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CLAUDE.md
CONTRIBUTING.md
LICENSE.md
MANIFEST.in
README.md
TODO.md
mkdocs.yml
pyproject.toml
setup.py
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archive/0001-Only-apply-gres-when-using-GPU-partition.patch
archive/ensemble.py
archive/extract.py
archive/flow.py
archive/examples/extend_chain.py
archive/examples/template_generation.py
archive/examples/configs/README.md
archive/examples/configs/inference_example.yaml
archive/examples/configs/inference_from_fasta.yaml
archive/examples/sweeps/flow.yaml
archive/examples/sweeps/latent_diffusion.yaml
archive/nn/pca_quantile.py
archive/nn/polymer.py
archive/nn/protocols.py
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archive/nn/io/save_load.py
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archive/nn/layers/causal.py
archive/nn/layers/mlp.py
archive/nn/layers/pairformer.py
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archive/nn/lightning/data/consolidated.py
archive/nn/lightning/data/flow.py
archive/nn/lightning/modules/consolidated_vae.py
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archive/nn/training/diagnostics.py
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archive/nn/training/split.py
archive/nn/vae/__init__.py
archive/nn/vae/losses.py
archive/scripts/EQUIVARIANT_REACTIVITY.md
archive/scripts/benchmark_compile.py
archive/scripts/benchmark_compile_fixed.py
archive/scripts/plot_predictions.py
archive/scripts/profile_transformer.py
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archive/tests/nn/test_polymer_flow.py
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ciffy/__init__.py
ciffy/_c.pyi
ciffy/_version.py
ciffy.egg-info/PKG-INFO
ciffy.egg-info/SOURCES.txt
ciffy.egg-info/dependency_links.txt
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ciffy/biochemistry/__init__.py
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ciffy/biochemistry/_generated_dihedraltypes.py
ciffy/biochemistry/_generated_elements.py
ciffy/biochemistry/_generated_linking.py
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ciffy/cli/__init__.py
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ciffy/data/ramachandran_gmm.npz
ciffy/data/rna_dihedrals.npz
ciffy/data/vdw_radii.json
ciffy/datasets/__init__.py
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ciffy/polymer/__init__.py
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codegen/__init__.py
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codegen/ccd.py
codegen/cli.py
codegen/config.py
codegen/elements.py
codegen/generate.py
codegen/monlib.py
codegen/names.py
codegen/python_codegen.py
codegen/residue.py
codegen/residues.yaml
codegen/validation.py
docs/api.md
docs/getting-started.md
docs/index.md
docs/guides/analysis.md
docs/guides/deep-learning.md
docs/guides/io.md
docs/guides/protein.md
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tests/__init__.py
tests/conftest.py
tests/test_imports.py
tests/utils.py
tests/analysis/__init__.py
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tests/nn/__init__.py
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tests/profiling/__init__.py
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