rcsb-embedding-model 0.0.34__tar.gz → 0.0.35__tar.gz

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  1. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/PKG-INFO +1 -1
  2. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/pyproject.toml +1 -1
  3. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py +2 -2
  4. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/.dockerignore +0 -0
  5. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/.github/workflows/_workflow-docker.yaml +0 -0
  6. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/.github/workflows/publish.yaml +0 -0
  7. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/.gitignore +0 -0
  8. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/Dockerfile +0 -0
  9. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/LICENSE.md +0 -0
  10. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/README.md +0 -0
  11. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/assets/embedding-model-architecture.png +0 -0
  12. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/examples/esm_embeddings.py +0 -0
  13. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/__init__.py +0 -0
  14. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/cli/args_utils.py +0 -0
  15. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/cli/inference.py +0 -0
  16. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/esm_prot_from_structure.py +0 -0
  17. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py +0 -0
  18. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py +0 -0
  19. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/residue_embedding_from_structure.py +0 -0
  20. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py +0 -0
  21. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/inference/assembly_inferece.py +0 -0
  22. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/inference/chain_inference.py +0 -0
  23. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/inference/esm_inference.py +0 -0
  24. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/inference/structure_inference.py +0 -0
  25. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/model/layers.py +0 -0
  26. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/model/residue_embedding_aggregator.py +0 -0
  27. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/modules/chain_module.py +0 -0
  28. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/modules/esm_module.py +0 -0
  29. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/modules/structure_module.py +0 -0
  30. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/rcsb_structure_embedding.py +0 -0
  31. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/types/api_types.py +0 -0
  32. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/utils/data.py +0 -0
  33. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/utils/model.py +0 -0
  34. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/utils/structure_parser.py +0 -0
  35. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/utils/structure_provider.py +0 -0
  36. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/writer/batch_writer.py +0 -0
  37. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/embeddings/1acb.A.pt +0 -0
  38. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/embeddings/1acb.B.pt +0 -0
  39. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/embeddings/2uzi.A.pt +0 -0
  40. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/embeddings/2uzi.B.pt +0 -0
  41. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/embeddings/2uzi.C.pt +0 -0
  42. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/pdb/1acb.cif +0 -0
  43. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/pdb/2uzi.cif +0 -0
  44. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/src_stream/assembly-complete-test.csv +0 -0
  45. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/src_stream/instance-complete-test.csv +0 -0
  46. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/resources/src_stream/instance.csv +0 -0
  47. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/test_cli_inference.py +0 -0
  48. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/test_embedding_model.py +0 -0
  49. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/test_inference.py +0 -0
  50. {rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/tests/test_remote_inference.py +0 -0
{rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/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: 0.0.34
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+ Version: 0.0.35
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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
{rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/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 = "0.0.34"
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+ version = "0.0.35"
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  authors = [
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  { name="Joan Segura", email="joan.segura@rcsb.org" },
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  ]
{rcsb_embedding_model-0.0.34 → rcsb_embedding_model-0.0.35}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py RENAMED
@@ -72,9 +72,9 @@ class EsmProtFromChain(Dataset):
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  for atom_ch in chain_iter(structure):
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  if len(atom_ch) == 0:
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  raise IOError(f"No atoms were found in structure chain {src_name}.{chain_id}")
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- atom_ch = filter_residues(atom_ch)
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- atom_ch = rename_atom_attr(atom_ch)
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  try:
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+ atom_ch = filter_residues(atom_ch)
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+ atom_ch = rename_atom_attr(atom_ch)
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  protein_chain = ProteinChain.from_atomarray(atom_ch)
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  protein_chain = ESMProtein.from_protein_chain(protein_chain)
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  except Exception as e: