CITATION.cff
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_SOFTWARE.md
mkdocs.yml
pyproject.toml
.github/workflows/documentation-pages.yml
.github/workflows/publish-pypi.yml
.github/workflows/quality.yml
docs/changelog.md
docs/contributing.md
docs/index.md
docs/api/modules/analytics.md
docs/api/modules/contracts.md
docs/api/modules/entities.md
docs/api/modules/input.md
docs/api/modules/utils.md
docs/api/recipes/bias.md
docs/api/recipes/oracle.md
docs/api/recipes/screen.md
docs/api/recipes/validate.md
docs/getting-started/configuration.md
docs/getting-started/installation.md
docs/getting-started/quickstart.md
docs/getting-started/repository-tour.md
docs/reference/cli.md
docs/reference/python-api/bias-recipe-flow.md
docs/reference/python-api/index.md
docs/reference/python-api/new-backend-runner.md
docs/reference/python-api/oracle-recipe-flow.md
docs/reference/python-api/screen-recipe-flow.md
docs/reference/python-api/validate-recipe-flow.md
docs/tutorials/advanced.md
docs/tutorials/backend-acceptance.md
docs/tutorials/basic.md
docs/tutorials/index.md
docs/tutorials/ligands.md
docs/tutorials/runners.md
docs/tutorials/screening.md
docs/tutorials/structure-gated-oracle.md
docs/user-guide/bias-training-data.md
docs/user-guide/bias.md
docs/user-guide/metric-reference.md
docs/user-guide/oracle.md
docs/user-guide/overview.md
docs/user-guide/public-output-contract.md
docs/user-guide/screen.md
docs/user-guide/troubleshooting.md
docs/user-guide/validate.md
examples/4HJO.cif
examples/4HJO.pdb
examples/README.md
examples/bias_matrix.yaml
examples/custom_bias_complexes.yaml
examples/ethanol.mol
examples/ethanol.sdf
examples/ifp_clustering_demo.py
examples/ligand_screen.csv
examples/options.yaml
examples/parameter_screen.csv
examples/system.yaml
examples/system_covalent.yaml
examples/system_custom_ccd.yaml
examples/system_nucleic_acid.yaml
examples/system_screen.yaml
scripts/README.md
scripts/fetch_bias_training_data.py
scripts/fetch_bias_training_data_tmp_mmseqs_env.sh
scripts/install_mmseqs_vendor.sh
scripts/run_test_lane.py
scripts/setup_openfold3.sh
scripts/verify_release_artifacts.py
src/cofolder/__init__.py
src/cofolder/__main__.py
src/cofolder/cli.py
src/cofolder.egg-info/PKG-INFO
src/cofolder.egg-info/SOURCES.txt
src/cofolder.egg-info/dependency_links.txt
src/cofolder.egg-info/entry_points.txt
src/cofolder.egg-info/requires.txt
src/cofolder.egg-info/top_level.txt
src/cofolder/acceptance/__init__.py
src/cofolder/acceptance/boltz1_backend_acceptance.py
src/cofolder/acceptance/boltz2_backend_acceptance.py
src/cofolder/acceptance/boltz_community_backend_acceptance.py
src/cofolder/acceptance/input_contract_backend_acceptance.py
src/cofolder/acceptance/openfold3_backend_acceptance.py
src/cofolder/acceptance/shared.py
src/cofolder/acceptance/data/ligand_screen.csv
src/cofolder/acceptance/data/ligand_training_data.csv
src/cofolder/acceptance/data/options_acceptance.yaml
src/cofolder/acceptance/data/options_boltz1_acceptance.yaml
src/cofolder/acceptance/data/options_openfold3_acceptance.yaml
src/cofolder/acceptance/data/protein_training_data.csv
src/cofolder/acceptance/data/system.yaml
src/cofolder/acceptance/data/system_constraints_boltz1.yaml
src/cofolder/acceptance/data/system_constraints_boltz2.yaml
src/cofolder/acceptance/data/system_constraints_openfold3.yaml
src/cofolder/acceptance/data/system_nucleic_acid.yaml
src/cofolder/acceptance/data/system_screen.yaml
src/cofolder/modules/__init__.py
src/cofolder/modules/analytics/__init__.py
src/cofolder/modules/analytics/_prolif_worker.py
src/cofolder/modules/analytics/aggregation.py
src/cofolder/modules/analytics/align.py
src/cofolder/modules/analytics/bias_database.py
src/cofolder/modules/analytics/bias_training.py
src/cofolder/modules/analytics/dataset.py
src/cofolder/modules/analytics/ifp_clustering.py
