CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
NOTICE
README.md
pyproject.toml
src/biotsr/__init__.py
src/biotsr/__main__.py
src/biotsr/api.py
src/biotsr/batch.py
src/biotsr/retrieval.py
src/biotsr.egg-info/PKG-INFO
src/biotsr.egg-info/SOURCES.txt
src/biotsr.egg-info/dependency_links.txt
src/biotsr.egg-info/entry_points.txt
src/biotsr.egg-info/requires.txt
src/biotsr.egg-info/top_level.txt
src/biotsr/analysis/__init__.py
src/biotsr/analysis/clustering.py
src/biotsr/analysis/common_keys.py
src/biotsr/analysis/features.py
src/biotsr/analysis/render.py
src/biotsr/analysis/samples.py
src/biotsr/analysis/similarity.py
src/biotsr/analysis/visualization.py
src/biotsr/binning/__init__.py
src/biotsr/binning/base.py
src/biotsr/binning/distance.py
src/biotsr/binning/theta.py
src/biotsr/candidates/__init__.py
src/biotsr/candidates/exhaustive.py
src/biotsr/cli/__init__.py
src/biotsr/cli/__main__.py
src/biotsr/cli/batch.py
src/biotsr/cli/commands.py
src/biotsr/cli/console.py
src/biotsr/cli/errors.py
src/biotsr/cli/main.py
src/biotsr/cli/manifest.py
src/biotsr/cli/output.py
src/biotsr/cli/parallel.py
src/biotsr/cli/parser.py
src/biotsr/cli/sheet.py
src/biotsr/cli/spec.py
src/biotsr/cross/__init__.py
src/biotsr/cross/candidates.py
src/biotsr/cross/pools.py
src/biotsr/cross/runner.py
src/biotsr/cross/sides.py
src/biotsr/domain/__init__.py
src/biotsr/domain/candidate.py
src/biotsr/domain/errors.py
src/biotsr/domain/identity.py
src/biotsr/domain/interpretation.py
src/biotsr/domain/keyspace.py
src/biotsr/domain/point.py
src/biotsr/domain/result.py
src/biotsr/domain/selection_record.py
src/biotsr/encoding/__init__.py
src/biotsr/encoding/key.py
src/biotsr/geometry/__init__.py
src/biotsr/geometry/conventions.py
src/biotsr/geometry/ordering.py
src/biotsr/geometry/triangle.py
src/biotsr/io/__init__.py
src/biotsr/io/input_columns.py
src/biotsr/io/naming.py
src/biotsr/io/native.py
src/biotsr/io/native_read.py
src/biotsr/labels/__init__.py
src/biotsr/labels/elements.py
src/biotsr/labels/schemes.py
src/biotsr/labels/resources/element_labels_v1.csv
src/biotsr/methods/__init__.py
src/biotsr/methods/arguments.py
src/biotsr/methods/engine.py
src/biotsr/methods/registry.py
src/biotsr/methods/builtin/__init__.py
src/biotsr/methods/builtin/amino_acid_atomic.py
src/biotsr/methods/builtin/carbohydrate.py
src/biotsr/methods/builtin/cross.py
src/biotsr/methods/builtin/drug.py
src/biotsr/methods/builtin/nucleotide.py
src/biotsr/methods/builtin/protein.py
src/biotsr/modifiers/__init__.py
src/biotsr/modifiers/aa_grouping.py
src/biotsr/modifiers/base.py
src/biotsr/modifiers/mirror.py
src/biotsr/modifiers/size_filter.py
src/biotsr/profiles/__init__.py
src/biotsr/profiles/atomic.py
src/biotsr/profiles/cross.py
src/biotsr/profiles/standard.py
src/biotsr/selection/__init__.py
src/biotsr/selection/atomic.py
src/biotsr/selection/base.py
src/biotsr/selection/completeness.py
src/biotsr/selection/integrity.py
src/biotsr/selection/protein.py
src/biotsr/selection/truncation.py
src/biotsr/sse/__init__.py
src/biotsr/sse/assignment.py
src/biotsr/sse/categories.py
src/biotsr/sse/states.py
src/biotsr/sse/stratification.py
src/biotsr/structure/__init__.py
src/biotsr/structure/model.py
src/biotsr/structure/backends/__init__.py
src/biotsr/structure/backends/pdb_legacy.py
tests/__init__.py
tests/conftest.py
tests/characterization/__init__.py
tests/characterization/test_1ubq_historical_difference.py
tests/data/legacy_outputs/before_adr101_hetatm_modified_residues/README.md
tests/data/legacy_outputs/before_adr101_hetatm_modified_residues/SYNPHOS_A_specific.keys
tests/data/legacy_outputs/before_adr101_hetatm_modified_residues/SYNPHOS_A_specific.meta.json
tests/data/legacy_outputs/before_adr101_hetatm_modified_residues/SYNPHOS_A_specific.run.json
tests/data/legacy_outputs/before_adr107_calpha_radix20/README.md
tests/data/legacy_outputs/before_adr107_calpha_radix20/SYNPHOS_A_protein.keys
tests/data/legacy_outputs/before_adr107_calpha_radix20/SYNPHOS_A_protein.meta.json
tests/data/legacy_outputs/before_adr107_calpha_radix20/SYNPHOS_A_protein.run.json
tests/data/legacy_outputs/before_adr113_adr114/1BNA_A_1-3_chain.keys
tests/data/legacy_outputs/before_adr113_adr114/1BNA_A_1-3_chain.meta.json
tests/data/legacy_outputs/before_adr113_adr114/1BNA_A_1-3_chain.run.json
tests/data/legacy_outputs/before_adr113_adr114/README.md
