Fixes the import paths for the internal imports.

openfold/features/data_pipeline.py

@@ -3,9 +3,9 @@ import os
 import numpy as np
 from typing import Mapping, Optional, Sequence
 
-from features import templates, parsers
-from features.tools import jackhmmer, hhblits, hhsearch
-from np import residue_constants
+from openfold.features import templates, parsers
+from openfold.features.tools import jackhmmer, hhblits, hhsearch
+from openfold.np import residue_constants
 
 FeatureDict = Mapping[str, np.ndarray]
 

openfold/features/data_transforms.py

@@ -6,7 +6,7 @@ import torch
 from operator import add
 
 from config import NUM_RES, NUM_EXTRA_SEQ, NUM_TEMPLATES, NUM_MSA_SEQ
-from np import residue_constants
+from openfold.np import residue_constants
 
 MSA_FEATURE_NAMES = [
     'msa', 'deletion_matrix', 'msa_mask', 'msa_row_mask', 'bert_mask', 'true_msa'

openfold/features/feature_pipeline.py

@@ -5,7 +5,7 @@ import torch
 from typing import Mapping, Tuple, List, Optional, Dict, Sequence
 import numpy as np
 
-from features import input_pipeline
+from openfold.features import input_pipeline
 
 FeatureDict = Mapping[str, np.ndarray]
 TensorDict = Dict[str, torch.Tensor]

openfold/features/input_pipeline.py

 import torch
 
-from features import data_transforms
+from openfold.features import data_transforms
 
 
 def nonensembled_transform_fns(data_config):

openfold/features/templates.py

@@ -10,9 +10,9 @@ from absl import logging
 
 import numpy as np
 
-from features import parsers, mmcif_parsing
-from features.tools import kalign
-from np import residue_constants
+from openfold.features import parsers, mmcif_parsing
+from openfold.features.tools import kalign
+from openfold.np import residue_constants
 
 
 class Error(Exception):

openfold/features/tools/hhblits.py

@@ -8,7 +8,7 @@ from typing import Any, Mapping, Optional, Sequence
 from absl import logging
 
 # Internal import (7716).
-from features.tools import utils
+from openfold.features.tools import utils
 
 _HHBLITS_DEFAULT_P = 20
 _HHBLITS_DEFAULT_Z = 500

openfold/features/tools/hhsearch.py

@@ -9,7 +9,7 @@ from absl import logging
 
 
 # Internal import (7716).
-from features.tools import utils
+from openfold.features.tools import utils
 
 
 class HHSearch:

openfold/features/tools/jackhmmer.py

@@ -12,7 +12,7 @@ from absl import logging
 
 
 # Internal import (7716).
-from features.tools import utils
+from openfold.features.tools import utils
 
 
 class Jackhmmer:

openfold/features/tools/kalign.py

@@ -6,7 +6,7 @@ from typing import Sequence
 
 from absl import logging
 
-from features.tools import utils
+from openfold.features.tools import utils
 
 
 def _to_a3m(sequences: Sequence[str]) -> str: