synkit 1.6.5__py3-none-win_amd64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- synkit/CRN/Benchmark/__init__.py +53 -0
- synkit/CRN/Benchmark/crosschecks.py +13 -0
- synkit/CRN/Benchmark/kegg.py +12 -0
- synkit/CRN/Benchmark/networks.py +13 -0
- synkit/CRN/Benchmark/scaling.py +13 -0
- synkit/CRN/Benchmark/validate.py +13 -0
- synkit/CRN/Construct/__init__.py +16 -0
- synkit/CRN/Construct/abstract.py +668 -0
- synkit/CRN/Construct/arity.py +36 -0
- synkit/CRN/Construct/builder.py +619 -0
- synkit/CRN/Construct/derivation.py +63 -0
- synkit/CRN/Construct/flattener.py +100 -0
- synkit/CRN/Construct/keys.py +14 -0
- synkit/CRN/Construct/mixtures.py +117 -0
- synkit/CRN/Construct/rdkit_worker.py +69 -0
- synkit/CRN/Construct/smiles.py +99 -0
- synkit/CRN/Construct/state.py +31 -0
- synkit/CRN/Construct/strategy.py +75 -0
- synkit/CRN/Construct/worker.py +42 -0
- synkit/CRN/IO/__init__.py +36 -0
- synkit/CRN/IO/sbml.py +925 -0
- synkit/CRN/Pathway/__init__.py +72 -0
- synkit/CRN/Pathway/_adapter.py +333 -0
- synkit/CRN/Pathway/pathfinder.py +500 -0
- synkit/CRN/Pathway/reachability.py +796 -0
- synkit/CRN/Pathway/realizability.py +1322 -0
- synkit/CRN/Petrinet/__init__.py +93 -0
- synkit/CRN/Petrinet/analyzer.py +486 -0
- synkit/CRN/Petrinet/minimal_semiflows.py +436 -0
- synkit/CRN/Petrinet/net.py +1041 -0
- synkit/CRN/Petrinet/persistence.py +97 -0
- synkit/CRN/Petrinet/semiflows.py +483 -0
- synkit/CRN/Petrinet/siphon_search.py +402 -0
- synkit/CRN/Petrinet/structure.py +286 -0
- synkit/CRN/Props/__init__.py +130 -0
- synkit/CRN/Props/_rank.py +29 -0
- synkit/CRN/Props/deficiency.py +953 -0
- synkit/CRN/Props/dynamics.py +832 -0
- synkit/CRN/Props/helper.py +151 -0
- synkit/CRN/Props/stoich.py +751 -0
- synkit/CRN/Props/thermo.py +584 -0
- synkit/CRN/Query/__init__.py +66 -0
- synkit/CRN/Query/cache.py +41 -0
- synkit/CRN/Query/kegg_api.py +99 -0
- synkit/CRN/Query/kegg_extract.py +714 -0
- synkit/CRN/Query/kegg_impute.py +707 -0
- synkit/CRN/Query/kegg_parse.py +480 -0
- synkit/CRN/Query/to_syncrn.py +290 -0
- synkit/CRN/README.md +234 -0
- synkit/CRN/Structure/__init__.py +12 -0
- synkit/CRN/Structure/_graph_io.py +713 -0
- synkit/CRN/Structure/_matrices.py +88 -0
- synkit/CRN/Structure/_parse.py +544 -0
- synkit/CRN/Structure/reaction.py +237 -0
- synkit/CRN/Structure/rule.py +55 -0
- synkit/CRN/Structure/species.py +46 -0
- synkit/CRN/Structure/syncrn.py +929 -0
- synkit/CRN/Symmetry/__init__.py +20 -0
- synkit/CRN/Symmetry/_common.py +1059 -0
- synkit/CRN/Symmetry/_ir.py +940 -0
- synkit/CRN/Symmetry/automorphism.py +472 -0
- synkit/CRN/Symmetry/canon.py +441 -0
- synkit/CRN/Symmetry/isomorphism.py +412 -0
- synkit/CRN/Symmetry/symmetry.py +61 -0
- synkit/CRN/Symmetry/wl_canon.py +967 -0
- synkit/CRN/Visualize/__init__.py +11 -0
- synkit/CRN/Visualize/labels.py +113 -0
- synkit/CRN/Visualize/layout.py +708 -0
- synkit/CRN/Visualize/palette.py +292 -0
- synkit/CRN/Visualize/validation.py +122 -0
- synkit/CRN/Visualize/vis.py +1152 -0
- synkit/CRN/__init__.py +233 -0
- synkit/CRN/_build.py +50 -0
- synkit/CRN/_native_build.py +175 -0
- synkit/CRN/analysis.py +629 -0
- synkit/CRN/backend.py +74 -0
- synkit/CRN/cpp/CMakeLists.txt +58 -0
- synkit/CRN/cpp/algebra.cpp +46 -0
- synkit/CRN/cpp/closure.cpp +29 -0
- synkit/CRN/cpp/exact.h +55 -0
- synkit/CRN/cpp/pathway.cpp +46 -0
- synkit/CRN/cpp/semiflows.cpp +209 -0
- synkit/CRN/cpp/structural.cpp +240 -0
- synkit/CRN/cpp/symmetry.cpp +45 -0
- synkit/CRN/cpp/write_manifest.cmake +28 -0
- synkit/CRN/kinds.py +137 -0
- synkit/CRN/lib/synkit_crn.dll +0 -0
- synkit/CRN/lib/synkit_crn.json +33 -0
- synkit/CRN/native.py +388 -0
- synkit/CRN/native_analysis.py +459 -0
- synkit/Chem/Cluster/__init__.py +0 -0
- synkit/Chem/Cluster/butina.py +140 -0
- synkit/Chem/Fingerprint/__init__.py +0 -0
- synkit/Chem/Fingerprint/fp_calculator.py +155 -0
- synkit/Chem/Fingerprint/smiles_featurizer.py +258 -0
- synkit/Chem/Fingerprint/transformation_fp.py +139 -0
- synkit/Chem/Mapper/README.rst +43 -0
- synkit/Chem/Mapper/__init__.py +255 -0
- synkit/Chem/Mapper/_compat.py +130 -0
- synkit/Chem/Mapper/adapters/__init__.py +1 -0
- synkit/Chem/Mapper/adapters/prediction.py +126 -0
- synkit/Chem/Mapper/adapters/template.py +412 -0
- synkit/Chem/Mapper/chem/__init__.py +52 -0
- synkit/Chem/Mapper/chem/aam.py +673 -0
- synkit/Chem/Mapper/chem/blind.py +160 -0
- synkit/Chem/Mapper/chem/its.py +309 -0
- synkit/Chem/Mapper/chem/smiles.py +564 -0
- synkit/Chem/Mapper/graph/__init__.py +66 -0
- synkit/Chem/Mapper/graph/automorphism.py +395 -0
- synkit/Chem/Mapper/graph/blockcut.py +98 -0
- synkit/Chem/Mapper/graph/labeled_graph.py +104 -0
- synkit/Chem/Mapper/graph/refine.py +176 -0
- synkit/Chem/Mapper/graph/synkit_adapter.py +110 -0
- synkit/Chem/Mapper/io/__init__.py +13 -0
- synkit/Chem/Mapper/io/idxmapstr.py +82 -0
- synkit/Chem/Mapper/mapper.py +685 -0
- synkit/Chem/Mapper/reaction_search.py +554 -0
- synkit/Chem/Mapper/reporting/__init__.py +1 -0
- synkit/Chem/Mapper/reporting/alternatives.py +451 -0
- synkit/Chem/Mapper/reporting/analysis.py +681 -0
- synkit/Chem/Mapper/reporting/native_analysis.py +485 -0
- synkit/Chem/Mapper/reporting/spectrum.py +642 -0
- synkit/Chem/Mapper/solvers/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/__init__.py +141 -0
- synkit/Chem/Mapper/solvers/exact/assignment/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/assignment/assignment_certificate.py +113 -0
- synkit/Chem/Mapper/solvers/exact/assignment/assignment_domains.py +162 -0
- synkit/Chem/Mapper/solvers/exact/assignment/assignment_verification.py +58 -0
- synkit/Chem/Mapper/solvers/exact/assignment/incremental_assignment.py +247 -0
- synkit/Chem/Mapper/solvers/exact/certificate.py +128 -0
- synkit/Chem/Mapper/solvers/exact/core.py +183 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/bounds.py +319 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/exhaustive.py +179 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/inputs.py +283 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/records.py +242 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/search.py +1025 -0
- synkit/Chem/Mapper/solvers/exact/distance_search/verify.py +378 -0
- synkit/Chem/Mapper/solvers/exact/edit_support.py +375 -0
- synkit/Chem/Mapper/solvers/exact/hybrid.py +224 -0
- synkit/Chem/Mapper/solvers/exact/hydrogen.py +264 -0
