rcsb-embedding-model 0.0.30__tar.gz → 0.0.31__tar.gz
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- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/PKG-INFO +2 -1
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/pyproject.toml +2 -1
- rcsb_embedding_model-0.0.31/src/rcsb_embedding_model/__init__.py +9 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/cli/inference.py +18 -0
- rcsb_embedding_model-0.0.30/src/rcsb_embedding_model/__init__.py +0 -4
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.dockerignore +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.github/workflows/_workflow-docker.yaml +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.github/workflows/publish.yaml +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.gitignore +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/Dockerfile +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/LICENSE.md +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/README.md +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/assets/embedding-model-architecture.png +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/examples/esm_embeddings.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/cli/args_utils.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/esm_prot_from_structure.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/residue_embedding_from_structure.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/assembly_inferece.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/chain_inference.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/esm_inference.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/structure_inference.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/model/layers.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/model/residue_embedding_aggregator.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/modules/chain_module.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/modules/esm_module.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/modules/structure_module.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/rcsb_structure_embedding.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/types/api_types.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/data.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/model.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/structure_parser.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/structure_provider.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/writer/batch_writer.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/1acb.A.pt +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/1acb.B.pt +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/2uzi.A.pt +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/2uzi.B.pt +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/2uzi.C.pt +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/pdb/1acb.cif +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/pdb/2uzi.cif +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/src_stream/assembly-complete-test.csv +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/src_stream/instance-complete-test.csv +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/src_stream/instance.csv +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_cli_inference.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_embedding_model.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_inference.py +0 -0
- {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_remote_inference.py +0 -0
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Metadata-Version: 2.4
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Name: rcsb-embedding-model
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Version: 0.0.
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Version: 0.0.31
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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
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@@ -11,6 +11,7 @@ Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.10
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Requires-Dist: esm>=3.2.0
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Requires-Dist: importlib-metadata>=8.7.0
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Requires-Dist: lightning>=2.5.0
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Requires-Dist: typer>=0.15.0
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Description-Content-Type: text/markdown
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[project]
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name = "rcsb-embedding-model"
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version = "0.0.
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version = "0.0.31"
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authors = [
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{ name="Joan Segura", email="joan.segura@rcsb.org" },
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]
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license = "BSD-3-Clause"
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license-files = ["LICEN[CS]E*"]
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dependencies=[
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"importlib-metadata >= 8.7.0",
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"esm >= 3.2.0",
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"lightning >= 2.5.0",
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"typer >= 0.15.0"
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from importlib_metadata import version, PackageNotFoundError
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from rcsb_embedding_model.rcsb_structure_embedding import RcsbStructureEmbedding
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try:
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__version__ = version("rcsb-embedding-model")
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except PackageNotFoundError:
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__version__ = "0.0.0"
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__all__ = ["RcsbStructureEmbedding", "__version__"]
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import typer
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from rcsb_embedding_model import __version__
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from rcsb_embedding_model.cli.args_utils import arg_devices
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from rcsb_embedding_model.types.api_types import StructureFormat, Accelerator, SrcLocation, SrcProteinFrom, \
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StructureLocation, SrcAssemblyFrom, SrcTensorFrom, OutFormat
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def version_callback(value: bool):
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if value:
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typer.echo(f"{__version__}")
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raise typer.Exit()
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@app.callback()
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def main(
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version: bool = typer.Option(
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None,
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"--version",
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callback=version_callback,
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is_eager=True,
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help="Show the version and exit",
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)
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):
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pass
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if __name__ == "__main__":
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app()
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