Coverage for biobb_structure_utils / utils / structure_check.py: 91%
47 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 13:23 +0000
1#!/usr/bin/env python3
3"""Module containing the StructureCheck class and the command line interface."""
5from typing import Optional
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.tools import file_utils as fu
9from biobb_common.tools.file_utils import launchlogger
11from biobb_structure_utils.utils.common import (
12 _from_string_to_list,
13 check_input_path,
14 check_output_path_json,
15)
18class StructureCheck(BiobbObject):
19 """
20 | biobb_structure_utils StructureCheck
21 | This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.
22 | 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.
24 Args:
25 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).
26 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).
27 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
28 * **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).
29 * **binary_path** (*string*) - ("check_structure") path to the check_structure application
30 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
31 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
32 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
34 Examples:
35 This is a use example of how to use the building block from Python::
37 from biobb_structure_utils.utils.structure_check import structure_check
38 prop = {
39 'features': ['models', 'chains', 'ligands']
40 }
41 structure_check(input_structure_path='/path/to/myInputStr.pdb',
42 output_summary_path='/path/to/newSummary.json',
43 properties=prop)
45 Info:
46 * wrapped_software:
47 * name: Structure Checking from MDWeb
48 * version: >=3.0.3
49 * license: Apache-2.0
50 * ontology:
51 * name: EDAM
52 * schema: http://edamontology.org/EDAM.owl
54 """
56 def __init__(
57 self, input_structure_path, output_summary_path, properties=None, **kwargs
58 ) -> 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_summary_path": output_summary_path},
69 }
71 # Properties specific for BB
72 self.binary_path = properties.get("binary_path", "check_structure")
73 self.features = _from_string_to_list(properties.get("features", None))
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:`StructureCheck <utils.structure_check.StructureCheck>` utils.structure_check.StructureCheck object."""
84 self.io_dict["in"]["input_structure_path"] = check_input_path(
85 self.io_dict["in"]["input_structure_path"],
86 self.out_log,
87 self.__class__.__name__,
88 )
89 self.io_dict["out"]["output_summary_path"] = check_output_path_json(
90 self.io_dict["out"]["output_summary_path"],
91 self.out_log,
92 self.__class__.__name__,
93 )
95 # Setup Biobb
96 if self.check_restart():
97 return 0
98 self.stage_files()
100 tmp_folder = None
102 if not self.features or self.features is None or self.features == "None":
103 fu.log(
104 "No features provided, all features will be computed: %s"
105 % "models, chains, altloc, metals, ligands, chiral, getss, cistransbck, backbone, amide, clashes",
106 self.out_log,
107 )
109 self.cmd = [
110 self.binary_path,
111 "-i",
112 self.stage_io_dict["in"]["input_structure_path"],
113 "--json",
114 self.stage_io_dict["out"]["output_summary_path"],
115 "--check_only",
116 "--non_interactive",
117 "checkall",
118 ]
119 else:
120 fu.log("Computing features: %s" % ", ".join(self.features), self.out_log)
122 # create temporary folder
123 tmp_folder = fu.create_unique_dir()
124 fu.log("Creating %s temporary folder" % tmp_folder, self.out_log)
126 command_list = tmp_folder + "/command_list.lst"
128 with open(command_list, "w") as f:
129 for item in self.features:
130 f.write("%s\n" % item)
132 self.cmd = [
133 self.binary_path,
134 "-i",
135 self.stage_io_dict["in"]["input_structure_path"],
136 "--json",
137 self.stage_io_dict["out"]["output_summary_path"],
138 "--check_only",
139 "--non_interactive",
140 "command_list",
141 "--list",
142 command_list,
143 ]
145 # Run Biobb block
146 self.run_biobb()
148 # Copy files to host
149 self.copy_to_host()
151 # Remove temporal files
152 self.tmp_files.append(tmp_folder)
153 self.remove_tmp_files()
155 self.check_arguments(output_files_created=True, raise_exception=False)
157 return self.return_code
160def structure_check(
161 input_structure_path: str,
162 output_summary_path: str,
163 properties: Optional[dict] = None,
164 **kwargs,
165) -> int:
166 """Create the :class:`StructureCheck <utils.structure_check.StructureCheck>` class and
167 execute the :meth:`launch() <utils.structure_check.StructureCheck.launch>` method."""
168 return StructureCheck(**dict(locals())).launch()
171structure_check.__doc__ = StructureCheck.__doc__
172main = StructureCheck.get_main(structure_check, "This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.")
174if __name__ == "__main__":
175 main()