- synkit/Chem/Mapper/solvers/exact/kernel_solvers/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/kernel_solvers/branching.py +499 -0
- synkit/Chem/Mapper/solvers/exact/kernel_solvers/enumerate.py +1050 -0
- synkit/Chem/Mapper/solvers/exact/kernel_solvers/enumeration_result.py +30 -0
- synkit/Chem/Mapper/solvers/exact/kernel_solvers/kernel.py +256 -0
- synkit/Chem/Mapper/solvers/exact/kernel_solvers/milp.py +194 -0
- synkit/Chem/Mapper/solvers/exact/native/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/native/build.py +154 -0
- synkit/Chem/Mapper/solvers/exact/native/candidates.py +593 -0
- synkit/Chem/Mapper/solvers/exact/native/canonical.py +396 -0
- synkit/Chem/Mapper/solvers/exact/native/disk_frontier.py +415 -0
- synkit/Chem/Mapper/solvers/exact/native/frontier.py +390 -0
- synkit/Chem/Mapper/solvers/exact/native/hydrogen_quotient.py +213 -0
- synkit/Chem/Mapper/solvers/exact/native/its.py +528 -0
- synkit/Chem/Mapper/solvers/exact/native/native_distance.cpp +2803 -0
- synkit/Chem/Mapper/solvers/exact/native/orbit_aggregation.py +328 -0
- synkit/Chem/Mapper/solvers/exact/native/parallel.py +205 -0
- synkit/Chem/Mapper/solvers/exact/native/pmcd.py +203 -0
- synkit/Chem/Mapper/solvers/exact/native/runtime.py +40 -0
- synkit/Chem/Mapper/solvers/exact/native/search.py +294 -0
- synkit/Chem/Mapper/solvers/exact/native/separator.py +224 -0
- synkit/Chem/Mapper/solvers/exact/native_build.py +12 -0
- synkit/Chem/Mapper/solvers/exact/pabs/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/pabs/cost_lattice.py +43 -0
- synkit/Chem/Mapper/solvers/exact/pabs/factor_spectrum.py +110 -0
- synkit/Chem/Mapper/solvers/exact/pabs/multi_shell.py +368 -0
- synkit/Chem/Mapper/solvers/exact/pabs/propagation.py +679 -0
- synkit/Chem/Mapper/solvers/exact/pabs/propagation_bounds.py +436 -0
- synkit/Chem/Mapper/solvers/exact/pabs/propagation_limits.py +13 -0
- synkit/Chem/Mapper/solvers/exact/pabs/propagation_search.py +856 -0
- synkit/Chem/Mapper/solvers/exact/pabs/propagation_symmetry.py +66 -0
- synkit/Chem/Mapper/solvers/exact/pabs/residual_typed_bonds.py +136 -0
- synkit/Chem/Mapper/solvers/exact/pabs/reward_frontier.py +201 -0
- synkit/Chem/Mapper/solvers/exact/pabs/separator_bound.py +258 -0
- synkit/Chem/Mapper/solvers/exact/pabs/separator_spectrum.py +308 -0
- synkit/Chem/Mapper/solvers/exact/pabs/sparse_reward_bound.py +207 -0
- synkit/Chem/Mapper/solvers/exact/pabs/suffix_spectrum.py +299 -0
- synkit/Chem/Mapper/solvers/exact/search.py +55 -0
- synkit/Chem/Mapper/solvers/exact/seeds/__init__.py +1 -0
- synkit/Chem/Mapper/solvers/exact/seeds/seed.py +104 -0
- synkit/Chem/Mapper/solvers/exact/seeds/seed_fragments.py +148 -0
- synkit/Chem/Mapper/solvers/exact/seeds/seed_relaxation.py +181 -0
- synkit/Chem/Mapper/solvers/exact/symmetry.py +223 -0
- synkit/Chem/Mapper/solvers/native/__init__.py +4 -0
- synkit/Chem/Mapper/solvers/native/assignment.py +99 -0
- synkit/Chem/Mapper/solvers/native/astar.py +22 -0
- synkit/Chem/Mapper/solvers/native/build.py +385 -0
- synkit/Chem/Mapper/solvers/native/classification.py +641 -0
- synkit/Chem/Mapper/solvers/native/core.py +378 -0
- synkit/Chem/Mapper/solvers/native/cpp/CMakeLists.txt +120 -0
- synkit/Chem/Mapper/solvers/native/cpp/examples/map_reaction.cpp +29 -0
- synkit/Chem/Mapper/solvers/native/cpp/examples/slap_graph.cpp +63 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/assignment/assignment.h +18 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/astar/astar.h +18 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/astar/bound.h +33 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/core/pmcd_witness.h +16 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/core/runtime.h +130 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/hydrogen/hydrogen.h +73 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/mapper.h +175 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/mces/mces.h +9 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/pabs/seed.h +34 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/reaction/reaction.h +30 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/sepdp/sepdp.h +21 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/slap.h +72 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/solvers/solvers.h +16 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/symmetry/classification.h +140 -0
- synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/symmetry/cpabs.h +33 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/assignment/abb.cpp +302 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/astar/CMakeLists.txt +12 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/astar/README.md +47 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/astar/astar.cpp +228 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/astar/astar_graph.cpp +37 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/astar/bound.cpp +212 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/core/dispatch.cpp +272 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/core/pmcd_witness.cpp +36 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/hydrogen/hydrogen.cpp +380 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/mces/README.md +57 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/mces/mces.cpp +287 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/bridge.cpp +334 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/chemical_floor.inc +181 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/endpoint_symmetry.inc +104 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/exact_helpers.h +20 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_assignment_certificate.h +165 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_certificate.h +125 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_model.h +365 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_provider.inc +319 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_rounding.inc +170 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_test_hooks.h +342 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/objective_reduction.inc +137 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/overlap_dual.inc +351 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/profile_seed.inc +214 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/seed_heuristics.inc +640 