PyVina

A Python Module implemented for using the Vina suite of molecular docking software.

Tested using QuickVina 2.1, AutoDock Vina, QuickVina2 GPU, Vina GPU 2, QuickVina2 GPU 2.1, and Vina GPU 2.1.

Installation

• open terminal in project directory

• git clone https://github.com/Pixelatory/PyVina/

• pip install meeko (for MeekoLigandPreparator)

• Note: installation of Vina docking program is done separately.

Example Usage: QuickVina2 GPU 2.1 with CPU fallback

from PyVina.ligand_preparators import MeekoLigandPreparator
from PyVina.dock import VinaDocking
from PyVina.exceptions import OutOfGPUMemoryError
import os

ligand_preparator = MeekoLigandPreparator(print_output=False,
                                          timeout_duration=None,
                                          n_workers=os.cpu_count())

docking_module_gpu = VinaDocking("path/to/QuickVina2-GPU-2-1",
                                 "path/to/cleaned/receptor/pdbqt",
                                 [7.750, -14.556, 6.747],
                                 [20, 20, 20],
                                 keep_ligand_file=True,
                                 keep_config_file=True,
                                 keep_log_file=True,
                                 keep_output_file=True,
                                 ligand_preparation_fn=ligand_preparator,
                                 timeout_duration=None,
                                 gpu_ids=[0],
                                 additional_vina_args={"thread": "5000",
                                                       "opencl_binary_path": "path/to/QuickVina2-GPU-2.1"})

docking_module_cpu = VinaDocking("path/to/qvina2.1",
                                 "path/to/cleaned/receptor/pdbqt",
                                 [7.750, -14.556, 6.747],
                                 [20, 20, 20],
                                 keep_ligand_file=True,
                                 keep_config_file=True,
                                 keep_log_file=True,
                                 keep_output_file=True,
                                 ligand_preparation_fn=ligand_preparator,
                                 timeout_duration=None,
                                 gpu_ids=None,
                                 additional_vina_args={"cpu": os.cpu_count()})

try:
  print(docking_module_gpu(["CCO", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"]))
except OutOfGPUMemoryError:
  print(docking_module_cpu(["CCO", "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"]))

docking_module_cpu.delete_files()
docking_module_gpu.delete_files()