Coverage for biobb_vs / fpocket / fpocket_run.py: 93%

1#!/usr/bin/env python3 

2 

3"""Module containing the FPocketRun class and the command line interface.""" 

4from typing import Optional 

5import shutil 

6from pathlib import PurePath 

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 

10from biobb_vs.fpocket.common import check_input_path, check_output_path, process_output_fpocket 

11 

12 

13class FPocketRun(BiobbObject): 

14 """ 

15 | biobb_vs FPocketRun 

16 | Wrapper of the fpocket software. 

17 | Finds the binding site of the input_pdb_path file via the `fpocket <https://github.com/Discngine/fpocket>`_ software. 

18 

19 Args: 

20 input_pdb_path (str): Path to the PDB structure where the binding site is to be found. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/fpocket_input.pdb>`_. Accepted formats: pdb (edam:format_1476). 

21 output_pockets_zip (str): Path to all the pockets found by fpocket in the input_pdb_path structure. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pockets.zip>`_. Accepted formats: zip (edam:format_3987). 

22 output_summary (str): Path to the JSON summary file. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_summary.json>`_. Accepted formats: json (edam:format_3464). 

23 properties (dic - Python dictionary object containing the tool parameters, not input/output files): 

24 * **min_radius** (*float*) - (None) [0.1~1000|0.1] The minimum radius in Ångstroms an alpha sphere might have in a binding pocket. 

25 * **max_radius** (*float*) - (None) [2~1000|0.1] The maximum radius in Ångstroms of alpha spheres in a pocket. 

26 * **num_spheres** (*int*) - (None) [1~1000|1] Indicates how many alpha spheres a pocket must contain at least in order to figure in the results. 

27 * **sort_by** (*str*) - ('druggability_score') From which property the output will be sorted. Values: druggability_score (this score intends to assess the likeliness of the pocket to bind a small drug like molecule), score (fpocket score as defined in the `fpocket paper <https://doi.org/10.1186/1471-2105-10-168>`_), volume (volume of the pocket). 

28 * **binary_path** (*string*) - ('fpocket') path to fpocket in your local computer. 

29 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. 

30 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 

31 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 

32 * **container_path** (*str*) - (None) Container path definition. 

33 * **container_image** (*str*) - ('fpocket/fpocket:latest') Container image definition. 

34 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. 

35 * **container_working_dir** (*str*) - (None) Container working directory definition. 

36 * **container_user_id** (*str*) - (None) Container user_id definition. 

37 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. 

38 

39 Examples: 

40 This is a use example of how to use the building block from Python:: 

41 

42 from biobb_vs.fpocket.fpocket_run import fpocket_run 

43 prop = { 

44 'min_radius': 3, 

45 'max_radius': 6, 

46 'num_spheres': 35, 

47 'sort_by': 'druggability_score' 

48 } 

49 fpocket_run(input_pdb_path='/path/to/myStructure.pdb', 

50 output_pockets_zip='/path/to/newPockets.zip', 

51 output_summary='/path/to/newSummary.json', 

52 properties=prop) 

53 

54 Info: 

55 * wrapped_software: 

56 * name: fpocket 

57 * version: ==4.1 

58 * license: MIT 

59 * ontology: 

60 * name: EDAM 

61 * schema: http://edamontology.org/EDAM.owl 

62 

63 """ 

64 

65 def __init__(self, input_pdb_path, output_pockets_zip, output_summary, 

66 properties=None, **kwargs) -> None: 

67 properties = properties or {} 

68 

69 # Call parent class constructor 

70 super().__init__(properties) 

71 self.locals_var_dict = locals().copy() 

72 

73 # Input/Output files 

74 self.io_dict = { 

75 "in": {"input_pdb_path": input_pdb_path}, 

76 "out": {"output_pockets_zip": output_pockets_zip, "output_summary": output_summary} 

77 } 

78 

79 # Properties specific for BB 

80 self.binary_path = properties.get('binary_path', 'fpocket') 