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/sparse_embedding.cpp +430 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/sparse_root_lp.h +176 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/pabs/test_hooks.inc +262 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/reaction/reaction.cpp +611 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/sepdp/README.md +61 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/sepdp/sepdp.cpp +253 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/slap.cpp +810 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/solvers/formulation.h +138 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/solvers/maxsat.cpp +526 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/solvers/ortools.cpp +475 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/solvers/seed.h +80 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/solvers/weighted_cnf.h +256 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/supporting/README.md +43 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/supporting/dfs.cpp +123 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/supporting/edit_support.cpp +224 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/classification.cpp +553 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/classification_pipeline.cpp +124 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/classification_stream.h +13 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/cpabs.cpp +455 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/edge_deck.cpp +743 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/COPYRIGHT +44 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt +202 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naugraph.c +732 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naurng.c +94 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naurng.h +49 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nausparse.c +1771 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nausparse.h +133 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nautil.c +750 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naututil.h +355 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nauty.c +1256 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nauty.h +1544 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/schreier.c +1131 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/schreier.h +70 -0
- synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/sorttemplates.c +580 -0
- synkit/Chem/Mapper/solvers/native/hydrogen.py +711 -0
- synkit/Chem/Mapper/solvers/native/implicit.py +506 -0
- synkit/Chem/Mapper/solvers/native/implicit_certificate.py +187 -0
- synkit/Chem/Mapper/solvers/native/implicit_preparation.py +309 -0
- synkit/Chem/Mapper/solvers/native/lib/synkit_mapper.dll +0 -0
- synkit/Chem/Mapper/solvers/native/mces.py +16 -0
- synkit/Chem/Mapper/solvers/native/reaction.py +179 -0
- synkit/Chem/Mapper/solvers/native/reaction_build.py +277 -0
- synkit/Chem/Mapper/solvers/native/reaction_text.py +26 -0
- synkit/Chem/Mapper/solvers/native/runtime.py +242 -0
- synkit/Chem/Mapper/solvers/native/sepdp.py +47 -0
- synkit/Chem/Mapper/solvers/native/slap.py +266 -0
- synkit/Chem/Mapper/solvers/native/solvers.py +67 -0
- synkit/Chem/Mapper/solvers/native/stereo.py +86 -0
- synkit/Chem/Mapper/solvers/native/supporting.py +34 -0
- synkit/Chem/Mapper/solvers/native/symmetry.py +91 -0
- synkit/Chem/Mapper/solvers/slap/__init__.py +29 -0
- synkit/Chem/Mapper/solvers/slap/lap.py +174 -0
- synkit/Chem/Mapper/solvers/slap/sequential.py +696 -0
- synkit/Chem/Mapper/validation/__init__.py +1 -0
- synkit/Chem/Mapper/validation/aam_validator.py +442 -0
- synkit/Chem/Mapper/validation/annotations.py +274 -0
- synkit/Chem/Mapper/validation/bonds.py +124 -0
- synkit/Chem/Mapper/validation/cohorts.py +72 -0
- synkit/Chem/Mapper/validation/identifiability.py +150 -0
- synkit/Chem/Mapper/validation/numerical_scope.py +36 -0
- synkit/Chem/Mapper/validation/orbits.py +137 -0
- synkit/Chem/Molecule/__init__.py +0 -0
- synkit/Chem/Molecule/_chirality_loci.py +165 -0
- synkit/Chem/Molecule/_chirality_types.py +231 -0
- synkit/Chem/Molecule/_helical_loci.py +167 -0
- synkit/Chem/Molecule/_stereo_axis_evidence.py +202 -0
- synkit/Chem/Molecule/_stereo_element_detection.py +193 -0
- synkit/Chem/Molecule/_stereo_orientation_constraints.py +511 -0
- synkit/Chem/Molecule/_tetrahedral_carriers.py +63 -0
- synkit/Chem/Molecule/atom_features.py +379 -0
- synkit/Chem/Molecule/chirality.py +1041 -0
- synkit/Chem/Molecule/cip_assignment.py +569 -0
- synkit/Chem/Molecule/cip_ranking.py +843 -0
- synkit/Chem/Molecule/coordinate_stereo.py +503 -0
- synkit/Chem/Molecule/derived_stereo_naming.py +165 -0
- synkit/Chem/Molecule/descriptors.py +452 -0
- synkit/Chem/Molecule/formula.py +249 -0
- synkit/Chem/Molecule/global_stereo.py +175 -0
- synkit/Chem/Molecule/graph_annotator.py +300 -0
- synkit/Chem/Molecule/standardize.py +817 -0
- synkit/Chem/Molecule/stereo_evidence.py +179 -0
- synkit/Chem/Molecule/stereo_perception.py +1032 -0
- synkit/Chem/Molecule/valence.py +123 -0
- synkit/Chem/Reaction/Mapper/__init__.py +44 -0
- synkit/Chem/Reaction/__init__.py +20 -0
- synkit/Chem/Reaction/aam_validator.py +5 -0
- synkit/Chem/Reaction/balance_check.py +138 -0
- synkit/Chem/Reaction/canon_rsmi.py +249 -0
- synkit/Chem/Reaction/cleaning.py +58 -0
- synkit/Chem/Reaction/deionize.py +199 -0
- synkit/Chem/Reaction/explicit_h_audit.py +232 -0
- synkit/Chem/Reaction/fix_aam.py +64 -0
- synkit/Chem/Reaction/neutralize.py +207 -0
- synkit/Chem/Reaction/radical_wildcard.py +224 -0
- synkit/Chem/Reaction/standardize.py +203 -0
- synkit/Chem/Reaction/tautomerize.py +205 -0
- synkit/Chem/__init__.py +1 -0
- synkit/Chem/utils.py +315 -0
- synkit/Data/__init__.py +0 -0
- synkit/Data/aldol.json.gz +1 -0
- synkit/Data/gen_partial_aam.py +147 -0
- synkit/Data/paracetamol.json.gz +1 -0
- synkit/Graph/Canon/__init__.py +16 -0
- synkit/Graph/Canon/_native/__init__.py +13 -0
- synkit/Graph/Canon/_native/build.py +93 -0
- synkit/Graph/Canon/_native/lib/synkit_canon.dll +0 -0
- synkit/Graph/Canon/_native/prepare.py +49 -0
- synkit/Graph/Canon/_native/runtime.py +140 -0
- synkit/Graph/Canon/_native/search.py +137 -0
- synkit/Graph/Canon/canon_algs.py +228 -0
- synkit/Graph/Canon/canon_graph.py +531 -0
- synkit/Graph/Canon/cpp/CMakeLists.txt +42 -0