src/cofolder/modules/analytics/ifp_filtering.py
src/cofolder/modules/analytics/plots.py
src/cofolder/modules/analytics/reference_ifp.py
src/cofolder/modules/analytics/reproduction.py
src/cofolder/modules/analytics/stats.py
src/cofolder/modules/analytics/structure.py
src/cofolder/modules/analytics/sucos.py
src/cofolder/modules/analytics/bias/__init__.py
src/cofolder/modules/analytics/bias/_artifacts.py
src/cofolder/modules/analytics/bias/_common.py
src/cofolder/modules/analytics/bias/_datasets.py
src/cofolder/modules/analytics/bias/_enrichment.py
src/cofolder/modules/analytics/bias/_references.py
src/cofolder/modules/analytics/bias/_similarity.py
src/cofolder/modules/analytics/bias/_workflow.py
src/cofolder/modules/contracts/__init__.py
src/cofolder/modules/contracts/adapters.py
src/cofolder/modules/contracts/metrics.py
src/cofolder/modules/contracts/models.py
src/cofolder/modules/contracts/serialization.py
src/cofolder/modules/contracts/validation.py
src/cofolder/modules/entities/__init__.py
src/cofolder/modules/entities/ligand.py
src/cofolder/modules/input/__init__.py
src/cofolder/modules/input/compound_library.py
src/cofolder/modules/input/config.py
src/cofolder/modules/input/ligand.py
src/cofolder/modules/input/system.py
src/cofolder/modules/input/system_mapping.py
src/cofolder/modules/input/validation.py
src/cofolder/modules/runners/__init__.py
src/cofolder/modules/runners/_boltz_command.py
src/cofolder/modules/runners/_command_reporting.py
src/cofolder/modules/runners/_ligand_preparation.py
src/cofolder/modules/runners/base.py
src/cofolder/modules/runners/boltz1_runner.py
src/cofolder/modules/runners/boltz2_runner.py
src/cofolder/modules/runners/boltz_community_runner.py
src/cofolder/modules/runners/boltz_runner.py
src/cofolder/modules/runners/contracts.py
src/cofolder/modules/runners/msa.py
src/cofolder/modules/runners/openfold3_runner.py
src/cofolder/modules/runners/validators.py
src/cofolder/modules/utils/__init__.py
src/cofolder/modules/utils/_optional_dependencies.py
src/cofolder/modules/utils/executables.py
src/cofolder/modules/utils/helpers.py
src/cofolder/modules/utils/log.py
src/cofolder/modules/utils/read.py
src/cofolder/modules/utils/timing.py
src/cofolder/modules/utils/write.py
src/cofolder/recipes/__init__.py
src/cofolder/recipes/_completion.py
src/cofolder/recipes/_diagnostics.py
src/cofolder/recipes/_execution.py
src/cofolder/recipes/_metrics.py
src/cofolder/recipes/_results.py
src/cofolder/recipes/_screen_postprocess.py
src/cofolder/recipes/bias.py
src/cofolder/recipes/oracle.py
src/cofolder/recipes/preflight.py
src/cofolder/recipes/screen.py
src/cofolder/recipes/validate.py
src/cofolder/resources/__init__.py
src/cofolder/resources/examples/4HJO.cif
src/cofolder/resources/examples/4HJO.pdb
src/cofolder/resources/examples/README.md
src/cofolder/resources/examples/__init__.py
src/cofolder/resources/examples/bias_matrix.yaml
src/cofolder/resources/examples/custom_bias_complexes.yaml
src/cofolder/resources/examples/ethanol.mol
src/cofolder/resources/examples/ethanol.sdf
src/cofolder/resources/examples/ifp_clustering_demo.py
src/cofolder/resources/examples/ligand_screen.csv
src/cofolder/resources/examples/options.yaml
src/cofolder/resources/examples/parameter_screen.csv
src/cofolder/resources/examples/system.yaml
src/cofolder/resources/examples/system_covalent.yaml
src/cofolder/resources/examples/system_custom_ccd.yaml
src/cofolder/resources/examples/system_nucleic_acid.yaml
src/cofolder/resources/examples/system_screen.yaml
src/cofolder/tools/__init__.py
src/cofolder/tools/__main__.py
src/cofolder/tools/bias_query_cache.py
src/cofolder/tools/build_bias_training_data.py
src/cofolder/tools/cache.py
src/cofolder/tools/cli.py
src/cofolder/tools/fetch_bias_training_data.py
src/cofolder/tools/install_mmseqs.py
