Added passing of sequence embedding mode flag from `data_modules` to `data_pipeline` for training and inference pipelines.

- Passing the config.data.seqemb_mode.enabled flag to the FASTA, PDB, and MMCIF data pipelines.

openfold/data/data_modules.py

@@ -186,7 +186,8 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
             mmcif=mmcif_object,
             alignment_dir=alignment_dir,
             chain_id=chain_id,
-            alignment_index=alignment_index
+            alignment_index=alignment_index,
+            seqemb_mode=self.config.seqemb_mode.enabled
         )
 
         return data
@@ -251,6 +252,7 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
                     chain_id=chain_id,
                     alignment_index=alignment_index,
                     _structure_index=structure_index,
+                    seqemb_mode=self.config.seqemb_mode.enabled,
                 )
             else:
                raise ValueError("Extension branch missing") 
@@ -260,6 +262,7 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
                 fasta_path=path,
                 alignment_dir=alignment_dir,
                 alignment_index=alignment_index,
+                seqemb_mode=self.config.seqemb_mode.enabled,
             )
 
         if(self._output_raw):