- synkit/Graph/Canon/cpp/README.md +123 -0
- synkit/Graph/Canon/cpp/examples/canonical_graph.cpp +16 -0
- synkit/Graph/Canon/cpp/include/synkit_canon/canon.h +85 -0
- synkit/Graph/Canon/cpp/src/canonical.cpp +391 -0
- synkit/Graph/Canon/cpp/src/symmetry.h +83 -0
- synkit/Graph/Canon/cpp/tests/symmetry.cpp +93 -0
- synkit/Graph/Canon/exact.py +1020 -0
- synkit/Graph/Canon/exact_refinement.py +368 -0
- synkit/Graph/Canon/nauty.py +143 -0
- synkit/Graph/Context/__init__.py +0 -0
- synkit/Graph/Context/hier_context.py +244 -0
- synkit/Graph/Context/radius_expand.py +252 -0
- synkit/Graph/FG/__init__.py +19 -0
- synkit/Graph/FG/api.py +39 -0
- synkit/Graph/FG/audit.py +155 -0
- synkit/Graph/FG/catalog.py +919 -0
- synkit/Graph/FG/detector.py +288 -0
- synkit/Graph/FG/model.py +97 -0
- synkit/Graph/FG/recognizers.py +274 -0
- synkit/Graph/FG/ring_system.py +154 -0
- synkit/Graph/Feature/Descriptors/topology.py +857 -0
- synkit/Graph/Feature/Fingerprint/__init__.py +0 -0
- synkit/Graph/Feature/Fingerprint/wl_rxn_fps.py +222 -0
- synkit/Graph/Feature/__init__.py +5 -0
- synkit/Graph/Feature/graph_descriptors.py +323 -0
- synkit/Graph/Feature/graph_fps.py +96 -0
- synkit/Graph/Feature/graph_signature.py +239 -0
- synkit/Graph/Feature/hash_fps.py +133 -0
- synkit/Graph/Feature/morgan_fps.py +88 -0
- synkit/Graph/Feature/path_fps.py +81 -0
- synkit/Graph/Feature/wl_hash.py +134 -0
- synkit/Graph/Fusion/__init__.py +85 -0
- synkit/Graph/Fusion/candidate.py +559 -0
- synkit/Graph/Fusion/constructor.py +877 -0
- synkit/Graph/Fusion/identity.py +184 -0
- synkit/Graph/Fusion/interface.py +700 -0
- synkit/Graph/Fusion/search.py +241 -0
- synkit/Graph/Hyrogen/__init__.py +6 -0
- synkit/Graph/Hyrogen/_misc.py +591 -0
- synkit/Graph/Hyrogen/hcomplete.py +995 -0
- synkit/Graph/Hyrogen/hcomplete_legacy.py +368 -0
- synkit/Graph/Hyrogen/hcompletion_algorithms.py +713 -0
- synkit/Graph/Hyrogen/hextend.py +570 -0
- synkit/Graph/Hyrogen/hextend_legacy.py +215 -0
- synkit/Graph/ITS/__init__.py +4 -0
- synkit/Graph/ITS/its_builder.py +120 -0
- synkit/Graph/ITS/its_construction.py +719 -0
- synkit/Graph/ITS/its_decompose.py +572 -0
- synkit/Graph/ITS/its_destruction.py +331 -0
- synkit/Graph/ITS/its_expand.py +1251 -0
- synkit/Graph/ITS/its_relabel.py +187 -0
- synkit/Graph/ITS/its_reverter.py +356 -0
- synkit/Graph/ITS/normalize_aam.py +145 -0
- synkit/Graph/ITS/partial_its.py +238 -0
- synkit/Graph/ITS/rc_extractor.py +656 -0
- synkit/Graph/ITS/stereo.py +74 -0
- synkit/Graph/MTG/__init__.py +107 -0
- synkit/Graph/MTG/gluing.py +451 -0
- synkit/Graph/MTG/history.py +928 -0
- synkit/Graph/MTG/inventory.py +118 -0
- synkit/Graph/MTG/local.py +447 -0
- synkit/Graph/MTG/mcs_matcher.py +246 -0
- synkit/Graph/MTG/mtg.py +611 -0
- synkit/Graph/MTG/mtg_explore.py +74 -0
- synkit/Graph/MTG/observation.py +209 -0
- synkit/Graph/MTG/process.py +577 -0
- synkit/Graph/MTG/queries.py +66 -0
- synkit/Graph/MTG/realization.py +95 -0
- synkit/Graph/MTG/series_parallel.py +107 -0
- synkit/Graph/MTG/utils.py +424 -0
- synkit/Graph/Matcher/__init__.py +10 -0
- synkit/Graph/Matcher/approx_mcs.py +1264 -0
- synkit/Graph/Matcher/auto_est.py +736 -0
- synkit/Graph/Matcher/automorphism.py +314 -0
- synkit/Graph/Matcher/batch_cluster.py +224 -0
- synkit/Graph/Matcher/dedup_matches.py +247 -0
- synkit/Graph/Matcher/graph_cluster.py +191 -0
- synkit/Graph/Matcher/graph_matcher.py +312 -0
- synkit/Graph/Matcher/graph_morphism.py +421 -0
- synkit/Graph/Matcher/mcs_matcher.py +804 -0
- synkit/Graph/Matcher/multi_turbo_iso.py +186 -0
- synkit/Graph/Matcher/orbit.py +284 -0
- synkit/Graph/Matcher/partial_matcher.py +694 -0
- synkit/Graph/Matcher/sing.py +544 -0
- synkit/Graph/Matcher/subgraph_matcher.py +812 -0
- synkit/Graph/Matcher/turbo_iso.py +272 -0
- synkit/Graph/Matcher/wl_sel.py +537 -0
- synkit/Graph/Mech/__init__.py +26 -0
- synkit/Graph/Mech/conversion.py +1466 -0
- synkit/Graph/Mech/conversion_debug.py +237 -0
- synkit/Graph/Mech/electron_accounting.py +200 -0
- synkit/Graph/Mech/lwg_editor.py +406 -0
- synkit/Graph/Mech/lwg_ops.py +313 -0
- synkit/Graph/Morphism/__init__.py +99 -0
- synkit/Graph/Morphism/constraints.py +460 -0
- synkit/Graph/Morphism/llg.py +999 -0
- synkit/Graph/Morphism/morphism.py +349 -0
- synkit/Graph/Morphism/stereo.py +258 -0
- synkit/Graph/Morphism/stereo_morphism.py +383 -0
- synkit/Graph/Morphism/stereo_morphism_helpers.py +957 -0
- synkit/Graph/Morphism/stereo_morphism_types.py +117 -0
- synkit/Graph/Stereo/__init__.py +376 -0
- synkit/Graph/Stereo/_descriptor_core.py +207 -0
- synkit/Graph/Stereo/_descriptor_serialization.py +138 -0
- synkit/Graph/Stereo/canonical.py +648 -0
- synkit/Graph/Stereo/changes.py +964 -0
- synkit/Graph/Stereo/composition.py +391 -0
- synkit/Graph/Stereo/configured.py +946 -0
- synkit/Graph/Stereo/couplings.py +245 -0
- synkit/Graph/Stereo/descriptors.py +1030 -0
- synkit/Graph/Stereo/enumeration.py +597 -0
- synkit/Graph/Stereo/extended_descriptors.py +406 -0
- synkit/Graph/Stereo/global_configured.py +152 -0
- synkit/Graph/Stereo/global_stereo.py +304 -0
- synkit/Graph/Stereo/identity.py +648 -0
- synkit/Graph/Stereo/interchange.py +496 -0
- synkit/Graph/Stereo/legacy.py +460 -0
- synkit/Graph/Stereo/matching.py +899 -0
- synkit/Graph/Stereo/native.py +154 -0
- synkit/Graph/Stereo/orbits.py +668 -0
- synkit/Graph/Stereo/outcomes.py +99 -0
- synkit/Graph/Stereo/pairwise.py +350 -0
- synkit/Graph/Stereo/rdkit_adapter.py +662 -0
- synkit/Graph/Stereo/rdkit_identity.py +118 -0
- synkit/Graph/Stereo/rdkit_resonance.py +140 -0
- synkit/Graph/Stereo/reaction_interchange.py +266 -0
- synkit/Graph/Stereo/semantics.py +296 -0
- synkit/Graph/Stereo/supports.py +257 -0
- synkit/Graph/Stereo/wire.py +339 -0
- synkit/Graph/Wildcard/__init__.py +0 -0
- synkit/Graph/Wildcard/fuse_graph.py +156 -0
- synkit/Graph/Wildcard/graph_wc.py +303 -0
- synkit/Graph/Wildcard/its_merge.py +857 -0
- synkit/Graph/Wildcard/radwc.py +114 -0
- synkit/Graph/Wildcard/wc_matcher.py +576 -0
- synkit/Graph/Wildcard/wildcard.py +225 -0
- synkit/Graph/__init__.py +17 -0
- synkit/Graph/canon_graph.py +14 -0
- synkit/Graph/syn_graph.py +199 -0
- synkit/Graph/utils.py +324 -0
- synkit/IO/__init__.py +4 -0
- synkit/IO/chem_converter.py +1059 -0
- synkit/IO/combinatorial/__init__.py +8 -0
- synkit/IO/combinatorial/gml_to_graph.py +223 -0
- synkit/IO/combinatorial/graph_to_gml.py +280 -0