tests/data/legacy_outputs/before_adr113_adr114/SYNPHOS_A_LIG101.keys
tests/data/legacy_outputs/before_adr113_adr114/SYNPHOS_A_LIG101.meta.json
tests/data/legacy_outputs/before_adr113_adr114/SYNPHOS_A_LIG101.run.json
tests/data/legacy_outputs/before_adr113_adr114/SYNPHOS_A_protein.keys
tests/data/legacy_outputs/before_adr113_adr114/SYNPHOS_A_protein.meta.json
tests/data/legacy_outputs/before_adr113_adr114/SYNPHOS_A_protein.run.json
tests/data/manifests/README.md
tests/data/manifests/dataset_sheet.csv
tests/data/manifests/wide_sheet.csv
tests/data/reference/README.md
tests/data/reference/atomic_element_labels.json
tests/data/reference/calpha_base30.json
tests/data/reference/standard_baseline.json
tests/data/reference/historical/1UBQ_A_TSR-Package_TSR_keys.txt.gz
tests/data/structures/1BNA.pdb
tests/data/structures/1BRS.pdb
tests/data/structures/1KX5.pdb
tests/data/structures/1TUP.pdb
tests/data/structures/1UBQ.pdb
tests/data/structures/2AC0.pdb
tests/data/structures/3EJ1.pdb
tests/data/structures/3PTB.pdb
tests/data/structures/5WT9.pdb
tests/data/structures/6G9M.pdb
tests/data/structures/7LF9.pdb
tests/data/structures/manifest.json
tests/data/synthetic/README.md
tests/data/synthetic/SYNPHOS.pdb
tests/data/synthetic/make_synthetic.py
tests/integration/__init__.py
tests/integration/test_analysis_comparison_rule.py
tests/integration/test_analysis_cross_method.py
tests/integration/test_api_guide.py
tests/integration/test_atomic_end_to_end.py
tests/integration/test_batch_engine.py
tests/integration/test_batch_interruption.py
tests/integration/test_cli_equivalence.py
tests/integration/test_cli_retrieval_regressions.py
tests/integration/test_cli_workflows.py
tests/integration/test_comparison_altloc_instance_rules.py
tests/integration/test_concurrent_invocations.py
tests/integration/test_cross_families.py
tests/integration/test_dataset_sheet_rows.py
tests/integration/test_download_cancellation.py
tests/integration/test_end_to_end.py
tests/integration/test_input_rules.py
tests/integration/test_ligand_carbohydrate_nucleotide_families.py
tests/integration/test_modified_residue_calpha.py
tests/integration/test_modified_residue_identifier_row_rules.py
tests/integration/test_modifier_composition.py
tests/integration/test_nucleotide_chain_available_atoms.py
tests/integration/test_output_containment.py
tests/integration/test_previous_outputs_element_labels.py
tests/integration/test_processing_identity.py
tests/integration/test_round_trip_families.py
tests/integration/test_selection_provenance_regressions.py
tests/integration/test_selection_rules.py
tests/integration/test_sse_composition.py
tests/integration/test_standard_references.py
tests/integration/test_tutorials.py
tests/integration/test_wide_sheet.py
tests/support/__init__.py
tests/support/stub_server.py
tests/unit/__init__.py
tests/unit/test_analysis_architecture.py
tests/unit/test_analysis_clustering.py
tests/unit/test_analysis_common_keys.py
tests/unit/test_analysis_features.py
tests/unit/test_analysis_math.py
tests/unit/test_analysis_render.py
tests/unit/test_analysis_similarity.py
tests/unit/test_atomic.py
tests/unit/test_binning.py
tests/unit/test_candidates_and_hygiene.py
tests/unit/test_cli_architecture.py
tests/unit/test_cli_manifest.py
tests/unit/test_cli_output.py
tests/unit/test_cli_parsing.py
tests/unit/test_cli_sheet.py
tests/unit/test_cross_candidates.py
tests/unit/test_cross_contact_rules.py
tests/unit/test_cross_keyspace.py
tests/unit/test_cross_ordering.py
tests/unit/test_cross_pools.py
tests/unit/test_cross_serialization.py
tests/unit/test_distance_top_class_and_theta_bounds.py
tests/unit/test_docs_links.py
tests/unit/test_domain.py
tests/unit/test_download_settings.py
tests/unit/test_element_labels.py
tests/unit/test_encoding.py
tests/unit/test_geometry.py
tests/unit/test_keyspace.py
tests/unit/test_label_space_and_selection.py
tests/unit/test_manifest_robustness.py
tests/unit/test_modifiers.py
tests/unit/test_native_round_trip.py
tests/unit/test_ordering.py
tests/unit/test_packaged_science_and_parser_semantics.py
tests/unit/test_platform_identities.py
tests/unit/test_release_readiness.py
tests/unit/test_retrieval.py
tests/unit/test_serialization.py
tests/unit/test_sse_architecture.py
tests/unit/test_sse_assignment.py
tests/unit/test_sse_categories.py
tests/unit/test_sse_serialization_and_analysis.py
tests/unit/test_structure_and_selection.py