Run molecular docking with AutoDock Vina — run

This function runs molecular docking using AutoDock Vina.

Usage

run_vina(
  receptor = NULL,
  ligand = NULL,
  center = NULL,
  size = NULL,
  config_paths = NULL,
  exhaustiveness = 8,
  output_dir = "docked",
  logs_dir = "logs",
  vina_path = NULL,
  seed = 12345,
  cpu = NULL
)

Arguments

receptor: Path to receptor PDBQT file (only for direct mode)
ligand: Path to ligand PDBQT file (only for direct mode)
center: Numeric vector of length 3 for box center (x,y,z) (only for direct mode)
size: Numeric vector of length 3 for box size (x,y,z) (only for direct mode)
config_paths: Character vector of paths to config files or directories containing config files
exhaustiveness: Integer, search intensity, default 8 (only for direct mode)
output_dir: Character, output directory for docked files, default "docked"
logs_dir: Character, output directory for log files, default "logs"
vina_path: Character, path to vina executable, default NULL
seed: Integer, random seed for reproducibility, default 12345
cpu: Integer, number of CPU cores to use for parallel computation, default NULL (auto-detect)

Examples

if (FALSE) { # \dontrun{
# Run molecular docking using AutoDock Vina
run_vina(
  config_paths = "configs",
  output_dir = "docked",
  logs_dir = "logs"
)
} # }