- synkit/IO/combinatorial/graph_to_smarts.py +186 -0
- synkit/IO/combinatorial/smarts_expander.py +147 -0
- synkit/IO/combinatorial/smarts_generalizer.py +133 -0
- synkit/IO/combinatorial/smarts_to_graph.py +179 -0
- synkit/IO/conversion.py +42 -0
- synkit/IO/data_io.py +269 -0
- synkit/IO/data_process.py +143 -0
- synkit/IO/debug.py +73 -0
- synkit/IO/gml_to_nx.py +150 -0
- synkit/IO/graph_to_mol.py +199 -0
- synkit/IO/mol_to_graph.py +1105 -0
- synkit/IO/mol_to_graph_chemistry.py +545 -0
- synkit/IO/nx_to_gml.py +209 -0
- synkit/IO/smiles_to_id.py +123 -0
- synkit/Mechanism/__init__.py +151 -0
- synkit/Mechanism/adapters.py +136 -0
- synkit/Mechanism/audit.py +323 -0
- synkit/Mechanism/benchmark.py +638 -0
- synkit/Mechanism/compatibility.py +13 -0
- synkit/Mechanism/drawing.py +85 -0
- synkit/Mechanism/electron_models.py +725 -0
- synkit/Mechanism/equivalence.py +521 -0
- synkit/Mechanism/evidence.py +262 -0
- synkit/Mechanism/interchange.py +141 -0
- synkit/Mechanism/model.py +918 -0
- synkit/Mechanism/neighbor_stereo.py +312 -0
- synkit/Mechanism/radical_data.py +740 -0
- synkit/Mechanism/replay.py +986 -0
- synkit/Mechanism/schema.py +264 -0
- synkit/Mechanism/stereo_state.py +416 -0
- synkit/Mechanism/symbols.py +91 -0
- synkit/Rule/Apply/__init__.py +35 -0
- synkit/Rule/Apply/conditions.py +45 -0
- synkit/Rule/Apply/dpo.py +998 -0
- synkit/Rule/Apply/rule_matcher.py +218 -0
- synkit/Rule/Apply/validation.py +354 -0
- synkit/Rule/Compose/__init__.py +106 -0
- synkit/Rule/Compose/_identity.py +43 -0
- synkit/Rule/Compose/composition.py +976 -0
- synkit/Rule/Compose/laws.py +439 -0
- synkit/Rule/Compose/search.py +771 -0
- synkit/Rule/Compose/synrule.py +170 -0
- synkit/Rule/Modify/__init__.py +0 -0
- synkit/Rule/Modify/implict_rule.py +56 -0
- synkit/Rule/Modify/longest_path.py +92 -0
- synkit/Rule/Modify/molecule_rule.py +115 -0
- synkit/Rule/Modify/prune_templates.py +78 -0
- synkit/Rule/Modify/rule_utils.py +194 -0
- synkit/Rule/Modify/strip_rule.py +97 -0
- synkit/Rule/__init__.py +28 -0
- synkit/Rule/generic_stereo.py +884 -0
- synkit/Rule/stereo_identity.py +271 -0
- synkit/Rule/syn_rule.py +1090 -0
- synkit/Synthesis/MSR/__init__.py +0 -0
- synkit/Synthesis/MSR/path_finder.py +239 -0
- synkit/Synthesis/Metrics/__init__.py +0 -0
- synkit/Synthesis/Metrics/_base.py +52 -0
- synkit/Synthesis/Metrics/_plot.py +129 -0
- synkit/Synthesis/Metrics/_ranking.py +179 -0
- synkit/Synthesis/RBL/__init__.py +80 -0
- synkit/Synthesis/RBL/engine.py +1249 -0
- synkit/Synthesis/RBL/matching.py +652 -0
- synkit/Synthesis/RBL/overlap.py +336 -0
- synkit/Synthesis/RBL/pipeline.py +376 -0
- synkit/Synthesis/RBL/policy.py +139 -0
- synkit/Synthesis/RBL/proof.py +370 -0
- synkit/Synthesis/RBL/reaction.py +506 -0
- synkit/Synthesis/RBL/state.py +169 -0
- synkit/Synthesis/RBL/validation.py +1060 -0
- synkit/Synthesis/Reactor/__init__.py +60 -0
- synkit/Synthesis/Reactor/core/__init__.py +1 -0
- synkit/Synthesis/Reactor/core/engine.py +967 -0
- synkit/Synthesis/Reactor/core/product.py +621 -0
- synkit/Synthesis/Reactor/core/rewrite.py +561 -0
- synkit/Synthesis/Reactor/core/strategy.py +44 -0
- synkit/Synthesis/Reactor/matching/__init__.py +1 -0
- synkit/Synthesis/Reactor/matching/mixin.py +920 -0
- synkit/Synthesis/Reactor/matching/policy.py +345 -0
- synkit/Synthesis/Reactor/matching/symmetry.py +309 -0
- synkit/Synthesis/Reactor/output/__init__.py +1 -0
- synkit/Synthesis/Reactor/output/deduplication.py +703 -0
- synkit/Synthesis/Reactor/output/policy.py +16 -0
- synkit/Synthesis/Reactor/output/serialization.py +485 -0
- synkit/Synthesis/Reactor/output/structural.py +893 -0
- synkit/Synthesis/Reactor/stereo/__init__.py +1 -0
- synkit/Synthesis/Reactor/stereo/assignment.py +35 -0
- synkit/Synthesis/Reactor/stereo/mixin.py +780 -0
- synkit/Synthesis/Reactor/variants/__init__.py +1 -0
- synkit/Synthesis/Reactor/variants/imbalanced.py +180 -0
- synkit/Synthesis/Reactor/variants/partial.py +84 -0
- synkit/Synthesis/Reactor/workflow/__init__.py +1 -0
- synkit/Synthesis/Reactor/workflow/batch.py +550 -0
- synkit/Synthesis/Reactor/workflow/benchmark.py +143 -0
- synkit/Synthesis/Reactor/workflow/postprocess.py +267 -0
- synkit/Synthesis/Reactor/workflow/rule_filter.py +210 -0
- synkit/Synthesis/__init__.py +0 -0
- synkit/Synthesis/reactor_utils.py +316 -0
- synkit/Utils/__init__.py +0 -0
- synkit/Utils/utils.py +172 -0
- synkit/Vis/__init__.py +91 -0
- synkit/Vis/crn/__init__.py +40 -0
- synkit/Vis/epd/__init__.py +20 -0
- synkit/Vis/epd/arrows.py +425 -0
- synkit/Vis/epd/chem.py +197 -0
- synkit/Vis/epd/constants.py +83 -0
- synkit/Vis/epd/layout.py +283 -0
- synkit/Vis/epd/mapping.py +51 -0
- synkit/Vis/epd/models.py +136 -0
- synkit/Vis/epd/render.py +543 -0
- synkit/Vis/epd/utils.py +108 -0
- synkit/Vis/epd/visualizer.py +811 -0
- synkit/Vis/graph_visualizer.py +375 -0
- synkit/Vis/its/__init__.py +19 -0
- synkit/Vis/its/drawer.py +615 -0
- synkit/Vis/its_drawer.py +35 -0
- synkit/Vis/molecule/__init__.py +31 -0
- synkit/Vis/molecule/drawer.py +563 -0
- synkit/Vis/molecule/reaction.py +285 -0
- synkit/Vis/molecule_drawer.py +33 -0
- synkit/Vis/mtg/__init__.py +17 -0
- synkit/Vis/mtg/drawer.py +769 -0
- synkit/Vis/mtg_drawer.py +34 -0
- synkit/Vis/pdf_writer.py +146 -0
- synkit/Vis/reaction/__init__.py +19 -0
- synkit/Vis/reaction/rule.py +141 -0
- synkit/Vis/reaction/rxn.py +532 -0
- synkit/Vis/reaction_drawer.py +41 -0
- synkit/Vis/space/__init__.py +17 -0
- synkit/Vis/space/chemical.py +80 -0
- synkit/Vis/space/embedding.py +87 -0
- synkit/Vis/vis_synedu/Vis/__init__.py +7 -0
- synkit/Vis/vis_synedu/Vis/dpo.py +862 -0
- synkit/Vis/vis_synedu/rxn_vis.py +377 -0
- synkit/Vis/vis_synedu/vis.py +501 -0
- synkit/Vis/visual_drawer.py +215 -0
- synkit/Vis/visual_model.py +520 -0
- synkit/__init__.py +3 -0
- synkit/_native.py +91 -0
- synkit/examples.py +50 -0
- synkit/version.py +23 -0
- synkit-1.6.5.dist-info/METADATA +156 -0
- synkit-1.6.5.dist-info/RECORD +636 -0
- synkit-1.6.5.dist-info/WHEEL +4 -0
- synkit-1.6.5.dist-info/licenses/LICENSE +21 -0
- synkit-1.6.5.dist-info/licenses/synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/COPYRIGHT +44 -0
- synkit-1.6.5.dist-info/licenses/synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt +202 -0
|
@@ -0,0 +1,700 @@
|
|
|
1
|
+
"""Explicit two-arm interfaces for verified graph fusion."""
