Prepare ligand files for molecular docking

This function processes molecule files to prepare them for molecular docking by converting them to PDBQT format using AutoDock Tools scripts.

Usage

prepare_ligand(
  mol_files,
  output_dir = "./",
  python_path = NULL,
  prepare_script = NULL,
  add_opts = "-A hydrogens"
)

Arguments

mol_files

Character vector of paths to molecule files (SDF, MOL, etc.)

output_dir

Character, output directory for prepared files, default "./"

python_path

Character, path to Python executable, default "python"

prepare_script

Character, path to prepare_ligand4.py script

add_opts

Character, additional options to pass to prepare_ligand4.py, default "-A hydrogens"

Value

Character vector of paths to successfully prepared PDBQT files

Examples

if (FALSE) { # \dontrun{
pdbqt_files <- prepare_ligand(sdf_files,
                              output_dir = "prepared",
                              prepare_script = "path/to/prepare_ligand4.py")
} # }