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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.
This commit is contained in:
Sachin Kadyan 2022-10-18 17:39:40 -04:00
parent 2ba07feb88
commit a6a467e09c
1 changed files with 4 additions and 1 deletions
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5
openfold/data/data_modules.py
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@ -186,7 +186,8 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
mmcif=mmcif_object, mmcif=mmcif_object,
alignment_dir=alignment_dir, alignment_dir=alignment_dir,
chain_id=chain_id, chain_id=chain_id,
alignment_index=alignment_index alignment_index=alignment_index,
seqemb_mode=self.config.seqemb_mode.enabled
) )
return data return data
@ -251,6 +252,7 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
chain_id=chain_id, chain_id=chain_id,
alignment_index=alignment_index, alignment_index=alignment_index,
_structure_index=structure_index, _structure_index=structure_index,
seqemb_mode=self.config.seqemb_mode.enabled,
) )
else: else:
raise ValueError("Extension branch missing") raise ValueError("Extension branch missing")
@ -260,6 +262,7 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
fasta_path=path, fasta_path=path,
alignment_dir=alignment_dir, alignment_dir=alignment_dir,
alignment_index=alignment_index, alignment_index=alignment_index,
seqemb_mode=self.config.seqemb_mode.enabled,
) )
if(self._output_raw): if(self._output_raw):