rcsb-embedding-model 0.0.24__py3-none-any.whl → 0.0.26__py3-none-any.whl

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Files changed (9) hide show
  1. rcsb_embedding_model/dataset/esm_prot_from_chain.py +5 -1
  2. rcsb_embedding_model/inference/chain_inference.py +4 -1
  3. rcsb_embedding_model/inference/esm_inference.py +4 -1
  4. rcsb_embedding_model/inference/structure_inference.py +7 -2
  5. {rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/METADATA +2 -2
  6. {rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/RECORD +9 -9
  7. {rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/WHEEL +0 -0
  8. {rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/entry_points.txt +0 -0
  9. {rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/licenses/LICENSE.md +0 -0
rcsb_embedding_model/dataset/esm_prot_from_chain.py CHANGED
@@ -49,6 +49,7 @@ class EsmProtFromChain(Dataset):
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  src_stream,
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  header=None,
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  index_col=None,
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+ keep_default_na=False,
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  dtype=str,
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  names=EsmProtFromChain.COLUMNS
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  )
@@ -82,7 +83,10 @@ if __name__ == '__main__':
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  args = parser.parse_args()
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  dataset = EsmProtFromChain(
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- args.file_list
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+ src_stream=args.file_list,
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+ src_location=SrcLocation.file,
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+ structure_location=StructureLocation.remote,
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+ structure_format=StructureFormat.mmcif,
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  )
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  esm3 = ESM3.from_pretrained(
rcsb_embedding_model/inference/chain_inference.py CHANGED
@@ -1,3 +1,4 @@
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+ import torch
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  from torch.utils.data import DataLoader
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  from lightning import Trainer
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@@ -53,7 +54,9 @@ def predict(
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  )
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  )
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- aggregator_model = get_aggregator_model()
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+ aggregator_model = get_aggregator_model(
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+ device=torch.device("cpu")
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+ )
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  module = ChainModule(
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  model=aggregator_model
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  )
rcsb_embedding_model/inference/esm_inference.py CHANGED
@@ -1,3 +1,4 @@
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+ import torch
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  from torch.utils.data import DataLoader
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  from lightning import Trainer
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@@ -47,7 +48,9 @@ def predict(
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  collate_fn=lambda _: _
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  )
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- esm_model = get_residue_model()
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+ esm_model = get_residue_model(
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+ device=torch.device("cpu")
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+ )
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  module = EsmModule(
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  model=esm_model
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  )
rcsb_embedding_model/inference/structure_inference.py CHANGED
@@ -1,3 +1,4 @@
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+ import torch
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  from torch.utils.data import DataLoader
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  from lightning import Trainer
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@@ -46,8 +47,12 @@ def predict(
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  collate_fn=lambda _: _
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  )
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- res_model = get_residue_model()
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- aggregator_model = get_aggregator_model()
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+ res_model = get_residue_model(
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+ device=torch.device("cpu")
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+ )
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+ aggregator_model = get_aggregator_model(
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+ device=torch.device("cpu")
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+ )
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  module = StructureModule(
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  res_model=res_model,
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  aggregator_model=aggregator_model
{rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: rcsb-embedding-model
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- Version: 0.0.24
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+ Version: 0.0.26
