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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 trainingCompared to OpenFoldDataModule, OpenFoldMultimerDataModulerequires 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_pathself.training_mode = self.train_data_dir is not Noneself.val_mmcif_data_cache_path = val_mmcif_data_cache_pathdef 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