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)[source]

Bases: biobb_common.generic.biobb_object.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) –
    • 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:
calculate_box(box_file_path)[source]
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, properties: dict = None, **kwargs) → int[source]

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

vina.autodock_vina_run.main()[source]

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