src/cofolder/tools/prepare_bias_custom_complexes.py
src/cofolder/tools/run_bias_matrix.py
src/cofolder/tools/setup_openfold3.py
tests/__init__.py
tests/conftest.py
tests/test_cli.py
tests/test_packaging.py
tests/test_structure_gated_oracle_tutorial.py
tests/test_test_lanes.py
tests/test_tutorials.py
tests/acceptance/test_setup_openfold3_script.py
tests/acceptance/test_shared.py
tests/fixtures/structural_parity_s6.json
tests/modules/__init__.py
tests/modules/analytics/__init__.py
tests/modules/analytics/test_aggregation.py
tests/modules/analytics/test_aggregation_orchestration.py
tests/modules/analytics/test_bias.py
tests/modules/analytics/test_bias_database.py
tests/modules/analytics/test_bias_training.py
tests/modules/analytics/test_ifp_clustering.py
tests/modules/analytics/test_optional_dependencies.py
tests/modules/analytics/test_reference_ifp.py
tests/modules/analytics/test_reproduction.py
tests/modules/analytics/test_structure.py
tests/modules/contracts/test_public_contracts.py
tests/modules/entities/__init__.py
tests/modules/entities/test_ligand.py
tests/modules/input/__init__.py
tests/modules/input/test_compound_library.py
tests/modules/input/test_config.py
tests/modules/input/test_system.py
tests/modules/input/test_system_mapping.py
tests/modules/input/test_validation.py
tests/modules/runners/test_boltz1_runner.py
tests/modules/runners/test_boltz_command.py
tests/modules/runners/test_boltz_community_runner.py
tests/modules/runners/test_boltz_runner.py
tests/modules/runners/test_command_reporting.py
tests/modules/runners/test_contracts.py
tests/modules/runners/test_ligand_preparation.py
tests/modules/runners/test_msa.py
tests/modules/runners/test_openfold3_runner.py
tests/modules/runners/test_registry.py
tests/modules/runners/test_validators.py
tests/modules/utils/__init__.py
tests/modules/utils/test_executables.py
tests/modules/utils/test_helpers.py
tests/modules/utils/test_log.py
tests/modules/utils/test_read.py
tests/recipes/__init__.py
tests/recipes/test_bias.py
tests/recipes/test_completion.py
tests/recipes/test_oracle.py
tests/recipes/test_screen.py
tests/recipes/test_screen_clustering.py
tests/recipes/test_screen_filter.py
tests/recipes/test_shared_internals.py
tests/recipes/test_structural_parity.py
tests/recipes/test_validate.py
tests/tools/test_bias_query_cache.py
tests/tools/test_build_bias_training_data.py
tests/tools/test_cache.py
tests/tools/test_cli.py
tests/tools/test_examples.py
tests/tools/test_fetch_bias_training_data.py
tests/tools/test_install_mmseqs.py
tests/tools/test_prepare_bias_custom_complexes.py
tests/tools/test_run_bias_matrix.py
tutorials/README.md
tutorials/_marimo_helpers.py
tutorials/_structure_gated_oracle.py
tutorials/_structure_gated_prolif_worker.py
tutorials/_workflow_examples.py
tutorials/bias.py
tutorials/boltz_system_inputs.py
tutorials/ligand_handling.py
tutorials/openfold3_system_inputs.py
tutorials/oracle.py
tutorials/runners.py
tutorials/screen.py
tutorials/structure_gated_oracle.py
tutorials/validate.py
tutorials/assets/structure_gated_oracle/acceptance-v1.json
tutorials/assets/structure_gated_oracle/acceptance-v2-interactions.json
tutorials/assets/structure_gated_oracle/acceptance-v2-provenance.json
tutorials/assets/structure_gated_oracle/acceptance-v2.csv
tutorials/assets/structure_gated_oracle/acceptance.json
tutorials/assets/structure_gated_oracle/config.yaml
tutorials/assets/structure_gated_oracle/illustrative_results.csv
tutorials/assets/structure_gated_oracle/ligands.csv
tutorials/assets/structure_gated_oracle/options.yaml
tutorials/assets/structure_gated_oracle/reference-validation.json
tutorials/assets/structure_gated_oracle/system.yaml
tutorials/assets/structure_gated_oracle/view_interactions.cxc
tutorials/assets/structure_gated_oracle/view_interactions.pml