|
|
2
|
+
|
|
3
|
+
from __future__ import annotations
|
|
4
|
+
|
|
5
|
+
from dataclasses import dataclass, field, replace
|
|
6
|
+
from enum import Enum
|
|
7
|
+
from typing import Any, Hashable, Mapping, Sequence
|
|
8
|
+
|
|
9
|
+
import networkx as nx
|
|
10
|
+
|
|
11
|
+
from synkit.Graph.Morphism import (
|
|
12
|
+
GraphMorphism,
|
|
13
|
+
NodeStateKind,
|
|
14
|
+
WildcardConstraint,
|
|
15
|
+
adapt_legacy_node_state,
|
|
16
|
+
)
|
|
17
|
+
from synkit.Graph.Morphism import StereoEffect
|
|
18
|
+
|
|
19
|
+
from .identity import FUSION_NODE_IDENTITY_KEYS, FUSION_WL_ITERATIONS
|
|
20
|
+
|
|
21
|
+
# A proof-bearing interface must compare the same chemical/Lewis state used by
|
|
22
|
+
# exact candidate identity. Matcher attributes remain independently
|
|
23
|
+
# configurable and may be deliberately coarser for candidate discovery.
|
|
24
|
+
# ``hcount`` is excluded at the interface because an overlap may resolve an
|
|
25
|
+
# implicit hydrogen against an explicit completion port. The completed graph
|
|
26
|
+
# identity still checks the effective hydrogen inventory after substitution.
|
|
27
|
+
DEFAULT_INTERFACE_NODE_KEYS = tuple(
|
|
28
|
+
key for key in FUSION_NODE_IDENTITY_KEYS if key != "hcount"
|
|
29
|
+
)
|
|
30
|
+
DEFAULT_INTERFACE_EDGE_KEYS = ("order",)
|
|
31
|
+
|
|
32
|
+
|
|
33
|
+
class FusionInterfaceIssueCode(str, Enum):
|
|
34
|
+
"""Stable failures raised before graph construction."""
|
|
35
|
+
|
|
36
|
+
SOURCE_MISMATCH = "FUSION_INTERFACE_SOURCE_MISMATCH"
|
|
37
|
+
TARGET_MISMATCH = "FUSION_INTERFACE_TARGET_MISMATCH"
|
|
38
|
+
NODE_CONFLICT = "FUSION_INTERFACE_NODE_CONFLICT"
|
|
39
|
+
EDGE_CONFLICT = "FUSION_INTERFACE_EDGE_CONFLICT"
|
|
40
|
+
WILDCARD_CONFLICT = "FUSION_INTERFACE_WILDCARD_CONFLICT"
|
|
41
|
+
OWNER_OUTSIDE_INTERFACE = "FUSION_INTERFACE_OWNER_OUTSIDE_INTERFACE"
|
|
42
|
+
INVALID_MAPPING = "FUSION_INTERFACE_INVALID_MAPPING"
|
|
43
|
+
|
|
44
|
+
|
|
45
|
+
@dataclass(frozen=True)
|
|
46
|
+
class FusionInterfaceIssue:
|
|
47
|
+
code: FusionInterfaceIssueCode
|
|
48
|
+
message: str
|
|
49
|
+
context: Mapping[str, Any] = field(default_factory=dict)
|
|
50
|
+
|
|
51
|
+
def to_dict(self) -> dict[str, Any]:
|
|
52
|
+
return {
|
|
53
|
+
"code": self.code.value,
|
|
54
|
+
"message": self.message,
|
|
55
|
+
"context": dict(self.context),
|
|
56
|
+
}
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
class FusionInterfaceError(ValueError):
|
|
60
|
+
"""Raised when a proposed common interface is not compatible."""
|
|
61
|
+
|
|
62
|
+
def __init__(self, *issues: FusionInterfaceIssue):
|
|
63
|
+
self.issues = tuple(issues)
|
|
64
|
+
super().__init__("; ".join(issue.message for issue in self.issues))
|
|
65
|
+
|
|
66
|
+
|
|
67
|
+
def _stable_value(value: Any) -> Any:
|
|
68
|
+
if isinstance(value, Mapping):
|
|
69
|
+
return tuple(
|
|
70
|
+
sorted(
|
|
71
|
+
((repr(key), _stable_value(item)) for key, item in value.items()),
|
|
72
|
+
key=repr,
|
|
73
|
+
)
|
|
74
|
+
)
|
|
75
|
+
if isinstance(value, (list, tuple, set, frozenset)):
|
|
76
|
+
items = tuple(_stable_value(item) for item in value)
|
|
77
|
+
return (
|
|
78
|
+
tuple(sorted(items, key=repr))
|
|
79
|
+
if isinstance(value, (set, frozenset))
|
|
80
|
+
else items
|
|
81
|
+
)
|
|
82
|
+
return value
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
def _attribute_signature(
|
|
86
|
+
attributes: Mapping[str, Any], keys: Sequence[str]
|
|
87
|
+
) -> tuple[Any, ...]:
|
|
88
|
+
return tuple((key, _stable_value(attributes.get(key))) for key in keys)
|
|
89
|
+
|
|
90
|
+
|
|
91
|
+
def _wildcard_values(wildcard_element: Any) -> tuple[Any, ...]:
|
|
92
|
+
scalar = (
|
|
93
|
+
wildcard_element[0]
|
|
94
|
+
if isinstance(wildcard_element, (tuple, list))
|
|
95
|
+
else wildcard_element
|
|
96
|
+
)
|
|
97
|
+
return (wildcard_element, scalar)
|
|
98
|
+
|
|
99
|
+
|
|
100
|
+
def _constraint_for_interface(
|
|
101
|
+
graph: nx.Graph,
|
|
102
|
+
node: Hashable,
|
|
103
|
+
inverse_arm: Mapping[Hashable, Hashable],
|
|
104
|
+
*,
|
|
105
|
+
element_key: str,
|
|
106
|
+
role_key: str,
|
|
107
|
+
wildcard_element: Any,
|
|
108
|
+
) -> WildcardConstraint | None:
|
|
109
|
+
state = adapt_legacy_node_state(
|
|
110
|
+
graph.nodes[node],
|
|
111
|
+
element_key=element_key,
|
|
112
|
+
role_key=role_key,
|
|
113
|
+
wildcard_values=_wildcard_values(wildcard_element),
|
|
114
|
+
)
|
|
115
|
+
if state.kind is not NodeStateKind.WILDCARD:
|
|
116
|
+
return None
|
|
117
|
+
constraint = state.constraint
|
|
118
|
+
if constraint is None:
|
|
119
|
+
return None
|
|
120
|
+
if constraint.owner is not None and constraint.owner not in inverse_arm:
|
|
121
|
+
raise FusionInterfaceError(
|
|
122
|
+
FusionInterfaceIssue(
|
|
123
|
+
FusionInterfaceIssueCode.OWNER_OUTSIDE_INTERFACE,
|
|
124
|
+
"A wildcard owner is absent from the proposed interface.",
|
|
125
|
+
{"node": repr(node), "owner": repr(constraint.owner)},
|
|
126
|
+
)
|
|
127
|
+
)
|
|
128
|
+
return constraint.relabel_owner(inverse_arm)
|
|
129
|
+
|
|
130
|
+
|
|
131
|
+
def _validated_mapping_pairs(
|
|
132
|
+
forward_graph: nx.Graph,
|
|
133
|
+
backward_graph: nx.Graph,
