AF3 from_pdb_string和from_mmcif_string函数解读

AlphaFold3的from_pdb_string和from_mmcif_string函数分别用来解析蛋白质PDB和mmCIF 格式结构数据并转换为 Protein 数据类。它通过 Biopython 提供的 PDBParser 和 MMCIFParser 解析 PDB/mmCIF 文件，再通过调用_from_bio_structure函数从 Biopython 解析出的 Structure 提取 原子坐标、残基类型、B 因子等信息，最终返回一个 Protein 对象。

源代码：

def _from_bio_structure(structure: Structure, chain_id: Optional[str] = None
) -> Protein:"""Takes a Biopython structure and creates a `Protein` instance.WARNING: All non-standard residue types will be converted into UNK. Allnon-standard atoms will be ignored.Args:structure: Structure from the Biopython library.chain_id: If chain_id is specified (e.g. A), then only that chain is parsed.Otherwise all chains are parsed.Returns:A new `Protein` created from the structure contents.Raises:ValueError: If the number of models included in the structure is not 1.ValueError: If insertion code is detected at a residue."""models = list(structure.get_models())if len(models) != 1:raise ValueError('Only single model PDBs/mmCIFs are supported. Found'f' {len(models)} models.')model = models[0]atom_positions = []aatype = []atom_mask = []residue_index = []chain_ids = []b_factors = []for chain in model:if chain_id is not None and chain.id != chain_id:continuefor res in chain:if res.id[2] != ' ':raise ValueError(f'PDB/mmCIF contains an insertion code at chain {chain.id} and'f' residue index {res.id[1]}. These are not supported.')res_shortname = residue_constants.restype_3to1.get(res.resname, 'X')restype_idx = residue_constants.restype_order.get(res_shortname, residue_constants.restype_num)pos = np.zeros((residue_constants.atom_type_num, 3))mask = np.zeros((residue_constants.atom_type_num,))res_b_factors = np.zeros((residue_constants.atom_type_num,))for atom in res:if atom.name not in residue_constants.atom_types: