Coverage for biobb_structure_utils/utils/structure_check.py: 77%
56 statements
« 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 StructureCheck 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.file_utils import launchlogger
8from biobb_common.tools import file_utils as fu
9from biobb_structure_utils.utils.common import check_input_path, check_output_path_json
12class StructureCheck(BiobbObject):
13 """
14 | biobb_structure_utils StructureCheck
15 | This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.
16 | Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to generate summary checking results on a json file from a given structure and a list of features.
18 Args:
19 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/2vgb.pdb>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
20 output_summary_path (str): Output summary checking results. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/summary.json>`_. Accepted formats: json (edam:format_3464).
21 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
22 * **features** (*list*) - (None) Features to summarize. If None, all the features will be computed. Values: models (multiple molecules or coordinate sets in a single file), chains (multiple chains in a single file), altloc (atom alternative conformation given an alternate location indicator and occupancy), metals (metals present in the structure), ligands (heteroatoms present in the structure), chiral (to say that a structure is chiral is to say that its mirror image is not the same as it self), getss (detect SS bonds or disulfides), cistransbck (detact cis/trans backbone), backbone (detect backbone breaks), amide (detect too close amides), clashes (detect clashes).
23 * **binary_path** (*string*) - ("check_structure") path to the check_structure application
24 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
25 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
26 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
28 Examples:
29 This is a use example of how to use the building block from Python::
31 from biobb_structure_utils.utils.structure_check import structure_check
32 prop = {
33 'features': ['models', 'chains', 'ligands']
34 }
35 structure_check(input_structure_path='/path/to/myInputStr.pdb',
36 output_summary_path='/path/to/newSummary.json',
37 properties=prop)
39 Info:
40 * wrapped_software:
41 * name: Structure Checking from MDWeb
42 * version: >=3.0.3
43 * license: Apache-2.0
44 * ontology:
45 * name: EDAM
46 * schema: http://edamontology.org/EDAM.owl
48 """
50 def __init__(self, input_structure_path, output_summary_path, properties=None, **kwargs) -> None:
51 properties = properties or {}
53 # Call parent class constructor
54 super().__init__(properties)
55 self.locals_var_dict = locals().copy()
57 # Input/Output files
58 self.io_dict = {
59 "in": {"input_structure_path": input_structure_path},
60 "out": {"output_summary_path": output_summary_path}
61 }
63 # Properties specific for BB
64 self.binary_path = properties.get('binary_path', 'check_structure')
65 self.features = properties.get('features', None)
66 self.properties = properties
68 # Check the properties
69 self.check_properties(properties)
70 self.check_arguments()
72 @launchlogger
73 def launch(self) -> int:
74 """Execute the :class:`StructureCheck <utils.structure_check.StructureCheck>` utils.structure_check.StructureCheck object."""
76 self.io_dict['in']['input_structure_path'] = check_input_path(self.io_dict['in']['input_structure_path'],
77 self.out_log, self.__class__.__name__)
78 self.io_dict['out']['output_summary_path'] = check_output_path_json(self.io_dict['out']['output_summary_path'],
79 self.out_log, self.__class__.__name__)
81 # Setup Biobb
82 if self.check_restart():
83 return 0
84 self.stage_files()
86 tmp_folder = None
88 if not self.features or self.features is None or self.features == 'None':
89 fu.log('No features provided, all features will be computed: %s' % 'models, chains, altloc, metals, ligands, chiral, getss, cistransbck, backbone, amide, clashes', self.out_log)
91 self.cmd = [self.binary_path,
92 '-i', self.stage_io_dict['in']['input_structure_path'],
93 '--json', self.stage_io_dict['out']['output_summary_path'],
94 '--check_only',
95 '--non_interactive',
96 'checkall']
97 else:
98 fu.log('Computing features: %s' % ', '.join(self.features), self.out_log)
100 # create temporary folder
101 tmp_folder = fu.create_unique_dir()
102 fu.log('Creating %s temporary folder' % tmp_folder, self.out_log)
104 command_list = tmp_folder + '/command_list.lst'
106 with open(command_list, 'w') as f:
107 for item in self.features:
108 f.write("%s\n" % item)
110 self.cmd = [self.binary_path,
111 '-i', self.stage_io_dict['in']['input_structure_path'],
112 '--json', self.stage_io_dict['out']['output_summary_path'],
113 '--check_only',
114 '--non_interactive',
115 'command_list',
116 '--list',
117 command_list]
119 # Run Biobb block
120 self.run_biobb()
122 # Copy files to host
123 self.copy_to_host()
125 # Remove temporal files
126 self.tmp_files.extend([
127 self.stage_io_dict.get("unique_dir"),
128 tmp_folder
129 ])
130 self.remove_tmp_files()
132 self.check_arguments(output_files_created=True, raise_exception=False)
134 return self.return_code
137def structure_check(input_structure_path: str, output_summary_path: str, properties: dict = None, **kwargs) -> int:
138 """Execute the :class:`StructureCheck <utils.structure_check.StructureCheck>` class and
139 execute the :meth:`launch() <utils.structure_check.StructureCheck.launch>` method."""
141 return StructureCheck(input_structure_path=input_structure_path,
142 output_summary_path=output_summary_path,
143 properties=properties, **kwargs).launch()
146def main():
147 """Command line execution of this building block. Please check the command line documentation."""
148 parser = argparse.ArgumentParser(description="This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
149 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
151 # Specific args of each building block
152 required_args = parser.add_argument_group('required arguments')
153 required_args.add_argument('-i', '--input_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.")
154 required_args.add_argument('-o', '--output_summary_path', required=True, help="Output summary checking results. Accepted formats: json.")
156 args = parser.parse_args()
157 config = args.config if args.config else None
158 properties = settings.ConfReader(config=config).get_prop_dic()
160 # Specific call of each building block
161 structure_check(input_structure_path=args.input_structure_path,
162 output_summary_path=args.output_summary_path,
163 properties=properties)
166if __name__ == '__main__':
167 main()