81 self.min_radius = properties.get('min_radius', None) 

82 self.max_radius = properties.get('max_radius', None) 

83 self.num_spheres = properties.get('num_spheres', None) 

84 self.sort_by = properties.get('sort_by', 'druggability_score') 

85 self.properties = properties 

86 

87 # Check the properties 

88 self.check_properties(properties) 

89 self.check_arguments() 

90 

91 def check_data_params(self, out_log, err_log): 

92 """ Checks all the input/output paths and parameters """ 

93 self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", out_log, self.__class__.__name__) 

94 self.io_dict["out"]["output_pockets_zip"] = check_output_path(self.io_dict["out"]["output_pockets_zip"], "output_pockets_zip", False, out_log, self.__class__.__name__) 

95 self.io_dict["out"]["output_summary"] = check_output_path(self.io_dict["out"]["output_summary"], "output_summary", True, out_log, self.__class__.__name__) 

96 

97 @launchlogger 

98 def launch(self) -> int: 

99 """Execute the :class:`FPocketRun <fpocket.fpocket_run.FPocketRun>` fpocket.fpocket_run.FPocketRun object.""" 

100 

101 # check input/output paths and parameters 

102 self.check_data_params(self.out_log, self.err_log) 

103 

104 # Setup Biobb 

105 if self.check_restart(): 

106 return 0 

107 self.stage_files() 

108 

109 if self.container_path: 

110 tmp_input = str(PurePath(self.container_volume_path).joinpath(PurePath(self.io_dict["in"]["input_pdb_path"]).name)) 

111 tmp_folder = self.stage_io_dict['unique_dir'] 

112 else: 

113 # create tmp_folder 

114 tmp_folder = fu.create_unique_dir() 

115 fu.log('Creating %s temporary folder' % tmp_folder, self.out_log) 

116 tmp_input = str(PurePath(tmp_folder).joinpath('input.pdb')) 

117 # copy input_pdb_path to tmp_folder 

118 shutil.copy(self.io_dict["in"]["input_pdb_path"], tmp_input) 

119 

120 # create cmd 

121 self.cmd = [self.binary_path, 

122 '-f', tmp_input] 

123 

124 # adding extra properties 

125 if self.min_radius: 

126 self.cmd.extend(['-m', str(self.min_radius)]) 

127 

128 if self.max_radius: 

129 self.cmd.extend(['-M', str(self.max_radius)]) 

130 

131 if self.num_spheres: 

132 self.cmd.extend(['-i', str(self.num_spheres)]) 

133 

134 fu.log('Executing fpocket', self.out_log, self.global_log) 

135 

136 # Run Biobb block 

137 self.run_biobb() 

138 

139 # Copy files to host 

140 self.copy_to_host() 

141 

142 process_output_fpocket(tmp_folder, 

143 self.io_dict["out"]["output_pockets_zip"], 

144 self.io_dict["out"]["output_summary"], 

145 self.sort_by, 

146 self.remove_tmp, 

147 self.container_path, 

148 self.out_log, 

149 self.__class__.__name__) 

150 

151 self.tmp_files.append(tmp_folder) 

152 self.remove_tmp_files() 

153 

154 return self.return_code 

155 

156 

157def fpocket_run(input_pdb_path: str, output_pockets_zip: str, output_summary: str, properties: Optional[dict] = None, **kwargs) -> int: 

158 """Create the :class:`FPocketRun <fpocket.fpocket_run.FPocketRun>` class and 

159 execute the :meth:`launch() <fpocket.fpocket_run.FPocketRun.launch>` method.""" 

160 return FPocketRun(**dict(locals())).launch() 

161 

162 

163fpocket_run.__doc__ = FPocketRun.__doc__ 

164main = FPocketRun.get_main(fpocket_run, "Finds the binding site of the input_pdb_path file via the fpocket software") 

165 

166 

167if __name__ == '__main__': 

168 main()