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CLAUDE.md
CONTRIBUTING.md
LICENSE.md
MANIFEST.in
README.md
TODO.md
mkdocs.yml
pyproject.toml
setup.py
uv.lock
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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
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archive/examples/configs/README.md
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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/layers/pairformer.py
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archive/nn/lightning/data/consolidated.py
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archive/nn/lightning/modules/consolidated_vae.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
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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/data/ramachandran_gmm.npz
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ciffy/polymer/__init__.py
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codegen/generate.py
codegen/monlib.py
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codegen/python_codegen.py
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codegen/residues.yaml
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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
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