|
|
134
|
+
mapping: Mapping[Hashable, Hashable],
|
|
135
|
+
) -> tuple[tuple[Hashable, Hashable], ...]:
|
|
136
|
+
pairs = tuple(
|
|
137
|
+
sorted(mapping.items(), key=lambda item: (repr(item[0]), repr(item[1])))
|
|
138
|
+
)
|
|
139
|
+
if not pairs:
|
|
140
|
+
raise FusionInterfaceError(
|
|
141
|
+
FusionInterfaceIssue(
|
|
142
|
+
FusionInterfaceIssueCode.INVALID_MAPPING,
|
|
143
|
+
"A fusion interface cannot be empty.",
|
|
144
|
+
)
|
|
145
|
+
)
|
|
146
|
+
if len({left for left, _ in pairs}) != len(pairs) or len(
|
|
147
|
+
{right for _, right in pairs}
|
|
148
|
+
) != len(pairs):
|
|
149
|
+
raise FusionInterfaceError(
|
|
150
|
+
FusionInterfaceIssue(
|
|
151
|
+
FusionInterfaceIssueCode.INVALID_MAPPING,
|
|
152
|
+
"Interface mappings must be injective.",
|
|
153
|
+
)
|
|
154
|
+
)
|
|
155
|
+
if any(
|
|
156
|
+
left not in forward_graph or right not in backward_graph
|
|
157
|
+
for left, right in pairs
|
|
158
|
+
):
|
|
159
|
+
raise FusionInterfaceError(
|
|
160
|
+
FusionInterfaceIssue(
|
|
161
|
+
FusionInterfaceIssueCode.TARGET_MISMATCH,
|
|
162
|
+
"Interface images must exist in both source graphs.",
|
|
163
|
+
)
|
|
164
|
+
)
|
|
165
|
+
return pairs
|
|
166
|
+
|
|
167
|
+
|
|
168
|
+
def _compatible_node_label(
|
|
169
|
+
forward_attrs: Mapping[str, Any],
|
|
170
|
+
backward_attrs: Mapping[str, Any],
|
|
171
|
+
*,
|
|
172
|
+
node_keys: Sequence[str],
|
|
173
|
+
element_key: str,
|
|
174
|
+
wildcard_values: tuple[Any, ...],
|
|
175
|
+
forward_node: Hashable,
|
|
176
|
+
backward_node: Hashable,
|
|
177
|
+
allow_hcount_resolution: bool,
|
|
178
|
+
) -> tuple[Any, ...]:
|
|
179
|
+
forward_wildcard = forward_attrs.get(element_key) in wildcard_values
|
|
180
|
+
backward_wildcard = backward_attrs.get(element_key) in wildcard_values
|
|
181
|
+
if forward_wildcard or backward_wildcard:
|
|
182
|
+
concrete = backward_attrs if forward_wildcard else forward_attrs
|
|
183
|
+
return _attribute_signature(concrete, node_keys)
|
|
184
|
+
left_label = _attribute_signature(forward_attrs, node_keys)
|
|
185
|
+
right_label = _attribute_signature(backward_attrs, node_keys)
|
|
186
|
+
forward_hcount = _effective_hcount(forward_attrs)
|
|
187
|
+
backward_hcount = _effective_hcount(backward_attrs)
|
|
188
|
+
hcount_conflict = (
|
|
189
|
+
not allow_hcount_resolution
|
|
190
|
+
and forward_hcount is not None
|
|
191
|
+
and backward_hcount is not None
|
|
192
|
+
and forward_hcount != backward_hcount
|
|
193
|
+
)
|
|
194
|
+
if left_label != right_label or hcount_conflict:
|
|
195
|
+
raise FusionInterfaceError(
|
|
196
|
+
FusionInterfaceIssue(
|
|
197
|
+
FusionInterfaceIssueCode.NODE_CONFLICT,
|
|
198
|
+
"Mapped concrete nodes disagree on interface attributes.",
|
|
199
|
+
{
|
|
200
|
+
"forward_node": repr(forward_node),
|
|
201
|
+
"backward_node": repr(backward_node),
|
|
202
|
+
"forward_hcount": forward_hcount,
|
|
203
|
+
"backward_hcount": backward_hcount,
|
|
204
|
+
},
|
|
205
|
+
)
|
|
206
|
+
)
|
|
207
|
+
return left_label
|
|
208
|
+
|
|
209
|
+
|
|
210
|
+
def _endpoint_scalar(value: Any) -> Any:
|
|
211
|
+
if isinstance(value, (tuple, list)) and len(value) == 2 and value[0] == value[1]:
|
|
212
|
+
return value[0]
|
|
213
|
+
return value
|
|
214
|
+
|
|
215
|
+
|
|
216
|
+
def _effective_hcount(attributes: Mapping[str, Any]) -> Any:
|
|
217
|
+
"""Normalize implicit H and explicit-H neighbor bookkeeping."""
|
|
218
|
+
hcount = attributes.get("hcount")
|
|
219
|
+
neighbours = attributes.get("neighbors")
|
|
220
|
+
if isinstance(hcount, (tuple, list)) and len(hcount) == 2:
|
|
221
|
+
if isinstance(neighbours, (tuple, list)) and len(neighbours) == 2:
|
|
222
|
+
return tuple(
|
|
223
|
+
hcount[index]
|
|
224
|
+
+ sum(item == "H" for item in (neighbours[index] or ()))
|
|
225
|
+
for index in range(2)
|
|
226
|
+
)
|
|
227
|
+
return tuple(hcount)
|
|
228
|
+
if isinstance(hcount, int) and isinstance(neighbours, (tuple, list)):
|
|
229
|
+
return hcount + sum(item == "H" for item in neighbours)
|
|
230
|
+
return hcount
|
|
231
|
+
|
|
232
|
+
|
|
233
|
+
def _owns_completion_port(
|
|
234
|
+
graph: nx.Graph,
|
|
235
|
+
node: Hashable,
|
|
236
|
+
*,
|
|
237
|
+
element_key: str,
|
|
238
|
+
role_key: str,
|
|
239
|
+
wildcard_values: tuple[Any, ...],
|
|
240
|
+
) -> bool:
|
|
241
|
+
completion_roles = {
|
|
242
|
+
"attachment_port",
|
|
243
|
+
"radical_completion",
|
|
244
|
+
"hydrogen_completion",
|
|
245
|
+
}
|
|
246
|
+
return any(
|
|
247
|
+
graph.nodes[neighbour].get(element_key) in wildcard_values
|
|
248
|
+
and graph.nodes[neighbour].get(role_key) in completion_roles
|
|
249
|
+
and graph.nodes[neighbour].get("owner") == node
|
|
250
|
+
for neighbour in graph.neighbors(node)
|
|
251
|
+
)
|
|
252
|
+
|
|
253
|
+
|
|
254
|
+
def _constraint_accepts_concrete(
|
|
255
|
+
constraint: WildcardConstraint,
|
|
256
|
+
attributes: Mapping[str, Any],
|
|
257
|
+
*,
|
|
258
|
+
graph: nx.Graph,
|
|
259
|
+
node: Hashable,
|
|
260
|
+
arm: Mapping[Hashable, Hashable],
|
|
261
|
+
element_key: str,
|
|
262
|
+
) -> bool:
|
|
263
|
+
"""Evaluate a concrete resolution through the canonical constraint API."""
