Source code for vina.autodock_vina_run

#!/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 import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_common.command_wrapper import cmd_wrapper
from biobb_vs.vina.common import *


[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): * **vina_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. 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 = { 'vina_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: >=1.1.2 * 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) # 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.vina_path = properties.get('vina_path', 'vina') self.properties = properties # Check the properties self.check_properties(properties)
[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.vina_path, '--ligand', self.io_dict["in"]["input_ligand_pdbqt_path"], '--receptor', self.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, '--out', self.io_dict["out"]["output_pdbqt_path"], '--log', self.io_dict["out"]["output_log_path"]] fu.log('Executing AutoDock Vina', self.out_log, self.global_log) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() 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()