZ7', 'res_id': '302', 'chain': 'B', 'model': '1' } ] } extract_heteroatoms(input_structure_path='/path/to/myStructure.pdb', output_heteroatom_path='/path/to/newHeteroatom.pdb', properties=prop) Info: * wrapped_software: * name: In house using Biopython * version: >=1.76 * license: other * ontology: * name: EDAM * schema: """ def __init__(self, input_structure_path, output_heteroatom_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_heteroatom_path": output_heteroatom_path} } # Properties specific for BB self.heteroatoms = properties.get('heteroatoms', []) self.water = properties.get('water', False) = properties # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` utils.extract_heteroatoms.ExtractHeteroAtoms 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_heteroatom_path'] = check_output_path(self.io_dict['out']['output_heteroatom_path'], self.out_log, self.__class__.__name__) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Business code # get list of heteroatoms from properties list_heteroatoms = check_format_heteroatoms(self.heteroatoms, 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 heteroatoms for residue in structure.get_residues(): r = create_biopython_residue(residue) if list_heteroatoms: for het in list_heteroatoms: match = True for code in het['code']: if het[code].strip() != r[code].strip(): match = False break if match: if not self.water and (r['name'] == 'HOH' or r['name'] == 'SOL' or r['name'] == 'WAT'): pass else: new_structure.append(r) else: if not self.water and (r['name'] == 'HOH' or r['name'] == 'SOL' or r['name'] == 'WAT'): pass else: new_structure.append(r) # if not heteroatoms found in structure, raise exit if not new_structure: fu.log(self.__class__.__name__ + ': The heteroatoms given by user were not found in input structure', self.out_log) raise SystemExit(self.__class__.__name__ + ': The heteroatoms given by user were not found in input structure') create_output_file(1, self.stage_io_dict['in']['input_structure_path'], new_structure, self.stage_io_dict['out']['output_heteroatom_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 extract_heteroatoms(input_structure_path: str, output_heteroatom_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` class and execute the :meth:`launch() <utils.extract_heteroatoms.ExtractHeteroAtoms.launch>` method.""" return ExtractHeteroAtoms(input_structure_path=input_structure_path, output_heteroatom_path=output_heteroatom_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="Extract a list of heteroatoms 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_heteroatom_path', required=True, help="Output heteroatom 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_heteroatoms(input_structure_path=args.input_structure_path, output_heteroatom_path=args.output_heteroatom_path, properties=properties)
if __name__ == '__main__': main()