General utilities

posebench.utils.utils.find_ligand_files(ligand_file_dir: Path, extension: str = 'sdf') → list[Path]

Find all ligand files in the specified directory.

Parameters:

• ligand_file_dir – The directory containing the ligand files.

• extension – The file extension of the ligand files.

Returns:

A list of Path objects representing the ligand files.

posebench.utils.utils.find_protein_files(protein_file_dir: Path, extension: str = 'pdb') → list[Path]

Find all protein files in the specified directory.

Parameters:

• protein_file_dir – The directory containing the protein files.

• extension – The file extension of the protein files.

Returns:

A list of Path objects representing the protein files.

posebench.utils.utils.run_command_with_timeout(command: str, timeout: int) → int

Run a command with a specified timeout in seconds.

Parameters:

• command – The command to run.

• timeout – The timeout for the command.

Returns:

The return code of the command.