#!/usr/bin/env python3
"""Module containing the AutoDockVinaRun class and the command line interface."""
import argparse
import os
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger
from biobb_vs.vina.common import check_input_path, check_output_path
[docs]class AutoDockVinaRun(BiobbObject):
"""
| biobb_vs AutoDockVinaRun
| Wrapper of the AutoDock Vina software.
| 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.
Args:
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).
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).
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).
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).
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).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **cpu** (*int*) - (1) [1~1000|1] the number of CPUs to use.
* **exhaustiveness** (*int*) - (8) [1~10000|1] exhaustiveness of the global search (roughly proportional to time).
* **num_modes** (*int*) - (9) [1~1000|1] maximum number of binding modes to generate.
* **min_rmsd** (*int*) - (1) [1~1000|1] minimum RMSD between output poses.
* **energy_range** (*int*) - (3) [1~1000|1] maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
* **binary_path** (*string*) - ('vina') path to vina in your local computer.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Container path definition.
* **container_image** (*str*) - ('biocontainers/autodock-vina:v1.1.2-5b1-deb_cv1') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_vs.vina.autodock_vina_run import autodock_vina_run
prop = {
'binary_path': 'vina'
}
autodock_vina_run(input_ligand_pdbqt_path='/path/to/myLigand.pdbqt',
input_receptor_pdbqt_path='/path/to/myReceptor.pdbqt',
input_box_path='/path/to/myBox.pdb',
output_pdbqt_path='/path/to/newStructure.pdbqt',
output_log_path='/path/to/newLog.log',
properties=prop)
Info:
* wrapped_software:
* name: Autodock Vina
* version: >=1.2.3
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box_path, output_pdbqt_path,
output_log_path=None, properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_ligand_pdbqt_path": input_ligand_pdbqt_path, "input_receptor_pdbqt_path": input_receptor_pdbqt_path, "input_box_path": input_box_path},
"out": {"output_pdbqt_path": output_pdbqt_path, "output_log_path": output_log_path}
}
# Properties specific for BB
self.cpu = properties.get('cpu', 1)
self.exhaustiveness = properties.get('exhaustiveness', 8)
self.num_modes = properties.get('num_modes', 9)
self.min_rmsd = properties.get('min_rmsd', 1)
self.energy_range = properties.get('energy_range', 3)
self.binary_path = properties.get('binary_path', 'vina')
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.io_dict["in"]["input_ligand_pdbqt_path"] = check_input_path(self.io_dict["in"]["input_ligand_pdbqt_path"], "input_ligand_pdbqt_path", self.out_log, self.__class__.__name__)
self.io_dict["in"]["input_receptor_pdbqt_path"] = check_input_path(self.io_dict["in"]["input_receptor_pdbqt_path"], "input_receptor_pdbqt_path", self.out_log, self.__class__.__name__)
self.io_dict["in"]["input_box_path"] = check_input_path(self.io_dict["in"]["input_box_path"], "input_box_path", self.out_log, self.__class__.__name__)
self.io_dict["out"]["output_pdbqt_path"] = check_output_path(self.io_dict["out"]["output_pdbqt_path"], "output_pdbqt_path", False, self.out_log, self.__class__.__name__)
self.io_dict["out"]["output_log_path"] = check_output_path(self.io_dict["out"]["output_log_path"], "output_log_path", True, self.out_log, self.__class__.__name__)
[docs] def calculate_box(self, box_file_path):
with open(box_file_path, 'r') as box_file:
for line in box_file:
line = line.rstrip(os.linesep)
if line.startswith("REMARK BOX CENTER"):
fields = line.split()
center = fields[3:6]
size = fields[-3:]
return list(map(str, [center[0], center[1], center[2], size[0], size[1], size[2]]))
return list(map(str, [0, 0, 0, 0, 0, 0]))
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`AutoDockVinaRun_run <vina.autodock_vina_run.AutoDockVinaRun_run>` vina.autodock_vina_run.AutoDockVinaRun_run object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# calculating box position and size
x0, y0, z0, sidex, sidey, sidez = self.calculate_box(self.io_dict["in"]["input_box_path"])
# in case ligand or receptor end with END, remove last line
# check_input_autodock(self.io_dict["in"]["input_ligand_pdbqt_path"], self.out_log)
# check_input_autodock(self.io_dict["in"]["input_receptor_pdbqt_path"], self.out_log)
# create cmd
self.cmd = [self.binary_path,
'--ligand', self.stage_io_dict["in"]["input_ligand_pdbqt_path"],
'--receptor', self.stage_io_dict["in"]["input_receptor_pdbqt_path"],
'--center_x=' + x0, '--center_y=' + y0, '--center_z=' + z0,
'--size_x=' + sidex, '--size_y=' + sidey, '--size_z=' + sidez,
'--cpu', str(self.cpu),
'--exhaustiveness', str(self.exhaustiveness),
'--num_modes', str(self.num_modes),
'--min_rmsd', str(self.min_rmsd),
'--energy_range', str(self.energy_range),
'--out', self.stage_io_dict["out"]["output_pdbqt_path"],
'--verbosity', '1',
'>', self.stage_io_dict["out"]["output_log_path"]]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def autodock_vina_run(input_ligand_pdbqt_path: str, input_receptor_pdbqt_path: str, input_box_path: str, output_pdbqt_path: str, output_log_path: str = None, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`AutoDockVinaRun <vina.autodock_vina_run.AutoDockVinaRun>` class and
execute the :meth:`launch() <vina.autodock_vina_run.AutoDockVinaRun.launch>` method."""
return AutoDockVinaRun(input_ligand_pdbqt_path=input_ligand_pdbqt_path,
input_receptor_pdbqt_path=input_receptor_pdbqt_path,
input_box_path=input_box_path,
output_pdbqt_path=output_pdbqt_path,
output_log_path=output_log_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Prepares input ligand for an Autodock Vina Virtual Screening.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_ligand_pdbqt_path', required=True, help='Path to the input PDBQT ligand. Accepted formats: pdbqt.')
required_args.add_argument('--input_receptor_pdbqt_path', required=True, help='Path to the input PDBQT receptor. Accepted formats: pdbqt.')
required_args.add_argument('--input_box_path', required=True, help='Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb.')
required_args.add_argument('--output_pdbqt_path', required=True, help='Path to the output PDBQT file. Accepted formats: pdbqt.')
parser.add_argument('--output_log_path', required=False, help='Path to the log file. Accepted formats: log.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
autodock_vina_run(input_ligand_pdbqt_path=args.input_ligand_pdbqt_path,
input_receptor_pdbqt_path=args.input_receptor_pdbqt_path,
input_box_path=args.input_box_path,
output_pdbqt_path=args.output_pdbqt_path,
output_log_path=args.output_log_path,
properties=properties)
if __name__ == '__main__':
main()