Coverage for biobb_vs / fpocket / fpocket_filter.py: 95%
74 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-16 15:25 +0000
1#!/usr/bin/env python3
3"""Module containing the FPocketFilter class and the command line interface."""
4import json
5from typing import Optional
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
10from biobb_vs.fpocket.common import (
11 check_input_path,
12 check_output_path,
13 check_range,
14 process_output_fpocket_filter,
15)
16from biobb_vs.utils.common import _from_string_to_list
19class FPocketFilter(BiobbObject):
20 """
21 | biobb_vs FPocketFilter
22 | Performs a search over the outputs of the fpocket building block.
23 | Finds one or more binding sites in the outputs of the fpocket building block from given parameters.
25 Args:
26 input_pockets_zip (str): Path to all the pockets found by fpocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_pockets.zip>`_. Accepted formats: zip (edam:format_3987).
27 input_summary (str): Path to the JSON summary file returned by fpocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_summary.json>`_. Accepted formats: json (edam:format_3464).
28 output_filter_pockets_zip (str): Path to the selected pockets after filtering. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip>`_. Accepted formats: zip (edam:format_3987).
29 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
30 * **score** (*list*) - (None) List of two float numbers between 0 and 1 indicating the score range. Indicates the fpocket score after the evaluation of pocket prediction accuracy as defined in the `fpocket paper <https://doi.org/10.1186/1471-2105-10-168>`_.
31 * **druggability_score** (*list*) - (None) List of two float numbers between 0 and 1 indicating the druggability_score range. It's a value between 0 and 1, 0 signifying that the pocket is likely to not bind a drug like molecule and 1, that it is very likely to bind the latter.
32 * **volume** (*list*) - (None) List of two float numbers indicating the volume range. Indicates the pocket volume.
33 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
34 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
35 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
37 Examples:
38 This is a use example of how to use the building block from Python::
40 from biobb_vs.fpocket.fpocket_filter import fpocket_filter
41 prop = {
42 'score': [0.2, 1],
43 'druggability_score': [0.2, 0.8],
44 'volume': [100, 600.2]
45 }
46 fpocket_filter(input_pockets_zip='/path/to/myPockets.zip',
47 input_summary='/path/to/mySummary.json',
48 output_filter_pockets_zip='/path/to/newPockets.json',
49 properties=prop)
51 Info:
52 * wrapped_software:
53 * name: In house
54 * license: Apache-2.0
55 * ontology:
56 * name: EDAM
57 * schema: http://edamontology.org/EDAM.owl
59 """
61 def __init__(
62 self,
63 input_pockets_zip,
64 input_summary,
65 output_filter_pockets_zip,
66 properties=None,
67 **kwargs,
68 ) -> None:
69 properties = properties or {}
71 # Call parent class constructor
72 super().__init__(properties)
73 self.locals_var_dict = locals().copy()
75 # Input/Output files
76 self.io_dict = {
77 "in": {
78 "input_pockets_zip": input_pockets_zip,
79 "input_summary": input_summary,
80 },
81 "out": {"output_filter_pockets_zip": output_filter_pockets_zip},
82 }
84 # Properties specific for BB
85 self.score = [
86 float(elem) for elem in _from_string_to_list(properties.get("score", None))
87 ]
88 self.druggability_score = [
89 float(elem)
90 for elem in _from_string_to_list(properties.get("druggability_score", None))
91 ]
93 self.volume = [
94 float(elem) for elem in _from_string_to_list(properties.get("volume", None))
95 ]
96 self.properties = properties
98 # Check the properties
99 self.check_properties(properties)
100 self.check_arguments()
102 def check_data_params(self, out_log, err_log):
103 """Checks all the input/output paths and parameters"""
104 self.io_dict["in"]["input_pockets_zip"] = check_input_path(
105 self.io_dict["in"]["input_pockets_zip"],
106 "input_pockets_zip",
107 out_log,
108 self.__class__.__name__,
109 )
110 self.io_dict["in"]["input_summary"] = check_output_path(
111 self.io_dict["in"]["input_summary"],
112 "input_summary",
113 False,
114 out_log,
115 self.__class__.__name__,
116 )
117 self.io_dict["out"]["output_filter_pockets_zip"] = check_output_path(
118 self.io_dict["out"]["output_filter_pockets_zip"],
119 "output_filter_pockets_zip",
120 True,
121 out_log,
122 self.__class__.__name__,
123 )
125 def score_matcher(self, score):
126 return lambda d: d["score"] > score[0] and d["score"] <= score[1]
128 def druggability_score_matcher(self, druggability_score):
129 return (
130 lambda d: d["druggability_score"] > druggability_score[0] and d["druggability_score"] <= druggability_score[1]
131 )
133 def volume_matcher(self, volume):
134 return lambda d: d["volume"] > volume[0] and d["volume"] <= volume[1]
136 @launchlogger
137 def launch(self) -> int:
138 """Execute the :class:`FPocketFilter <fpocket.fpocket_filter.FPocketFilter>` fpocket.fpocket_filter.FPocketFilter object."""