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  Summary: Protein Embedding Model for Structure Search
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  Project-URL: Homepage, https://github.com/rcsb/rcsb-embedding-model
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  Project-URL: Issues, https://github.com/rcsb/rcsb-embedding-model/issues
@@ -17,7 +17,7 @@ Description-Content-Type: text/markdown
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  # RCSB Embedding Model
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- **Version** 0.0.24
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+ **Version** 0.0.26
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  ## Overview
{rcsb_embedding_model-0.0.24.dist-info → rcsb_embedding_model-0.0.26.dist-info}/RECORD RENAMED
@@ -2,16 +2,16 @@ rcsb_embedding_model/__init__.py,sha256=r3gLdeBIXkQEQA_K6QcRPO-TtYuAQSutk6pXRUE_
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  rcsb_embedding_model/rcsb_structure_embedding.py,sha256=dKp9hXQO0JAnO4SEfjJ_mG_jHu3UxAPguv6jkOjp-BI,4487
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  rcsb_embedding_model/cli/args_utils.py,sha256=7nP2q8pL5dWK_U7opxtWmoFcYVwasky6elHk-dASFaI,165
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  rcsb_embedding_model/cli/inference.py,sha256=tfMvHAhkUIzJ2RbTtQjq7eWmOUrSyVfH5bjTkCCSIS8,19500
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- rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=Dh8BVWVT5gdzJKYvQHMEnD8stpMTdvKK1yJVhCBI2bw,3702
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+ rcsb_embedding_model/dataset/esm_prot_from_chain.py,sha256=mYk3Xnm_QK25iyWGPyWRQLpNzpXfZcUbNUSLSXOJe7Q,3889
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  rcsb_embedding_model/dataset/esm_prot_from_structure.py,sha256=TeITPdi1uc3qLQ-Pgn807oH6eM0LYv-67RE50ZT4dLI,2551
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  rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py,sha256=worRiNqOJRjyr693TaillsS65bdTdGOoHfwyT9yE1O4,2866
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  rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py,sha256=JG4rrhziIUtdTmbuTbMbEYHrvlda4m5VWvdJXe_Sv3c,3449
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  rcsb_embedding_model/dataset/residue_embedding_from_structure.py,sha256=dxfUNcVmdl8LrtQf1UJQ4E79e7R9LRsL0fjsq2GJQRk,2796
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  rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py,sha256=ehHQuLI2TrE5l4_4n6p3e30i17O1pXW92KOCn7bGtcg,1274
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  rcsb_embedding_model/inference/assembly_inferece.py,sha256=8fPJjEXy1WsM5XB5U7KfdO5-Du6nEsawsaAjmWoXA9I,2329
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- rcsb_embedding_model/inference/chain_inference.py,sha256=YGSCEYQWQvew_UGhM6Ehqd77vPUWXt2XrQuCuQvjM0o,2872
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- rcsb_embedding_model/inference/esm_inference.py,sha256=EmLsP4a0nCQKPIaMNuzY1MZQ7YZuj15FBqymV6WZMfc,2493
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- rcsb_embedding_model/inference/structure_inference.py,sha256=VMjUZFj5zGnW7HB6-7rnuBrNhXby5yCQgQoiK9g_PDo,2498
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+ rcsb_embedding_model/inference/chain_inference.py,sha256=6f5wVzjtRtHU3BPMTe5k3nH_Nl440Am8BL8h1vmK1jI,2925
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+ rcsb_embedding_model/inference/esm_inference.py,sha256=rn6H43D8BYzMZbMu7UPsLYg2dgERmmpci5weNItrG5Q,2546
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+ rcsb_embedding_model/inference/structure_inference.py,sha256=0wqCW5wee_UQ8WJo9KG6SBHmosdNRzoJYEm7rMn4veA,2591
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  rcsb_embedding_model/model/layers.py,sha256=lhKaWC4gTS_T5lHOP0mgnnP8nKTPEOm4MrjhESA4hE8,743
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  rcsb_embedding_model/model/residue_embedding_aggregator.py,sha256=k3UW63Ax8DtjCMdD3O5xNxtyAu28l2n3-Ab6nS0atm0,1967
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  rcsb_embedding_model/modules/chain_module.py,sha256=KsZw2uagO4rpAKWv6ivqEMxIEzgtfQFliHV_vX8kqtc,435
@@ -23,8 +23,8 @@ rcsb_embedding_model/utils/model.py,sha256=xr3p02ohOgJ5UInwdIupN68Oq4yvNFhxobZRa
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  rcsb_embedding_model/utils/structure_parser.py,sha256=IWMQ8brlEMe6_ND-DBESOli8vlqHxladTssjbM9RSKw,2751
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  rcsb_embedding_model/utils/structure_provider.py,sha256=eWtxjkPpmRfmil_DKR1J6miaXR3lQ28DF5O0qrqSgGA,786
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  rcsb_embedding_model/writer/batch_writer.py,sha256=rTFNasB0Xp4-XCNTXKeEWZxSrb7lvZytoRldJUWn9Jg,3312
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- rcsb_embedding_model-0.0.24.dist-info/METADATA,sha256=SCMQPP_lMB1_udpJfSCZDl92Pm3GbBhtXpIj5PF8Dok,5310
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- rcsb_embedding_model-0.0.24.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- rcsb_embedding_model-0.0.24.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
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- rcsb_embedding_model-0.0.24.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
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- rcsb_embedding_model-0.0.24.dist-info/RECORD,,
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+ rcsb_embedding_model-0.0.26.dist-info/METADATA,sha256=eQ2PQmXlSEWkXQHW9dXQaPN-_YzcQq_tYGmGygT_WM4,5310
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+ rcsb_embedding_model-0.0.26.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ rcsb_embedding_model-0.0.26.dist-info/entry_points.txt,sha256=MK11jTIEmaV-x4CkPX5IymDaVs7Ky_f2xxU8BJVZ_9Q,69
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+ rcsb_embedding_model-0.0.26.dist-info/licenses/LICENSE.md,sha256=oUaHiKgfBkChth_Sm67WemEvatO1U0Go8LHjaskXY0w,1522
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+ rcsb_embedding_model-0.0.26.dist-info/RECORD,,