AutoParser

AutoParser 是解析化学文件的主要入口。它会根据文件扩展名自动选择合适的解析器。

The Entrypoint of MolOP

Parameters:

Name	Type	Description	Default
file_path	str	use regax to match files.	required
total_charge	int | None	forced charge of the molecule, if not given, will use the charge written in the file or 0.	None
total_multiplicity	int | None	forced multiplicity of the molecule, if not given, will use the charge written in the file or 1.	None
n_jobs	int	number of jobs to use, if -1, use cpu with default max number.	-1
only_extract_structure	bool	if True, only extract the structure, else extract the whole file.	False
only_last_frame	bool	if True, only extract the last frame, else extract all frames.	False
release_file_content	bool	if True, release the file content after parsing, else keep the file content in memory.	True
parser_detection	str	if “auto”, use the file extension to detect the parser, else use the given format id.	'auto'

Returns:

Type	Description
FileBatchModelDisk[FileDiskObj]	FileBatchParserDisk

How to use

Python

from molop import AutoParser

parser = AutoParser("/path/to/file")  # return FileBatchParserDisk with singlefile_parser
parser = AutoParser("/path/to/files/*.log")  # return FileBatchParserDisk

Source code in src/molop/io/__init__.py

Python

def AutoParser(
    file_path: str,
    *,
    total_charge: int | None = None,
    total_multiplicity: int | None = None,
    n_jobs: int = -1,
    only_extract_structure=False,
    only_last_frame=False,
    release_file_content: bool = True,
    parser_detection: str = "auto",
) -> FileBatchModelDisk["FileDiskObj"]:
    """
    The Entrypoint of MolOP

    Parameters:
        file_path (str):
            use regax to match files.
        total_charge (int | None):
            forced charge of the molecule, if not given, will use the charge written in the file or 0.
        total_multiplicity (int | None):
            forced multiplicity of the molecule, if not given, will use the charge written in the file or 1.
        n_jobs (int):
            number of jobs to use, if -1, use cpu with default max number.
        only_extract_structure (bool):
            if True, only extract the structure, else extract the whole file.
        only_last_frame (bool):
            if True, only extract the last frame, else extract all frames.
        release_file_content (bool):
            if True, release the file content after parsing, else keep the file content in memory.
        parser_detection (str):
            if "auto", use the file extension to detect the parser, else use the given format id.

    Returns:
        FileBatchParserDisk

    How to use
    ----------
    ```python
    from molop import AutoParser

    parser = AutoParser("/path/to/file")  # return FileBatchParserDisk with singlefile_parser
    parser = AutoParser("/path/to/files/*.log")  # return FileBatchParserDisk
    ```
    """
    if os.path.isfile(file_path) and os.path.exists(file_path):
        files = [file_path]
    else:
        base_path, pattern = split_path_pattern(file_path)
        files = [str(p) for p in base_path.glob(pattern)]
    return FileBatchParserDisk(n_jobs=n_jobs).parse(
        files,
        total_charge=total_charge,
        total_multiplicity=total_multiplicity,
        only_extract_structure=only_extract_structure,
        only_last_frame=only_last_frame,
        release_file_content=release_file_content,
        parser_detection=parser_detection,
    )