140 # check input/output paths and parameters
141 self.check_data_params(self.out_log, self.err_log)
143 # Setup Biobb
144 if self.check_restart():
145 return 0
146 self.stage_files()
148 # load input_summary into a dictionary
149 with open(self.io_dict["in"]["input_summary"]) as json_file:
150 data = json.load(json_file)
152 # build search_list
153 search_list = []
154 ranges = {}
155 if self.score:
156 check_range(
157 "score", self.score, [0, 1], self.out_log, self.__class__.__name__
158 )
159 search_list.append(self.score_matcher(self.score))
160 ranges["score"] = self.score
161 if self.druggability_score:
162 check_range(
163 "druggability_score",
164 self.druggability_score,
165 [0, 1],
166 self.out_log,
167 self.__class__.__name__,
168 )
169 search_list.append(self.druggability_score_matcher(self.druggability_score))
170 ranges["druggability_score"] = self.druggability_score
171 if self.volume:
172 check_range(
173 "volume", self.volume, [0, 10000], self.out_log, self.__class__.__name__
174 )
175 search_list.append(self.volume_matcher(self.volume))
176 ranges["volume"] = self.volume
178 fu.log(
179 "Performing a search under the next parameters: %s"
180 % (", ".join(["{0}: {1}".format(k, v) for k, v in ranges.items()])),
181 self.out_log,
182 )
184 # perform search
185 search = [x for x in data if all([f(data[x]) for f in search_list])]
187 if len(search) == 0:
188 fu.log("No matches found", self.out_log)
189 return 0
191 str_out = ""
192 for s in search:
193 str_out = str_out + (
194 "\n**********\n%s\n**********\nscore: %s\ndruggability_score: %s\nvolume: %s\n"
195 % (
196 s,
197 data[s]["score"],
198 data[s]["druggability_score"],
199 data[s]["volume"],
200 )
201 )
203 fu.log("Found %d matches:%s" % (len(search), str_out), self.out_log)
205 # create tmp_folder
206 self.tmp_folder = fu.create_unique_dir()
207 fu.log("Creating %s temporary folder" % self.tmp_folder, self.out_log)
209 process_output_fpocket_filter(
210 search,
211 self.tmp_folder,
212 self.io_dict["in"]["input_pockets_zip"],
213 self.io_dict["out"]["output_filter_pockets_zip"],
214 self.remove_tmp,
215 self.out_log,
216 )
218 # Copy files to host
219 self.copy_to_host()
221 self.tmp_files.extend([
222 self.tmp_folder
223 ])
224 self.remove_tmp_files()
226 self.check_arguments(output_files_created=True, raise_exception=False)
228 return 0
231def fpocket_filter(
232 input_pockets_zip: str,
233 input_summary: str,
234 output_filter_pockets_zip: str,
235 properties: Optional[dict] = None,
236 **kwargs,
237) -> int:
238 """Create the :class:`FPocketFilter <fpocket.fpocket_filter.FPocketFilter>` class and
239 execute the :meth:`launch() <fpocket.fpocket_filter.FPocketFilter.launch>` method."""
240 return FPocketFilter(**dict(locals())).launch()
243fpocket_filter.__doc__ = FPocketFilter.__doc__
244main = FPocketFilter.get_main(fpocket_filter, "Finds one or more binding sites in the outputs of the fpocket building block from given parameters.")
247if __name__ == "__main__":
248 main()