AF3 _build_query_to_hit_index_mapping函数解读

AlphaFold3 中templates模块的_build_query_to_hit_index_mapping函数是将原始查询序列（original_query_sequence）中的索引与hit 序列（hit_sequence）中的索引进行映射。

在蛋白质序列比对（如 HHsearch）中，hit 是与查询序列部分匹配的区域。由于存在缺口（-）和部分比对，该函数修正索引，使得可以将原始序列的每个氨基酸位置正确映射到 hit 序列中。

该函数输入参数主要来自 HHsearch/HMMsearch 解析器 生成TemplateHit数据，返回的索引映射map可以用于提取模版特征（_extract_template_features函数参数）。

源代码：

def _build_query_to_hit_index_mapping(
        hit_query_sequence: str,
        hit_sequence: str,
        indices_hit: Sequence[int],
        indices_query: Sequence[int],
        original_query_sequence: str,
) -> Mapping[int, int]:
    """Gets mapping from indices in original query sequence to indices in the hit.

    hit_query_sequence and hit_sequence are two aligned sequences containing gap
    characters. hit_query_sequence contains only the part of the original query
    sequence that matched the hit. When interpreting the indices from the .hhr, we
    need to correct for this to recover a mapping from original query sequence to
    the hit sequence.

    Args:
        hit_query_sequence: The portion of the query sequence that is in the .hhr
            hit
        hit_sequence: The portion of the hit sequence that is in the .hhr