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AGENTS.md
CHANGELOG.md
LICENSE
LICENSING.md
MANIFEST.in
README.md
pyproject.toml
uv.lock
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docs/images/report-kinetics.png
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docs/methods/binding-and-qmmm.md
docs/methods/candidate-models.md
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docs/methods/proteins.md
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src/alambiq/core/store.py
src/alambiq/engines/P2RankOffline.java
src/alambiq/engines/__init__.py
src/alambiq/engines/_runner.py
src/alambiq/engines/boltz_download.py
src/alambiq/engines/boltz_predict.py
src/alambiq/engines/echo_probe.py
src/alambiq/engines/esm3_predict.py
src/alambiq/engines/esmc_embed.py
src/alambiq/engines/esmc_score.py
src/alambiq/engines/hints.py
src/alambiq/engines/mmseqs_msa.py
src/alambiq/engines/mmseqs_panel.py
src/alambiq/engines/mmseqs_profiles.py
src/alambiq/engines/mmseqs_search.py
src/alambiq/engines/openfe_prepare_binding.py
src/alambiq/engines/openfe_rbfe.py
src/alambiq/engines/openff_finite_environment.py
src/alambiq/engines/openff_prepare_complex.py
src/alambiq/engines/openff_prepare_system.py
src/alambiq/engines/openmm_common.py
src/alambiq/engines/openmm_md.py
src/alambiq/engines/openmm_metadynamics.py
src/alambiq/engines/openmm_prepare.py
src/alambiq/engines/openmm_xml.py
src/alambiq/engines/p2rank_predict.py
src/alambiq/engines/qmmm_coupling.py
src/alambiq/engines/qmmm_dynamics_runner.py
src/alambiq/engines/qmmm_native.py
src/alambiq/engines/qmmm_pyscf.py
src/alambiq/engines/qmmm_runner.py
src/alambiq/engines/thermompnn_predict.py
src/alambiq/engines/umbrella_analysis.py
src/alambiq/report/__init__.py
src/alambiq/report/charts.py
src/alambiq/report/page.py
src/alambiq/report/viewers.py
src/alambiq/report/assets/3Dmol-min.js
src/alambiq/report/assets/3Dmol-min.js.LICENSE.txt
src/alambiq/report/assets/LICENSE
src/alambiq/report/assets/README.md
src/alambiq/resources/THIRD_PARTY_NOTICES.md
src/alambiq/resources/__init__.py
src/alambiq/resources/boltz2-2.2.1.json
src/alambiq/resources/esm3-small.json
src/alambiq/resources/esmc-300m.json
src/alambiq/resources/p2rank-2.5.1.json
src/alambiq/resources/pfam-38.2-profiles.json
src/alambiq/resources/thermompnn.json
src/alambiq/resources/uniref50-2026_02.json
tests/core/__init__.py
tests/core/native_signal_fixture.py
tests/core/test_candidate_strategies.py
tests/core/test_cli_resources.py
tests/core/test_condition_fits.py
tests/core/test_conformance.py
tests/core/test_connected_investigation.py
tests/core/test_construct_capabilities.py
tests/core/test_core_imports.py
tests/core/test_determinism.py
tests/core/test_docker_files.py
tests/core/test_documentation.py
tests/core/test_engine_launcher.py
tests/core/test_engine_openff_finite.py
tests/core/test_engine_qmmm_coupling.py
tests/core/test_engine_qmmm_dynamics.py
tests/core/test_engine_qmmm_native.py
tests/core/test_engine_qmmm_pyscf.py
tests/core/test_engine_qmmm_state.py
tests/core/test_engine_suites.py
tests/core/test_engine_umbrella_analysis.py
tests/core/test_engineering_capabilities.py
tests/core/test_enzyme_capabilities.py
tests/core/test_esm3_capabilities.py
tests/core/test_examples.py
tests/core/test_execution.py
tests/core/test_first_mistakes.py
tests/core/test_genome_inspect_context.py
tests/core/test_licenses.py
tests/core/test_loader.py
tests/core/test_measurement_options.py
tests/core/test_native_capture.py
tests/core/test_native_descendants.py
tests/core/test_native_process.py
tests/core/test_native_signal.py
tests/core/test_operating_conditions.py
tests/core/test_operation_capabilities.py
tests/core/test_operation_define.py
tests/core/test_operation_propagate.py
tests/core/test_option_coverage.py
