CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
docs/benchmark_config.example.json
docs/benchmark_manifest_template.csv
docs/benchmark_quickstart.example.json
docs/benchmark_schema.md
docs/sensitivity_axes.example.json
docs/assets/topoppi-gui-sanitized.png
installer/macos/Info.plist.in
installer/macos/README.md
installer/macos/TopoPPI
installer/macos/build_app.sh
installer/macos/collect_licenses.py
installer/macos/launcher.c
installer/windows/README.md
installer/windows/TopoPPI.iss
installer/windows/install_topoppi.ps1
installer/windows/launch_gui.pyw
installer/windows/uninstall_topoppi.ps1
src/topoppi/__init__.py
src/topoppi/_version.py
src/topoppi/benchmark_cli.py
src/topoppi/benchmark_methods.py
src/topoppi/cli.py
src/topoppi/config.py
src/topoppi/errors.py
src/topoppi/file_utils.py
src/topoppi/gui.py
src/topoppi/install_optcuts.py
src/topoppi/json_utils.py
src/topoppi/logging_utils.py
src/topoppi/pipeline.py
src/topoppi/rigid_geometry.py
src/topoppi/sequence_alignment.py
src/topoppi.egg-info/PKG-INFO
src/topoppi.egg-info/SOURCES.txt
src/topoppi.egg-info/dependency_links.txt
src/topoppi.egg-info/entry_points.txt
src/topoppi.egg-info/requires.txt
src/topoppi.egg-info/top_level.txt
src/topoppi/assets/__init__.py
src/topoppi/assets/topoppi.ico
src/topoppi/assets/topoppi.png
src/topoppi/atlas/__init__.py
src/topoppi/atlas/footprints.py
src/topoppi/atlas/metrics.py
src/topoppi/atlas/packing.py
src/topoppi/atlas/seams.py
src/topoppi/atlas/uv.py
src/topoppi/benchmarking/__init__.py
src/topoppi/benchmarking/coordinate_audit.py
src/topoppi/benchmarking/evidence_bundle.py
src/topoppi/benchmarking/manifest_metadata.py
src/topoppi/benchmarking/metrics_utils.py
src/topoppi/benchmarking/reporting.py
src/topoppi/benchmarking/runner.py
src/topoppi/benchmarking/sensitivity.py
src/topoppi/benchmarking/statistics.py
src/topoppi/benchmarking/worker.py
src/topoppi/gui_app/__init__.py
src/topoppi/gui_app/app.py
src/topoppi/gui_app/constants.py
src/topoppi/gui_app/forms.py
src/topoppi/gui_app/plot_mixin.py
src/topoppi/gui_app/ui_mixin.py
src/topoppi/gui_app/workflow_mixin.py
src/topoppi/interactions/__init__.py
src/topoppi/interactions/interaction_engine.py
src/topoppi/interactions/metadata.py
src/topoppi/io/__init__.py
src/topoppi/io/afdb_download.py
src/topoppi/io/io_loader.py
src/topoppi/io/pdb_records.py
src/topoppi/mesh/__init__.py
src/topoppi/mesh/parameterization.py
src/topoppi/mesh/provenance.py
src/topoppi/mesh/surface.py
src/topoppi/mesh/topology.py
src/topoppi/optimization/__init__.py
src/topoppi/optimization/optcuts/__init__.py
src/topoppi/optimization/optcuts/joint_optimizer.py
src/topoppi/visualization/__init__.py
src/topoppi/visualization/visualizer.py
tests/test_atlas_metrics.py
tests/test_benchmark_audit.py
tests/test_benchmark_end_to_end.py
tests/test_benchmark_metrics.py
tests/test_benchmark_reporting.py
tests/test_benchmark_runner_preprocess.py
tests/test_benchmark_sensitivity.py
tests/test_benchmark_statistics.py
tests/test_cli.py
tests/test_config.py
tests/test_file_utils.py
tests/test_gui_forms.py
tests/test_gui_workflow.py
tests/test_imports.py
tests/test_install_optcuts.py
tests/test_interaction_engine.py
tests/test_io_loader.py
tests/test_macos_packaging.py
tests/test_optcuts_footprint_cpp.py
tests/test_optcuts_optimizer.py
tests/test_parameterization_domains.py
tests/test_pipeline.py
tests/test_publication_afdb.py
tests/test_publication_paired_analysis.py
tests/test_publication_prepare_manifest_prolif.py
tests/test_publication_weight_selection.py
tests/test_release_metadata.py
tests/test_residue_footprints.py
tests/test_sequence_alignment.py
tests/test_surface_adaptive.py
tests/test_topology.py
tests/test_uv_layout.py
tests/test_visualizer.py
tests/fixtures/1bvk.pdb
tests/fixtures/prolif_interactions.json
tests/fixtures/tiny_complex.pdb
tools/OptCuts/LICENSE.txt
tools/OptCuts/NOTICE.md
tools/OptCuts/THIRD_PARTY_LICENSES.txt
tools/OptCuts/build_residue_aware_optcuts.sh
tools/OptCuts/build_windows_optcuts.ps1
tools/OptCuts/install_optcuts.sh
tools/OptCuts/reproducible/candidate-validity-cd230267.patch
tools/OptCuts/reproducible/modern-compiler-compatibility-cd230267.patch
tools/OptCuts/reproducible/mpl2-sparse-solver-cd230267.patch
tools/OptCuts/reproducible/obj-output-precision-cd230267.patch
tools/OptCuts/reproducible/oscillation-tolerance-cd230267.patch
tools/OptCuts/reproducible/sparse-local-solves-cd230267.patch
tools/OptCuts/reproducible/static-stb-cd230267.patch
tools/OptCuts/reproducible/topology-cycle-acceleration-cd230267.patch
tools/OptCuts/residue_aware/README.md
tools/OptCuts/residue_aware/ResidueFootprintEnergy.cpp
tools/OptCuts/residue_aware/ResidueFootprintEnergy.hpp
tools/OptCuts/residue_aware/optcuts-cd230267.patch
tools/OptCuts/residue_aware/source-vertex-provenance-cd230267.patch
tools/publication/README.md
tools/publication/analyze_paired_benchmarks.py
tools/publication/audit_manifest_coordinates.py
tools/publication/audit_paired_structures.py
tools/publication/build_afdb_monomer_replacements.py
tools/publication/cluster_pdbbind_manifest.py
tools/publication/download_afdb_matches.py
tools/publication/match_afdb_complexes.py
tools/publication/prepare_formal_benchmarks.py
tools/publication/prepare_manifest_prolif.py
tools/publication/prepare_pdbbind_r1.py
tools/publication/prepare_residue_aware_optcuts_weight_study.py
tools/publication/select_benchmark_subset.py
tools/publication/select_residue_aware_optcuts_weight.py
tools/publication/stage_manifest_inputs.py
tools/publication/stratify_afdb_paired_geometry.py