Converter API

docksuitex.utils.converter

Format conversion utilities for DockSuiteX.

convert

convert(
    input: Union[str, Path, list[Union[str, Path]]],
    output_format: str,
    gen3d: bool = False,
    split: bool = False,
    output_dir: Optional[Union[str, Path]] = None,
    extra_args: Optional[list[str]] = None,
) -> Union[Path, list[Path]]

Convert molecular file(s) from one format to another using Open Babel.

Supports single files, lists of file paths, or a directory path. The output filename is automatically derived by replacing the input extension with the specified output_format.

Parameters:

Name	Type	Description	Default
input	str | Path | list	Path to the input file, a list of paths, or a directory containing molecular files.	required
output_format	str	The target format identifier (e.g. "sdf", "pdbqt").	required
gen3d	bool	Generate 3D coordinates. Essential when converting from SMILES or other 2D/text formats. Defaults to False.	False
split	bool	Split multi-molecule/model files into individual files. Appends suffixes (1, 2, 3...) to the output filename. Defaults to False.	False
output_dir	str | Path	Directory to save the converted files. If not provided, files are saved in the same directory as the input.	None
extra_args	list[str]	Additional command-line arguments passed directly to Open Babel (e.g. ["-h", "--minimize"]).	None

Returns:

Type	Description
Union[Path, list[Path]]	Path | list[Path]: Path to the created output file (single input) or a list of paths (batch input).

Raises:

Type	Description
FileNotFoundError	If input files or Open Babel executable are missing.
RuntimeError	If the Open Babel conversion fails.

get_supported_formats

get_supported_formats() -> dict[str, str]

Query Open Babel for all supported file formats.

Returns:

Type	Description
dict[str, str]	dict[str, str]: Mapping of format identifier to description.

Raises:

Type	Description
FileNotFoundError	If the Open Babel executable is not found.
RuntimeError	If Open Babel fails to list formats.