tests/core/test_pilot_capabilities.py
tests/core/test_protein_embed.py
tests/core/test_protein_explore_embeddings.py
tests/core/test_protein_inspect.py
tests/core/test_protein_match_profiles.py
tests/core/test_protein_predict_stability_change.py
tests/core/test_protein_score_substitutions.py
tests/core/test_reaction_analyze_enzyme_panel.py
tests/core/test_reaction_estimate_thermodynamics.py
tests/core/test_reaction_explore_routes.py
tests/core/test_reaction_inspect.py
tests/core/test_relocation.py
tests/core/test_report_lint.py
tests/core/test_report_visuals.py
tests/core/test_resources.py
tests/core/test_reuse_identity.py
tests/core/test_run_records.py
tests/core/test_runtime_budgets.py
tests/core/test_sequence_generate_msa.py
tests/core/test_sequence_inspect_msa.py
tests/core/test_simulation_analyze_binding_free_energy.py
tests/core/test_simulation_analyze_reaction_free_energy.py
tests/core/test_simulation_compare_replica_structures.py
tests/core/test_simulation_compare_scalar_couplings.py
tests/core/test_simulation_evaluate_qmmm_state.py
tests/core/test_simulation_inspect_trajectory.py
tests/core/test_simulation_run_metadynamics.py
tests/core/test_simulation_run_molecular_dynamics.py
tests/core/test_simulation_run_qmmm_dynamics.py
tests/core/test_simulation_run_relative_free_energy.py
tests/core/test_structure_compare.py
tests/core/test_structure_detect_binding_pockets.py
tests/core/test_structure_predict_biomolecular_complex.py
tests/core/test_structure_prepare_finite_environment.py
tests/core/test_structure_prepare_predicted_complex_for_dynamics.py
tests/core/test_structure_prepare_protein_ligand_system.py
tests/core/test_structure_prepare_protein_system.py
tests/core/test_structure_prepare_reactive_coordinates.py
tests/core/test_structure_prepare_relative_binding_inputs.py
tests/core/test_temporary_server.py
tests/core/test_variant_benchmark.py
tests/core/test_variant_propose.py
tests/core/test_writing.py
tests/fixtures/README.md
tests/fixtures/constructs/puc19.gb
tests/fixtures/enzyme-reaction-panel/panel.json
tests/fixtures/enzyme-reaction-panel/parameters.json
tests/fixtures/enzyme-reaction-panel/source-accounting.json
tests/fixtures/hemoglobin/P69905.json
tests/fixtures/hemoglobin/hemoglobin-alpha.fasta
tests/fixtures/operation/ensemble-observations.json
tests/fixtures/operation/enzyme-assessment.json
tests/fixtures/operation/enzyme-batch.json
tests/fixtures/operation/first-order-fit.json
tests/fixtures/operation/first-order-observations.json
tests/fixtures/operation/first-order.json
tests/fixtures/operation/member-0.json
tests/fixtures/operation/member-1.json
tests/fixtures/operation/member-2.json
tests/fixtures/operation/resources.json
tests/fixtures/reactions/chorismate/manifest.json
tests/fixtures/structures/181L.cif
tests/fixtures/structures/1A3N.cif
tests/fixtures/structures/1L2Y.cif
tests/fixtures/structures/1P7E.cif
tests/fixtures/variant-benchmark/bslipa-t50-observations.csv
tests/snapshots/reports/cofactor-regeneration.txt
tests/snapshots/reports/connected-investigation.txt
tests/snapshots/reports/kinetics-from-measurements.txt
tests/snapshots/reports/lanmodulin-comparison.txt
tests/snapshots/reports/measured-variant-rounds.txt
tests/snapshots/reports/operation-from-progress-curves.txt
tests/snapshots/reports/pockets-and-complex.txt
tests/snapshots/reports/protein-first-look.txt
tests/snapshots/reports/relatives-and-context.txt
tests/snapshots/reports/representative-panel.txt
tests/snapshots/reports/transformation-and-routes.txt
tests/snapshots/reports/transformation-to-enzymes.txt
tests/snapshots/reports/variant-to-construct.txt
tools/README.md
tools/benchmark_variant_proposal.py
tools/check_distribution.py
tools/check_getting_started.py
tools/check_installed_package.py
tools/scan_licenses.py