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AlphaFold3 中mmcif_parsing模块的parse函数的主要作用是 解析 mmCIF 文件内容，提取蛋白质结构信息，转换为 MmcifObject，并返回解析结果。

源代码：

@functools.lru_cache(16, typed=False)
def parse(*, file_id: str, mmcif_string: str, catch_all_errors: bool = True
) -> ParsingResult:"""Entry point, parses an mmcif_string.Args:file_id: A string identifier for this file. Should be unique within thecollection of files being processed.mmcif_string: Contents of an mmCIF file.catch_all_errors: If True, all exceptions are caught and error messages arereturned as part of the ParsingResult. If False exceptions will be allowedto propagate.Returns:A ParsingResult."""errors = {}try:parser = PDB.MMCIFParser(QUIET=True)handle = io.StringIO(mmcif_string)full_structure = parser.get_structure("", handle)first_model_structure = _get_first_model(full_structure)# Extract the _mmcif_dict from the parser, which contains useful fields not# reflected in the Biopython structure.parsed_info = parser._mmcif_dict  # pylint:disable=protected-access# Ensure all values are lists, even if singletons.for key, value in parsed_info.items():if not isinstance(value, list):parsed_info[key] = [value]header = _get_header(parsed_info)# Determine the protein chains, and their start numbers according to the# internal mmCIF numbering scheme (likely but not guaranteed to be 1).valid_chains = _get_protein_chains(parsed_info=parsed_info)if not valid_chains:return ParsingResult(None, {(file_id, ""): "No protein chains found in this file."})seq_start_num = {chain_id: min([monomer.num for monomer in seq])for chain_id, seq in valid_chains.items()}# Loop over the atoms for which we have coordinates. Populate two mappings:# -mmcif_to_author_chain_id (maps internal mmCIF chain ids to chain ids used# the authors / Biopython).# -seq_to_structure_mappings (maps idx into sequence to ResidueAtPosition).mmcif_to_author_chain_id = {}seq_to_structure_mappings = {}for atom in _get_atom_site_list(parsed_info):if atom.model_num != "1":# We only process the first model at the moment.continuemmcif_to_author_chain_id[atom.mmcif_chain_id] = atom.author_chain_idif atom.mmcif_chain_id in valid_chains:hetflag = " "if atom.hetatm_atom == "HETATM":# Water atoms are assigned a special hetflag