vina package

Submodules

vina.autodock_vina_run module

Module containing the AutoDockVinaRun class and the command line interface.

class vina.autodock_vina_run.AutoDockVinaRun(input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box_path, output_pdbqt_path, output_log_path=None, properties=None, **kwargs)

Bases: 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 software.

Parameters:

• input_ligand_pdbqt_path (str) – Path to the input PDBQT ligand. File type: input. Sample file. Accepted formats: pdbqt (edam:format_1476).

• input_receptor_pdbqt_path (str) –

  Path to the input PDBQT receptor. File type: input. Sample file. 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. Accepted formats: pdb (edam:format_1476).

• output_pdbqt_path (str) –

  Path to the output PDBQT file. File type: output. Sample file. Accepted formats: pdbqt (edam:format_1476).

• output_log_path (str) (Optional) –

  Path to the log file. File type: output. Sample file. 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.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

  • 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

calculate_box(box_file_path)

check_data_params(out_log, err_log)

Checks all the input/output paths and parameters

launch() → int

Execute the AutoDockVinaRun_run vina.autodock_vina_run.AutoDockVinaRun_run object.

vina.autodock_vina_run.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 = None, properties: dict | None = None, **kwargs) → int

Execute the AutoDockVinaRun class and execute the launch() method.

vina.autodock_vina_run.main()

Command line execution of this building block. Please check the command line documentation.