AF3 OpenFoldMultimerDataModule类解读

AlphaFold3 data_modules 模块的 OpenFoldMultimerDataModule 类继承自OpenFoldDataModule 类，并且针对多聚体（multimer）蛋白质训练做了特化。在 OpenFoldMultimerDataModule 中，除了继承自 OpenFoldDataModule 的所有功能外，还额外要求提供与多聚体相关的数据缓存路径 (mmcif_data_cache_path)。

源代码：

class OpenFoldMultimerDataModule(OpenFoldDataModule):
    """
    Create a datamodule specifically for multimer training

    Compared to OpenFoldDataModule, OpenFoldMultimerDataModule
    requires mmcif_data_cache_path which is the product of 
    scripts/generate_mmcif_cache.py mmcif_data_cache_path should be 
    a file that record what chain(s) each mmcif file has 
    """

    def __init__(self,
                 config: mlc.ConfigDict,
                 template_mmcif_dir: str,
                 max_template_date: str,
                 train_data_dir: Optional[str] = None,
                 train_mmcif_data_cache_path: Optional[str] = None,
                 val_mmcif_data_cache_path: Optional[str] = None,
                 **kwargs):
        super(OpenFoldMultimerDataModule, self).__init__(config,
                                                         template_mmcif_dir,
                                                         max_template_date,
                                                         train_data_dir,
                                                         **kwargs)

        self.train_mmcif_data_cache_path = train_mmcif_data_cache_path
        self.training_mode = self.train_data_dir is not None
        self.val_mmcif_data_cache_path = val_mmcif_data_cache_path

    def setup(self, setup=None):
        # Most of the arguments are the same for the three datasets 
        dataset_gen = partial(OpenFoldSingleMultimerDataset,
                              template_mmcif_dir=self.template_mmcif_dir,
                              max_template_date=self.max_template_date,
                              config=self.config,
                              kalign_binary_path=self.kalign_binary_path,
                              template_release_dates_cache_path=self.template_release_dates_cache_path,
                              obsolete_pdbs_f