Restore missing license notices

openfold/features/data_pipeline.py → openfold/data/data_pipeline.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import os
 import datetime
+from typing import Mapping, Optional, Sequence, Any
 
 import numpy as np
-from typing import Mapping, Optional, Sequence, Any
 
-from openfold.features import templates, parsers, mmcif_parsing
-from openfold.features.np import jackhmmer, hhblits, hhsearch
-from openfold.features.np.utils import to_date
+from openfold.data import templates, parsers, mmcif_parsing
+from openfold.data.tools import jackhmmer, hhblits, hhsearch
+from openfold.data.tools.utils import to_date
 from openfold.np import residue_constants
 
 
@@ -286,7 +301,7 @@ class DataPipeline:
                 alignments['mgnify_deletion_matrix']
             )
         )
-        return {**sequence_features, **msa_features, **templates_result.features}
+        return {**sequence_features, **msa_features, **templates_result.data}
 
     def process_mmcif(self,
         mmcif: mmcif_parsing.MmcifObject, # parsing is expensive, so no path
@@ -333,4 +348,4 @@ class DataPipeline:
             )
         )
 
-        return {**mmcif_feats, **templates_result.features, **msa_features}
+        return {**mmcif_feats, **templates_result.data, **msa_features}

openfold/features/data_transforms.py → openfold/data/data_transforms.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import itertools
 from functools import reduce
+from operator import add
 
 import numpy as np
 import torch
-from operator import add
 
 from openfold.config import NUM_RES, NUM_EXTRA_SEQ, NUM_TEMPLATES, NUM_MSA_SEQ
-from openfold.np import residue_constants as rc
+from openfold.tools import residue_constants as rc
 from openfold.utils.affine_utils import T
 from openfold.utils.tensor_utils import tree_map, tensor_tree_map, batched_gather
 

openfold/features/feature_pipeline.py → openfold/data/feature_pipeline.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 import copy
+from typing import Mapping, Tuple, List, Optional, Dict, Sequence
 
 import ml_collections
-import torch
-from typing import Mapping, Tuple, List, Optional, Dict, Sequence
 import numpy as np
+import torch
+
+from openfold.data import input_pipeline
 
-from openfold.features import input_pipeline
 
 FeatureDict = Mapping[str, np.ndarray]
 TensorDict = Dict[str, torch.Tensor]
 
-
 def np_to_tensor_dict(
     np_example: Mapping[str, np.ndarray],
     features: Sequence[str],

openfold/features/input_pipeline.py → openfold/data/input_pipeline.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from functools import partial
+
 import torch
 
-from openfold.features import data_transforms
+from openfold.data import data_transforms
 
 
 def nonensembled_transform_fns(common_cfg, mode_cfg):

openfold/features/mmcif_parsing.py → openfold/data/mmcif_parsing.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """Parses the mmCIF file format."""
 import collections
 import dataclasses

openfold/features/parsers.py → openfold/data/parsers.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """Functions for parsing various file formats."""
 import collections
 import dataclasses
@@ -5,8 +20,8 @@ import re
 import string
 from typing import Dict, Iterable, List, Optional, Sequence, Tuple
 
-DeletionMatrix = Sequence[Sequence[int]]
 
+DeletionMatrix = Sequence[Sequence[int]]
 
 @dataclasses.dataclass(frozen=True)
 class TemplateHit:

openfold/features/templates.py → openfold/data/templates.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """Functions for getting templates and calculating template features."""
 import dataclasses
 import datetime
@@ -10,9 +25,9 @@ from typing import Any, Dict, Mapping, Optional, Sequence, Tuple
 
 import numpy as np
 
-from openfold.features import parsers, mmcif_parsing
-from openfold.features.np import kalign
-from openfold.features.np.utils import to_date
+from openfold.data import parsers, mmcif_parsing
+from openfold.data.tools import kalign
+from openfold.data.tools.utils import to_date
 from openfold.np import residue_constants
 
 

openfold/features/np/hhblits.py → openfold/data/tools/hhblits.py

-"""Library to run HHblits from Python."""
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
+"""Library to run HHblits from Python."""
 import glob
+import logging
 import os
 import subprocess
 from typing import Any, Mapping, Optional, Sequence
 
-from absl import logging
-
+from openfold.data.tools import utils
 
-from openfold.features.np import utils
 
 _HHBLITS_DEFAULT_P = 20
 _HHBLITS_DEFAULT_Z = 500

openfold/features/np/hhsearch.py → openfold/data/tools/hhsearch.py

-"""Library to run HHsearch from Python."""
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
+"""Library to run HHsearch from Python."""
 import glob
+import logging
 import os
 import subprocess
 from typing import Sequence
 
-from absl import logging
-
-
-from openfold.features.np import utils
+from openfold.data.np import utils
 
 
 class HHSearch:

openfold/features/np/jackhmmer.py → openfold/data/tools/jackhmmer.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 """Library to run Jackhmmer from Python."""
 
@@ -9,7 +23,7 @@ import subprocess
 from typing import Any, Callable, Mapping, Optional, Sequence
 from urllib import request
 
-from openfold.features.np import utils
+from openfold.data.tools import utils
 
 
 class Jackhmmer:

openfold/features/np/kalign.py → openfold/data/tools/kalign.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 """A Python wrapper for Kalign."""
 import os
@@ -6,7 +20,7 @@ from typing import Sequence
 
 from absl import logging
 
-from openfold.features.np import utils
+from openfold.data.tools import utils
 
 
 def _to_a3m(sequences: Sequence[str]) -> str:

openfold/features/np/utils.py → openfold/data/tools/utils.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 """Common utilities for data pipeline tools."""
 import contextlib
 import datetime
+import logging
 import shutil
 import tempfile
 import time
 from typing import Optional
 
-from absl import logging
-
 
 @contextlib.contextmanager
 def tmpdir_manager(base_dir: Optional[str] = None):

run_pretrained_openfold.py

@@ -16,6 +16,7 @@
 import argparse
 from datetime import date
 import logging
+import numpy as np
 import os
 
 # A hack to get OpenMM and PyTorch to peacefully coexist
@@ -24,15 +25,11 @@ os.environ["OPENMM_DEFAULT_PLATFORM"] = "OpenCL"
 import pickle
 import random
 import sys
-
-from openfold.features import templates, feature_pipeline, data_pipeline
-
 import time
-
-import numpy as np
 import torch
 
 from openfold.config import model_config
+from openfold.data import templates, feature_pipeline, data_pipeline
 from openfold.model.model import AlphaFold
 from openfold.np import residue_constants, protein
 import openfold.np.relax.relax as relax