Coverage for biobb_vs / vina / autodock_vina_run.py: 95%

1#!/usr/bin/env python3 

2 

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

4import os 

5from typing import Optional 

6from biobb_common.generic.biobb_object import BiobbObject 

7from biobb_common.tools.file_utils import launchlogger 

8from biobb_vs.vina.common import check_input_path, check_output_path 

9 

10 

11class AutoDockVinaRun(BiobbObject): 

12 """ 

13 | biobb_vs AutoDockVinaRun 

14 | Wrapper of the AutoDock Vina software. 

15 | This class performs docking of the ligand to a set of grids describing the target protein via the `AutoDock Vina <http://vina.scripps.edu/index.html>`_ software. 

16 

17 Args: 

18 input_ligand_pdbqt_path (str): Path to the input PDBQT ligand. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt>`_. Accepted formats: pdbqt (edam:format_1476). 

19 input_receptor_pdbqt_path (str): Path to the input PDBQT receptor. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt>`_. Accepted formats: pdbqt (edam:format_1476). 

20 input_box_path (str): Path to the PDB containig the residues belonging to the binding site. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb>`_. Accepted formats: pdb (edam:format_1476). 

21 output_pdbqt_path (str): Path to the output PDBQT file. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt>`_. Accepted formats: pdbqt (edam:format_1476). 

22 output_log_path (str) (Optional): Path to the log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log>`_. Accepted formats: log (edam:format_2330). 

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

24 * **cpu** (*int*) - (1) [1~1000|1] the number of CPUs to use. 

25 * **exhaustiveness** (*int*) - (8) [1~10000|1] exhaustiveness of the global search (roughly proportional to time). 

26 * **num_modes** (*int*) - (9) [1~1000|1] maximum number of binding modes to generate. 

27 * **min_rmsd** (*int*) - (1) [1~1000|1] minimum RMSD between output poses. 

28 * **energy_range** (*int*) - (3) [1~1000|1] maximum energy difference between the best binding mode and the worst one displayed (kcal/mol). 

29 * **binary_path** (*string*) - ('vina') path to vina in your local computer. 

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. 

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

34 * **container_image** (*str*) - ('biocontainers/autodock-vina:v1.1.2-5b1-deb_cv1') Container image definition. 

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

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

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

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

39 

40 Examples: 

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

42 

43 from biobb_vs.vina.autodock_vina_run import autodock_vina_run 

44 prop = { 

45 'binary_path': 'vina' 

46 } 

47 autodock_vina_run(input_ligand_pdbqt_path='/path/to/myLigand.pdbqt', 

48 input_receptor_pdbqt_path='/path/to/myReceptor.pdbqt', 

49 input_box_path='/path/to/myBox.pdb', 

50 output_pdbqt_path='/path/to/newStructure.pdbqt', 

51 output_log_path='/path/to/newLog.log', 

52 properties=prop) 

53 

54 Info: 

55 * wrapped_software: 

56 * name: Autodock Vina 

57 * version: >=1.2.3 

58 * license: Apache-2.0 

59 * ontology: 

60 * name: EDAM 

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

62 

63 """ 

64 

65 def __init__( 

66 self, 

67 input_ligand_pdbqt_path, 

68 input_receptor_pdbqt_path, 

69 input_box_path, 

70 output_pdbqt_path, 

71 output_log_path=None, 

72 properties=None, 

73 **kwargs, 

74 ) -> None: 

75 properties = properties or {} 

76 

77 # Call parent class constructor 

78 super().__init__(properties) 

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

80 

81 # Input/Output files 

82 self.io_dict = { 

83 "in": { 

84 "input_ligand_pdbqt_path": input_ligand_pdbqt_path, 

85 "input_receptor_pdbqt_path": input_receptor_pdbqt_path, 

86 "input_box_path": input_box_path, 

87 }, 

88 "out": { 

89 "output_pdbqt_path": output_pdbqt_path, 

90 "output_log_path": output_log_path, 

91 }, 

92 } 

93 

94 # Properties specific for BB 

95 self.cpu = properties.get("cpu", 1) 

96 self.exhaustiveness = properties.get("exhaustiveness", 8) 

97 self.num_modes = properties.get("num_modes", 9) 

98 self.min_rmsd = properties.get("min_rmsd", 1) 

99 self.energy_range = properties.get("energy_range", 3) 

100 self.binary_path = properties.get("binary_path", "vina") 

101 self.properties = properties 

102 

103 # Check the properties 

104 self.check_properties(properties) 

105 self.check_arguments() 

106 

107 def check_data_params(self, out_log, err_log): 

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

109 self.io_dict["in"]["input_ligand_pdbqt_path"] = check_input_path( 

110 self.io_dict["in"]["input_ligand_pdbqt_path"], 

111 "input_ligand_pdbqt_path", 

112 self.out_log, 

113 self.__class__.__name__, 

114 ) 

115 self.io_dict["in"]["input_receptor_pdbqt_path"] = check_input_path( 

116 self.io_dict["in"]["input_receptor_pdbqt_path"], 

117 "input_receptor_pdbqt_path", 

118 self.out_log, 

119 self.__class__.__name__, 

120 ) 

121 self.io_dict["in"]["input_box_path"] = check_input_path( 

122 self.io_dict["in"]["input_box_path"], 

123 "input_box_path", 

124 self.out_log, 

125 self.__class__.__name__, 

126 ) 

127 self.io_dict["out"]["output_pdbqt_path"] = check_output_path( 

128 self.io_dict["out"]["output_pdbqt_path"], 

129 "output_pdbqt_path", 

130 False, 

131 self.out_log, 

132 self.__class__.__name__, 

133 ) 

134 self.io_dict["out"]["output_log_path"] = check_output_path( 

135 self.io_dict["out"]["output_log_path"], 

136 "output_log_path", 

137 True, 

138 self.out_log, 

139 self.__class__.__name__, 

140 ) 

141 

142 def calculate_box(self, box_file_path): 

143 with open(box_file_path, "r") as box_file: 

144 for line in box_file: 

145 line = line.rstrip(os.linesep) 

146 if line.startswith("REMARK BOX CENTER"): 

147 fields = line.split() 

148 center = fields[3:6] 

149 size = fields[-3:] 

150 return list( 

151 map( 

152 str, 

153 [ 

154 center[0], 

155 center[1], 

156 center[2], 

157 size[0], 

158 size[1], 

159 size[2], 

160 ], 

161 ) 

162 ) 

163 return list(map(str, [0, 0, 0, 0, 0, 0])) 

164 

165 @launchlogger 

166 def launch(self) -> int: 

167 """Execute the :class:`AutoDockVinaRun_run <vina.autodock_vina_run.AutoDockVinaRun_run>` vina.autodock_vina_run.AutoDockVinaRun_run object.""" 

168 

169 # check input/output paths and parameters 

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

171 

172 # Setup Biobb 

173 if self.check_restart(): 

174 return 0 

175 self.stage_files() 

176 

177 # calculating box position and size 

178 x0, y0, z0, sidex, sidey, sidez = self.calculate_box( 

179 self.io_dict["in"]["input_box_path"] 

180 ) 

181 

182 # in case ligand or receptor end with END, remove last line 

183 # check_input_autodock(self.io_dict["in"]["input_ligand_pdbqt_path"], self.out_log) 

184 # check_input_autodock(self.io_dict["in"]["input_receptor_pdbqt_path"], self.out_log) 

185 

186 # create cmd 

187 self.cmd = [ 

188 self.binary_path, 

189 "--ligand", 

190 self.stage_io_dict["in"]["input_ligand_pdbqt_path"], 

191 "--receptor", 

192 self.stage_io_dict["in"]["input_receptor_pdbqt_path"], 

193 "--center_x=" + x0, 

194 "--center_y=" + y0, 

195 "--center_z=" + z0, 

196 "--size_x=" + sidex, 

197 "--size_y=" + sidey, 

198 "--size_z=" + sidez, 

199 "--cpu", 

200 str(self.cpu), 

201 "--exhaustiveness", 

202 str(self.exhaustiveness), 

203 "--num_modes", 

204 str(self.num_modes), 

205 "--min_rmsd", 

206 str(self.min_rmsd), 

207 "--energy_range", 

208 str(self.energy_range), 

209 "--out", 

210 self.stage_io_dict["out"]["output_pdbqt_path"], 

211 "--verbosity", 

212 "1", 

213 ">", 

214 self.stage_io_dict["out"]["output_log_path"], 

215 ] 

216 

217 # Run Biobb block 

218 self.run_biobb() 

219 

220 # Copy files to host 

221 self.copy_to_host() 

222 

223 # remove temporary folder(s) 

224 self.remove_tmp_files() 

225 

226 self.check_arguments(output_files_created=True, raise_exception=False) 

227 

228 return self.return_code 

229 

230 

231def autodock_vina_run( 

232 input_ligand_pdbqt_path: str, 

233 input_receptor_pdbqt_path: str, 

234 input_box_path: str, 

235 output_pdbqt_path: str, 

236 output_log_path: Optional[str] = None, 

237 properties: Optional[dict] = None, 

238 **kwargs, 

239) -> int: 

240 """Create the :class:`AutoDockVinaRun <vina.autodock_vina_run.AutoDockVinaRun>` class and 

241 execute the :meth:`launch() <vina.autodock_vina_run.AutoDockVinaRun.launch>` method.""" 

242 return AutoDockVinaRun(**dict(locals())).launch() 

243 

244 

245autodock_vina_run.__doc__ = AutoDockVinaRun.__doc__ 

246main = AutoDockVinaRun.get_main(autodock_vina_run, "Prepares input ligand for an Autodock Vina Virtual Screening.") 

247 

248 

249if __name__ == "__main__": 

250 main()