.gitignore
CONTRIBUTING.md
LICENSE.md
MANIFEST.in
README.md
TODO.md
mkdocs.yml
pyproject.toml
requirements.txt
setup.py
setup_cuda.py
test.cif
.github/workflows/docs.yml
.github/workflows/pypi-cuda.yml
.github/workflows/pypi.yml
ciffy/__init__.py
ciffy/ensemble.py
ciffy/polymer.py
ciffy/template.py
ciffy.egg-info/PKG-INFO
ciffy.egg-info/SOURCES.txt
ciffy.egg-info/dependency_links.txt
ciffy.egg-info/entry_points.txt
ciffy.egg-info/requires.txt
ciffy.egg-info/top_level.txt
ciffy/backend/__init__.py
ciffy/backend/autograd.py
ciffy/backend/core.py
ciffy/backend/cuda_ops.py
ciffy/backend/dispatch.py
ciffy/backend/graph.py
ciffy/backend/numpy_ops.py
ciffy/backend/ops.py
ciffy/backend/torch_ops.py
ciffy/biochemistry/__init__.py
ciffy/biochemistry/_generated_atoms.py
ciffy/biochemistry/_generated_dihedrals.py
ciffy/biochemistry/_generated_dihedraltypes.py
ciffy/biochemistry/_generated_elements.py
ciffy/biochemistry/_generated_molecule.py
ciffy/biochemistry/_generated_residues.py
ciffy/biochemistry/_generated_zmatrix.py
ciffy/biochemistry/constants.py
ciffy/biochemistry/linking.py
ciffy/cli/__init__.py
ciffy/cli/__main__.py
ciffy/data/ramachandran_gmm.npz
ciffy/data/rna_dihedrals.npz
ciffy/internal/__init__.py
ciffy/internal/coordinates.py
ciffy/io/__init__.py
ciffy/io/loader.py
ciffy/io/writer.py
ciffy/nn/__init__.py
ciffy/nn/base_trainer.py
ciffy/nn/dataset.py
ciffy/nn/embedding.py
ciffy/nn/experiment_runner.py
ciffy/nn/inference.py
ciffy/nn/inference_config.py
ciffy/nn/inference_runner.py
ciffy/nn/loggers.py
ciffy/nn/model_registry.py
ciffy/nn/protocols.py
ciffy/nn/training.py
ciffy/nn/transformer.py
ciffy/nn/vae/__init__.py
ciffy/nn/vae/decoder.py
ciffy/nn/vae/distributions.py
ciffy/nn/vae/encoder.py
ciffy/nn/vae/inference.py
ciffy/nn/vae/losses.py
ciffy/nn/vae/trainer.py
ciffy/nn/vae/vae.py
ciffy/operations/__init__.py
ciffy/operations/alignment.py
ciffy/operations/extract.py
ciffy/operations/metrics.py
ciffy/operations/reduction.py
ciffy/sampling/__init__.py
ciffy/sampling/backbone.py
ciffy/src/common.h
ciffy/src/error.h
ciffy/src/log.h
ciffy/src/lookup.h
ciffy/src/module.c
ciffy/src/module.h
ciffy/src/profile.h
ciffy/src/pyutils.c
ciffy/src/pyutils.h
ciffy/src/cif/io.c
ciffy/src/cif/io.h
ciffy/src/cif/parser.c
ciffy/src/cif/parser.h
ciffy/src/cif/registry.c
ciffy/src/cif/registry.h
ciffy/src/cif/writer.c
ciffy/src/cif/writer.h
ciffy/src/hash/atom.c
ciffy/src/hash/element.c
ciffy/src/hash/entity.c
ciffy/src/hash/ion.c
ciffy/src/hash/molecule.c
ciffy/src/hash/residue.c
ciffy/src/hash/reverse.h
ciffy/src/internal/batch.c
ciffy/src/internal/batch.cu
ciffy/src/internal/batch.h
ciffy/src/internal/bond_patterns.h
ciffy/src/internal/cuda_compat.h
ciffy/src/internal/cuda_module.cu
ciffy/src/internal/geometry.c
ciffy/src/internal/geometry.h
ciffy/src/internal/geometry_impl.h
ciffy/src/internal/graph.c
ciffy/src/internal/graph.h
ciffy/src/internal/internal_module.c
ciffy/src/internal/internal_module.h
ciffy/src/internal/primitives.h
ciffy/types/__init__.py
ciffy/types/dihedral.py
ciffy/types/molecule.py
ciffy/types/scale.py
ciffy/utils/__init__.py
ciffy/utils/enum_base.py
ciffy/utils/formatting.py
ciffy/utils/gmm.py
ciffy/utils/helpers.py
ciffy/visualize/__init__.py
ciffy/visualize/alignment.py
ciffy/visualize/chimerax.py
ciffy/visualize/defattr.py
ciffy/visualize/plots.py
codegen/__init__.py
codegen/c_codegen.py
codegen/ccd.py
codegen/cli.py
codegen/config.py
codegen/generate.py
codegen/names.py
codegen/python_codegen.py
codegen/residue.py
cuda/README.md
cuda/pyproject.toml
cuda/setup.py
cuda/ciffy/__init__.py
cuda/ciffy_cuda/__init__.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
docs/guides/rna.md
docs/guides/selection.md
docs/guides/visualization.md
examples/energy_minimization.py
examples/ramachandran_plot.py
examples/template_generation.py
examples/configs/inference_example.yaml
examples/configs/inference_from_fasta.yaml
scripts/check_api_docs.py
scripts/check_indices.py
scripts/fit_ramachandran_gmm.py
scripts/fit_rna_dihedrals.py
scripts/run_inference.py
scripts/train_vae.py
tests/__init__.py
tests/conftest.py
tests/test_backend_consistency.py
tests/test_device.py
tests/test_documentation.py
tests/test_imports.py
tests/test_internal.py
tests/test_metrics.py
tests/test_visualize.py
tests/utils.py
tests/io/test_errors.py
tests/io/test_read_write.py
tests/ml/test_nn.py
tests/ml/test_sampling.py
tests/ml/test_training.py
tests/ml/test_transformer.py
tests/ml/test_vae.py
tests/polymer/test_edges.py
tests/polymer/test_geometry.py
tests/polymer/test_reduction.py
tests/polymer/test_selection.py
tests/polymer/test_template.py
tests/profiling/__init__.py
tests/profiling/profile_internal.py
tests/profiling/profile_io.py
tests/profiling/profile_to_internal_breakdown.py
tests/profiling/timing.py
tests/testing/__init__.py
tests/testing/assertions.py
tests/testing/backend_registry.py
tests/testing/expectations.py
tests/testing/patterns.py
tests/testing/tolerances.py