vina package


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)[source]

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.
  • 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.

    • 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.


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'
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() int[source]

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[source]

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


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