Coverage for biobb_structure_utils/utils/extract_heteroatoms.py: 75%
68 statements
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 19:03 +0000
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 19:03 +0000
1#!/usr/bin/env python3
3"""Module containing the ExtractHeteroAtoms class and the command line interface."""
4import argparse
5from biobb_common.configuration import settings
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.tools import file_utils as fu
8from biobb_common.tools.file_utils import launchlogger
9from Bio.PDB.PDBParser import PDBParser
10from biobb_structure_utils.utils.common import check_input_path, check_format_heteroatoms, check_output_path, create_biopython_residue, create_output_file
13class ExtractHeteroAtoms(BiobbObject):
14 """
15 | biobb_structure_utils ExtractHeteroAtoms
16 | Class to extract hetero-atoms from a 3D structure using Biopython.
17 | Extracts a list of heteroatoms from a 3D structure using Biopython.
19 Args:
20 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).
21 output_heteroatom_path (str): Output heteroatom file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_heteroatom.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
22 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
23 * **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.
24 * **water** (*bool*) - (False) Add or not waters.
25 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
26 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
27 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
29 Examples:
30 This is a use example of how to use the building block from Python::
32 from biobb_structure_utils.utils.extract_heteroatoms import extract_heteroatoms
33 prop = {
34 'heteroatoms': [
35 {
36 'name': 'ZZ7',
37 'res_id': '302',
38 'chain': 'B',
39 'model': '1'
40 }
41 ]
42 }
43 extract_heteroatoms(input_structure_path='/path/to/myStructure.pdb',
44 output_heteroatom_path='/path/to/newHeteroatom.pdb',
45 properties=prop)
47 Info:
48 * wrapped_software:
49 * name: In house using Biopython
50 * version: >=1.76
51 * license: other
52 * ontology:
53 * name: EDAM
54 * schema: http://edamontology.org/EDAM.owl
56 """
58 def __init__(self, input_structure_path, output_heteroatom_path, properties=None, **kwargs) -> None:
59 properties = properties or {}
61 # Call parent class constructor
62 super().__init__(properties)
63 self.locals_var_dict = locals().copy()
65 # Input/Output files
66 self.io_dict = {
67 "in": {"input_structure_path": input_structure_path},
68 "out": {"output_heteroatom_path": output_heteroatom_path}
69 }
71 # Properties specific for BB
72 self.heteroatoms = properties.get('heteroatoms', [])
73 self.water = properties.get('water', False)
74 self.properties = properties
76 # Check the properties
77 self.check_properties(properties)
78 self.check_arguments()
80 @launchlogger
81 def launch(self) -> int:
82 """Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` utils.extract_heteroatoms.ExtractHeteroAtoms object."""
84 self.io_dict['in']['input_structure_path'] = check_input_path(self.io_dict['in']['input_structure_path'],
85 self.out_log, self.__class__.__name__)
86 self.io_dict['out']['output_heteroatom_path'] = check_output_path(self.io_dict['out']['output_heteroatom_path'],
87 self.out_log, self.__class__.__name__)
89 # Setup Biobb
90 if self.check_restart():
91 return 0
92 self.stage_files()
94 # Business code
95 # get list of heteroatoms from properties
96 list_heteroatoms = check_format_heteroatoms(self.heteroatoms, self.out_log)
98 # load input into BioPython structure
99 structure = PDBParser(QUIET=True).get_structure('structure', self.stage_io_dict['in']['input_structure_path'])
101 new_structure = []
102 # get desired heteroatoms
103 for residue in structure.get_residues():
104 r = create_biopython_residue(residue)
105 if list_heteroatoms:
106 for het in list_heteroatoms:
107 match = True
108 for code in het['code']:
109 if het[code].strip() != r[code].strip():
110 match = False
111 break
113 if match:
114 if not self.water and (r['name'] == 'HOH' or r['name'] == 'SOL' or r['name'] == 'WAT'):
115 pass
116 else:
117 new_structure.append(r)
118 else:
119 if not self.water and (r['name'] == 'HOH' or r['name'] == 'SOL' or r['name'] == 'WAT'):
120 pass
121 else:
122 new_structure.append(r)
124 # if not heteroatoms found in structure, raise exit
125 if not new_structure:
126 fu.log(self.__class__.__name__ + ': The heteroatoms given by user were not found in input structure', self.out_log)
127 raise SystemExit(self.__class__.__name__ + ': The heteroatoms given by user were not found in input structure')
129 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)
131 self.return_code = 0
133 # Copy files to host
134 self.copy_to_host()
136 # Remove temporal files
137 self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
138 self.remove_tmp_files()
140 self.check_arguments(output_files_created=True, raise_exception=False)
142 return self.return_code
145def extract_heteroatoms(input_structure_path: str, output_heteroatom_path: str, properties: dict = None, **kwargs) -> int:
146 """Execute the :class:`ExtractHeteroAtoms <utils.extract_heteroatoms.ExtractHeteroAtoms>` class and
147 execute the :meth:`launch() <utils.extract_heteroatoms.ExtractHeteroAtoms.launch>` method."""
149 return ExtractHeteroAtoms(input_structure_path=input_structure_path,
150 output_heteroatom_path=output_heteroatom_path,
151 properties=properties, **kwargs).launch()
154def main():
155 """Command line execution of this building block. Please check the command line documentation."""
156 parser = argparse.ArgumentParser(description="Extract a list of heteroatoms from a 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
157 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
159 # Specific args of each building block
160 required_args = parser.add_argument_group('required arguments')
161 required_args.add_argument('-i', '--input_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.")
162 required_args.add_argument('-o', '--output_heteroatom_path', required=True, help="Output heteroatom file path. Accepted formats: pdb.")
164 args = parser.parse_args()
165 config = args.config if args.config else None
166 properties = settings.ConfReader(config=config).get_prop_dic()
168 # Specific call of each building block
169 extract_heteroatoms(input_structure_path=args.input_structure_path,
170 output_heteroatom_path=args.output_heteroatom_path,
171 properties=properties)
174if __name__ == '__main__':
175 main()