AF3 MmcifObject类解读

AlphaFold3 中 MmcifObject类 是 解析 mmCIF 文件的核心数据结构，用于存储解析后的蛋白质结构信息，包含PDB 头部信息、Biopython 解析的结构、链序列信息等。

下面代码包含 Monomer 、AtomSite、ResiduePosition、ResidueAtPosition、 MmcifObject以及ParsingResult数据类的定义。

源代码：

# Type aliases:
ChainId = str
PdbHeader = Mapping[str, Any]
PdbStructure = PDB.Structure.Structure
SeqRes = str
MmCIFDict = Mapping[str, Sequence[str]]


@dataclasses.dataclass(frozen=True)
class Monomer:
    id: str
    num: int


# Note - mmCIF format provides no guarantees on the type of author-assigned
# sequence numbers. They need not be integers.
@dataclasses.dataclass(frozen=True)
class AtomSite:
    residue_name: str
    author_chain_id: str
    mmcif_chain_id: str
    author_seq_num: str
    mmcif_seq_num: int
    insertion_code: str
    hetatm_atom: str
    model_num: int


# Used to map SEQRES index to a residue in the structure.
@dataclasses.dataclass(frozen=True)
class ResiduePosition:
    chain_id: str
    residue_number: int
    insertion_code: str


@dataclasses.dataclass(frozen=True)
class ResidueAtPosition:
    position: Optional[ResiduePosition]
    name: str
    is_missing: bool
    hetflag: str


@dataclasses.dataclass(frozen=True)
class MmcifObject:
    """Representation of a parsed mmCIF file.

    Contains:
      file_id: A meaningful name, e.g. a pdb_id. Should be unique amongst all
        files being processed.
      header: Biopython header.
      structure: Biopython structure.
      chain_to_seqres: Dict mapping chain_id to 1 letter amino acid sequence. E.g.
        {'A': 'ABCDEFG'}
      seqres_to_structure: Dict; for each chain_id contains a mapping between
        SEQRES index and a ResidueAtPosition. e.g. {'A': {0: ResidueAtPosition,
                                                          1: ResidueAtPosition,
                                                          ...}}
      raw_string: The raw string used to construct the MmcifObject.
    """

    file_id: str
    header: PdbHeader
    structure: PdbStructure
    chain_to_seqres: Mapping[ChainId, SeqRes]
    seqres_to_structure: Mapping[ChainId, Mapping[int, ResidueAtPosition]]
    raw_string: Any


@dataclasses.dataclass(frozen=True)
class ParsingResult:
    """Returned by the parse function.

    Contains:
      mmcif_object: A MmcifObject, may be None if no chain could be successfully
        parsed.
      errors: A dict mapping (file_id, chain_id) to any exception generated.
    """

    mmcif_object: Optional[MmcifObject]
    errors: Mapping[Tuple[str, str], Any]

代码解读：

类型别名 (Type Aliases)

类型别名是对复杂类型的简写，方便代码的可读性和维护。

ChainId = str  
PdbHeader = Mapping[str, Any]  
PdbStructure = PDB.Structure.Structure  
SeqRes = str  
MmCIFDict = Mapping[str, Sequence[str]]  

• ChainId = str
  • 表示蛋白质链的 ID，例如 "A"、"B"。
• PdbHeader = Mapping[str, Any]
  • 表