Coverage for biobb_vs/vina/autodock_vina_run.py: 77%
69 statements
« prev ^ index » next coverage.py v7.6.10, created at 2025-01-28 12:00 +0000
1#!/usr/bin/env python3
3"""Module containing the AutoDockVinaRun class and the command line interface."""
5import argparse
6import os
7from typing import Optional
9from biobb_common.configuration import settings
10from biobb_common.generic.biobb_object import BiobbObject
11from biobb_common.tools.file_utils import launchlogger
13from biobb_vs.vina.common import check_input_path, check_output_path
16class AutoDockVinaRun(BiobbObject):
17 """
18 | biobb_vs AutoDockVinaRun
19 | Wrapper of the AutoDock Vina software.
20 | 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.
22 Args:
23 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).
24 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).
25 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).
26 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).
27 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).
28 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
29 * **cpu** (*int*) - (1) [1~1000|1] the number of CPUs to use.
30 * **exhaustiveness** (*int*) - (8) [1~10000|1] exhaustiveness of the global search (roughly proportional to time).
31 * **num_modes** (*int*) - (9) [1~1000|1] maximum number of binding modes to generate.
32 * **min_rmsd** (*int*) - (1) [1~1000|1] minimum RMSD between output poses.
33 * **energy_range** (*int*) - (3) [1~1000|1] maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
34 * **binary_path** (*string*) - ('vina') path to vina in your local computer.
35 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
36 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
37 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
38 * **container_path** (*str*) - (None) Container path definition.
39 * **container_image** (*str*) - ('biocontainers/autodock-vina:v1.1.2-5b1-deb_cv1') Container image definition.
40 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
41 * **container_working_dir** (*str*) - (None) Container working directory definition.
42 * **container_user_id** (*str*) - (None) Container user_id definition.
43 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
45 Examples:
46 This is a use example of how to use the building block from Python::
48 from biobb_vs.vina.autodock_vina_run import autodock_vina_run
49 prop = {
50 'binary_path': 'vina'
51 }
52 autodock_vina_run(input_ligand_pdbqt_path='/path/to/myLigand.pdbqt',
53 input_receptor_pdbqt_path='/path/to/myReceptor.pdbqt',
54 input_box_path='/path/to/myBox.pdb',
55 output_pdbqt_path='/path/to/newStructure.pdbqt',
56 output_log_path='/path/to/newLog.log',
57 properties=prop)
59 Info:
60 * wrapped_software:
61 * name: Autodock Vina
62 * version: >=1.2.3
63 * license: Apache-2.0
64 * ontology:
65 * name: EDAM
66 * schema: http://edamontology.org/EDAM.owl
68 """
70 def __init__(
71 self,
72 input_ligand_pdbqt_path,
73 input_receptor_pdbqt_path,
74 input_box_path,
75 output_pdbqt_path,
76 output_log_path=None,
77 properties=None,
78 **kwargs,
79 ) -> None:
80 properties = properties or {}
82 # Call parent class constructor
83 super().__init__(properties)
84 self.locals_var_dict = locals().copy()
86 # Input/Output files
87 self.io_dict = {
88 "in": {
89 "input_ligand_pdbqt_path": input_ligand_pdbqt_path,
90 "input_receptor_pdbqt_path": input_receptor_pdbqt_path,
91 "input_box_path": input_box_path,
92 },
93 "out": {
94 "output_pdbqt_path": output_pdbqt_path,
95 "output_log_path": output_log_path,
96 },
97 }
99 # Properties specific for BB
100 self.cpu = properties.get("cpu", 1)
101 self.exhaustiveness = properties.get("exhaustiveness", 8)
102 self.num_modes = properties.get("num_modes", 9)
103 self.min_rmsd = properties.get("min_rmsd", 1)
104 self.energy_range = properties.get("energy_range", 3)
105 self.binary_path = properties.get("binary_path", "vina")
106 self.properties = properties
108 # Check the properties
109 self.check_properties(properties)
110 self.check_arguments()
112 def check_data_params(self, out_log, err_log):
113 """Checks all the input/output paths and parameters"""
114 self.io_dict["in"]["input_ligand_pdbqt_path"] = check_input_path(
115 self.io_dict["in"]["input_ligand_pdbqt_path"],
116 "input_ligand_pdbqt_path",
117 self.out_log,
118 self.__class__.__name__,
119 )
120 self.io_dict["in"]["input_receptor_pdbqt_path"] = check_input_path(
121 self.io_dict["in"]["input_receptor_pdbqt_path"],
122 "input_receptor_pdbqt_path",
123 self.out_log,
124 self.__class__.__name__,
125 )
126 self.io_dict["in"]["input_box_path"] = check_input_path(
127 self.io_dict["in"]["input_box_path"],
128 "input_box_path",
129 self.out_log,
130 self.__class__.__name__,
131 )
132 self.io_dict["out"]["output_pdbqt_path"] = check_output_path(
133 self.io_dict["out"]["output_pdbqt_path"],
134 "output_pdbqt_path",
135 False,
136 self.out_log,
137 self.__class__.__name__,
138 )
139 self.io_dict["out"]["output_log_path"] = check_output_path(
140 self.io_dict["out"]["output_log_path"],
141 "output_log_path",
142 True,
143 self.out_log,
144 self.__class__.__name__,
145 )
147 def calculate_box(self, box_file_path):
148 with open(box_file_path, "r") as box_file:
149 for line in box_file:
150 line = line.rstrip(os.linesep)
151 if line.startswith("REMARK BOX CENTER"):
152 fields = line.split()
153 center = fields[3:6]
154 size = fields[-3:]
155 return list(
156 map(
157 str,
158 [
159 center[0],
160 center[1],
161 center[2],
162 size[0],
163 size[1],
164 size[2],
165 ],
166 )
167 )
168 return list(map(str, [0, 0, 0, 0, 0, 0]))
170 @launchlogger
171 def launch(self) -> int:
172 """Execute the :class:`AutoDockVinaRun_run <vina.autodock_vina_run.AutoDockVinaRun_run>` vina.autodock_vina_run.AutoDockVinaRun_run object."""
