rcsb-embedding-model 0.0.23__tar.gz → 0.0.25__tar.gz

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  1. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/PKG-INFO +2 -2
  2. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/README.md +1 -1
  3. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/pyproject.toml +1 -1
  4. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py +2 -1
  5. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/.github/workflows/_workflow-docker.yaml +0 -0
  6. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/.github/workflows/publish.yaml +0 -0
  7. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/.gitignore +0 -0
  8. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/Dockerfile +0 -0
  9. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/LICENSE.md +0 -0
  10. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/assets/embedding-model-architecture.png +0 -0
  11. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/examples/esm_embeddings.py +0 -0
  12. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/__init__.py +0 -0
  13. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/cli/args_utils.py +0 -0
  14. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/cli/inference.py +0 -0
  15. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/esm_prot_from_structure.py +0 -0
  16. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py +0 -0
  17. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py +0 -0
  18. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/residue_embedding_from_structure.py +0 -0
  19. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py +0 -0
  20. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/inference/assembly_inferece.py +0 -0
  21. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/inference/chain_inference.py +0 -0
  22. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/inference/esm_inference.py +0 -0
  23. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/inference/structure_inference.py +0 -0
  24. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/model/layers.py +0 -0
  25. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/model/residue_embedding_aggregator.py +0 -0
  26. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/modules/chain_module.py +0 -0
  27. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/modules/esm_module.py +0 -0
  28. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/modules/structure_module.py +0 -0
  29. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/rcsb_structure_embedding.py +0 -0
  30. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/types/api_types.py +0 -0
  31. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/utils/data.py +0 -0
  32. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/utils/model.py +0 -0
  33. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/utils/structure_parser.py +0 -0
  34. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/utils/structure_provider.py +0 -0
  35. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/writer/batch_writer.py +0 -0
  36. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/embeddings/1acb.A.pt +0 -0
  37. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/embeddings/1acb.B.pt +0 -0
  38. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/embeddings/2uzi.A.pt +0 -0
  39. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/embeddings/2uzi.B.pt +0 -0
  40. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/embeddings/2uzi.C.pt +0 -0
  41. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/pdb/1acb.cif +0 -0
  42. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/resources/pdb/2uzi.cif +0 -0
  43. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/test_embedding_model.py +0 -0
  44. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/test_inference.py +0 -0
  45. {rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/tests/test_remote_inference.py +0 -0
{rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/PKG-INFO 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: 0.0.23
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+ Version: 0.0.25
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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** 0.0.23
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+ **Version** 0.0.25
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  ## Overview
{rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/README.md RENAMED
@@ -1,6 +1,6 @@
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  # RCSB Embedding Model
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- **Version** 0.0.23
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+ **Version** 0.0.25
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  ## Overview
{rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "rcsb-embedding-model"
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- version = "0.0.23"
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+ version = "0.0.25"
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  authors = [
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  { name="Joan Segura", email="joan.segura@rcsb.org" },
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  ]
{rcsb_embedding_model-0.0.23 → rcsb_embedding_model-0.0.25}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py RENAMED
@@ -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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  )
@@ -72,7 +73,7 @@ class EsmProtFromChain(Dataset):
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  raise IOError(f"No atoms were found in structure chain {src_name}.{chain_id}")
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  protein_chain = ProteinChain.from_atomarray(rename_atom_ch(atom_ch))
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  return ESMProtein.from_protein_chain(protein_chain), item_name
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- raise IOError(f"No chain was found for structure {src_name}")
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+ raise IOError(f"No atoms were found in structure chain {src_name}.{chain_id}")
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  if __name__ == '__main__':