Convert molecule file formats using OpenBabel — convert

This function converts molecular structure files between different formats using the OpenBabel chemical toolbox. It supports converting a single file, multiple files, or all files in a directory.

Usage

convert_molecule(
  input_file,
  input_format = NULL,
  output_file = NULL,
  output_format = NULL,
  output_dir = "converted",
  pattern = NULL,
  recursive = FALSE,
  obabel_path = NULL
)

Arguments

input_file: Character, path to the input molecule file, or a character vector of file paths, or a directory containing molecule files to convert
input_format: Character, format of the input file, default NULL (auto-detect from file extension)
output_file: Character, path to the output file, default NULL (auto-generate based on input file name)
output_format: Character, format for the output file, default NULL (auto-detect from output file extension)
output_dir: Character, directory to save output files, default converted
pattern: Character, file pattern to match when input_file is a directory, default NULL (all files)
recursive: Logical, whether to search recursively in directories, default FALSE
obabel_path: Character, path to OpenBabel executable, default NULL (uses GLUEDOCK_OBABEL_PATH environment variable)

Value

Character vector of paths to successfully converted files, or NULL if conversion failed

Examples

if (FALSE) { # \dontrun{
# Convert a single file
convert_molecule("ligand.sdf", output_format = "mol2")
} # }