174 # check input/output paths and parameters
175 self.check_data_params(self.out_log, self.err_log)
177 # Setup Biobb
178 if self.check_restart():
179 return 0
180 self.stage_files()
182 # calculating box position and size
183 x0, y0, z0, sidex, sidey, sidez = self.calculate_box(
184 self.io_dict["in"]["input_box_path"]
185 )
187 # in case ligand or receptor end with END, remove last line
188 # check_input_autodock(self.io_dict["in"]["input_ligand_pdbqt_path"], self.out_log)
189 # check_input_autodock(self.io_dict["in"]["input_receptor_pdbqt_path"], self.out_log)
191 # create cmd
192 self.cmd = [
193 self.binary_path,
194 "--ligand",
195 self.stage_io_dict["in"]["input_ligand_pdbqt_path"],
196 "--receptor",
197 self.stage_io_dict["in"]["input_receptor_pdbqt_path"],
198 "--center_x=" + x0,
199 "--center_y=" + y0,
200 "--center_z=" + z0,
201 "--size_x=" + sidex,
202 "--size_y=" + sidey,
203 "--size_z=" + sidez,
204 "--cpu",
205 str(self.cpu),
206 "--exhaustiveness",
207 str(self.exhaustiveness),
208 "--num_modes",
209 str(self.num_modes),
210 "--min_rmsd",
211 str(self.min_rmsd),
212 "--energy_range",
213 str(self.energy_range),
214 "--out",
215 self.stage_io_dict["out"]["output_pdbqt_path"],
216 "--verbosity",
217 "1",
218 ">",
219 self.stage_io_dict["out"]["output_log_path"],
220 ]
222 # Run Biobb block
223 self.run_biobb()
225 # Copy files to host
226 self.copy_to_host()
228 # remove temporary folder(s)
229 # self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
230 self.remove_tmp_files()
232 self.check_arguments(output_files_created=True, raise_exception=False)
234 return self.return_code
237def autodock_vina_run(
238 input_ligand_pdbqt_path: str,
239 input_receptor_pdbqt_path: str,
240 input_box_path: str,
241 output_pdbqt_path: str,
242 output_log_path: Optional[str] = None,
243 properties: Optional[dict] = None,
244 **kwargs,
245) -> int:
246 """Execute the :class:`AutoDockVinaRun <vina.autodock_vina_run.AutoDockVinaRun>` class and
247 execute the :meth:`launch() <vina.autodock_vina_run.AutoDockVinaRun.launch>` method."""
249 return AutoDockVinaRun(
250 input_ligand_pdbqt_path=input_ligand_pdbqt_path,
251 input_receptor_pdbqt_path=input_receptor_pdbqt_path,
252 input_box_path=input_box_path,
253 output_pdbqt_path=output_pdbqt_path,
254 output_log_path=output_log_path,
255 properties=properties,
256 **kwargs,
257 ).launch()
259 autodock_vina_run.__doc__ = AutoDockVinaRun.__doc__
262def main():
263 """Command line execution of this building block. Please check the command line documentation."""
264 parser = argparse.ArgumentParser(
265 description="Prepares input ligand for an Autodock Vina Virtual Screening.",
266 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
267 )
268 parser.add_argument("--config", required=False, help="Configuration file")
270 # Specific args of each building block
271 required_args = parser.add_argument_group("required arguments")
272 required_args.add_argument(
273 "--input_ligand_pdbqt_path",
274 required=True,
275 help="Path to the input PDBQT ligand. Accepted formats: pdbqt.",
276 )
277 required_args.add_argument(
278 "--input_receptor_pdbqt_path",
279 required=True,
280 help="Path to the input PDBQT receptor. Accepted formats: pdbqt.",
281 )
282 required_args.add_argument(
283 "--input_box_path",
284 required=True,
285 help="Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb.",
286 )
287 required_args.add_argument(
288 "--output_pdbqt_path",
289 required=True,
290 help="Path to the output PDBQT file. Accepted formats: pdbqt.",
291 )
292 parser.add_argument(
293 "--output_log_path",
294 required=False,
295 help="Path to the log file. Accepted formats: log.",
296 )
298 args = parser.parse_args()
299 args.config = args.config or "{}"
300 properties = settings.ConfReader(config=args.config).get_prop_dic()
302 # Specific call of each building block
303 autodock_vina_run(
304 input_ligand_pdbqt_path=args.input_ligand_pdbqt_path,
305 input_receptor_pdbqt_path=args.input_receptor_pdbqt_path,
306 input_box_path=args.input_box_path,
307 output_pdbqt_path=args.output_pdbqt_path,
308 output_log_path=args.output_log_path,
309 properties=properties,
310 )
313if __name__ == "__main__":
314 main()