|
|
264
|
+
concrete: dict[str, Any] = {
|
|
265
|
+
"element": _endpoint_scalar(attributes.get(element_key)),
|
|
266
|
+
"charge": _endpoint_scalar(attributes.get("charge", 0)),
|
|
267
|
+
"radical": _endpoint_scalar(attributes.get("radical", 0)),
|
|
268
|
+
"side": _endpoint_scalar(attributes.get("side")),
|
|
269
|
+
"stereo_slot": _endpoint_scalar(attributes.get("stereo_slot")),
|
|
270
|
+
"virtual_kind": _endpoint_scalar(attributes.get("virtual_kind")),
|
|
271
|
+
"mapped_identity": _endpoint_scalar(attributes.get("mapped_identity")),
|
|
272
|
+
"materialization": _endpoint_scalar(attributes.get("materialization")),
|
|
273
|
+
# Resolving one wildcard consumes one unit of its capacity/resource.
|
|
274
|
+
"capacity": 1,
|
|
275
|
+
"resource_usage": 1,
|
|
276
|
+
}
|
|
277
|
+
if constraint.owner is not None:
|
|
278
|
+
concrete_owner = arm.get(constraint.owner)
|
|
279
|
+
if concrete_owner is not None and graph.has_edge(node, concrete_owner):
|
|
280
|
+
concrete["owner"] = constraint.owner
|
|
281
|
+
edge = graph.edges[node, concrete_owner]
|
|
282
|
+
concrete["bond_order"] = _endpoint_scalar(edge.get("order"))
|
|
283
|
+
else:
|
|
284
|
+
concrete["owner"] = None
|
|
285
|
+
return constraint.satisfies(concrete)
|
|
286
|
+
|
|
287
|
+
|
|
288
|
+
def _common_interface_edges(
|
|
289
|
+
forward_graph: nx.Graph,
|
|
290
|
+
backward_graph: nx.Graph,
|
|
291
|
+
forward_arm: Mapping[Hashable, Hashable],
|
|
292
|
+
backward_arm: Mapping[Hashable, Hashable],
|
|
293
|
+
edge_keys: Sequence[str],
|
|
294
|
+
) -> tuple[tuple[Hashable, Hashable, tuple[Any, ...]], ...]:
|
|
295
|
+
edges: list[tuple[Hashable, Hashable, tuple[Any, ...]]] = []
|
|
296
|
+
inverse_forward = {target: source for source, target in forward_arm.items()}
|
|
297
|
+
for f_left, f_right in forward_graph.edges:
|
|
298
|
+
if f_left not in inverse_forward or f_right not in inverse_forward:
|
|
299
|
+
continue
|
|
300
|
+
left, right = inverse_forward[f_left], inverse_forward[f_right]
|
|
301
|
+
b_left, b_right = backward_arm[left], backward_arm[right]
|
|
302
|
+
if not backward_graph.has_edge(b_left, b_right):
|
|
303
|
+
continue
|
|
304
|
+
f_label = _attribute_signature(forward_graph.edges[f_left, f_right], edge_keys)
|
|
305
|
+
b_label = _attribute_signature(backward_graph.edges[b_left, b_right], edge_keys)
|
|
306
|
+
if f_label != b_label:
|
|
307
|
+
raise FusionInterfaceError(
|
|
308
|
+
FusionInterfaceIssue(
|
|
309
|
+
FusionInterfaceIssueCode.EDGE_CONFLICT,
|
|
310
|
+
"Mapped interface edges disagree on bond attributes.",
|
|
311
|
+
{"edge": (repr(left), repr(right))},
|
|
312
|
+
)
|
|
313
|
+
)
|
|
314
|
+
edges.append((left, right, f_label))
|
|
315
|
+
return tuple(sorted(edges, key=repr))
|
|
316
|
+
|
|
317
|
+
|
|
318
|
+
@dataclass(frozen=True)
|
|
319
|
+
class FusionInterface:
|
|
320
|
+
"""A common graph ``K`` with injective arms into two source graphs."""
|
|
321
|
+
|
|
322
|
+
forward_morphism: GraphMorphism
|
|
323
|
+
backward_morphism: GraphMorphism
|
|
324
|
+
node_labels: tuple[tuple[Hashable, tuple[Any, ...]], ...] = ()
|
|
325
|
+
edges: tuple[tuple[Hashable, Hashable, tuple[Any, ...]], ...] = ()
|
|
326
|
+
stereo_effects: tuple[tuple[str, str, str, StereoEffect], ...] = ()
|
|
327
|
+
|
|
328
|
+
def __post_init__(self) -> None:
|
|
329
|
+
forward = self.forward_morphism
|
|
330
|
+
backward = self.backward_morphism
|
|
331
|
+
if (
|
|
332
|
+
forward.source != backward.source
|
|
333
|
+
or forward.source_nodes != backward.source_nodes
|
|
334
|
+
):
|
|
335
|
+
raise FusionInterfaceError(
|
|
336
|
+
FusionInterfaceIssue(
|
|
337
|
+
FusionInterfaceIssueCode.SOURCE_MISMATCH,
|
|
338
|
+
"Both fusion arms must have the same interface source.",
|
|
339
|
+
)
|
|
340
|
+
)
|
|
341
|
+
labels = tuple(sorted(tuple(self.node_labels), key=lambda item: repr(item[0])))
|
|
342
|
+
if labels and {node for node, _ in labels} != set(forward.source_nodes):
|
|
343
|
+
raise FusionInterfaceError(
|
|
344
|
+
FusionInterfaceIssue(
|
|
345
|
+
FusionInterfaceIssueCode.INVALID_MAPPING,
|
|
346
|
+
"Interface node labels must be total on K.",
|
|
347
|
+
)
|
|
348
|
+
)
|
|
349
|
+
normalized_edges = tuple(
|
|
350
|
+
sorted(
|
|
351
|
+
(
|
|
352
|
+
(
|
|
353
|
+
(left, right, label)
|
|
354
|
+
if repr(left) <= repr(right)
|
|
355
|
+
else (right, left, label)
|
|
356
|
+
)
|
|
357
|
+
for left, right, label in self.edges
|
|
358
|
+
),
|
|
359
|
+
key=repr,
|
|
360
|
+
)
|
|
361
|
+
)
|
|
362
|
+
if any(
|
|
363
|
+
left not in forward.source_nodes or right not in forward.source_nodes
|
|
364
|
+
for left, right, _ in normalized_edges
|
|
365
|
+
):
|
|
366
|
+
raise FusionInterfaceError(
|
|
367
|
+
FusionInterfaceIssue(
|
|
368
|
+
FusionInterfaceIssueCode.INVALID_MAPPING,
|
|
369
|
+
"Interface edges must have endpoints in K.",
|
|
370
|
+
)
|
|
371
|
+
)
|
|
372
|
+
object.__setattr__(self, "node_labels", labels)
|
|
373
|
+
object.__setattr__(self, "edges", normalized_edges)
|
|
374
|
+
effects = tuple(
|
|
375
|
+
sorted(
|
|
376
|
+
(
|
|
377
|
+
(
|
|
378
|
+
side,
|
|
379
|
+
layer,
|
|
380
|
+
descriptor_id,
|
|
381
|
+
(
|
|
382
|
+
effect
|
|
383
|
+
if isinstance(effect, StereoEffect)
|
|
384
|
+
else StereoEffect(effect)
|
|
385
|
+
),
|
|
386
|
+
)
|
|
387
|
+
for side, layer, descriptor_id, effect in self.stereo_effects
|
|
388
|
+
),
|
|
389
|
+
key=repr,
|
|
390
|
+
)
|
|
391
|
+
)
|
|
392
|
+
if any(side not in {"forward", "backward"} for side, _, _, _ in effects):
|
|
393
|
+
raise ValueError("Stereo effects require side 'forward' or 'backward'.")
|
|
394
|
+
object.__setattr__(self, "stereo_effects", effects)
|
|
395
|
+
|
|
396
|
+
f_theta = forward.substitutions
|
|
397
|
+
b_theta = backward.substitutions
|
|
398
|
+
for node in forward.source_nodes:
|
|
399
|
+
left = f_theta.get(node)
|
|
400
|
+
right = b_theta.get(node)
|
|
401
|
+
if (
|
|
402
|
+
left is not None
|
|
403
|
+
and right is not None
|
|
404
|
+
and not left.intersect(right).valid
|
|
405
|
+
):
|
|
406
|
+
raise FusionInterfaceError(
|
|
407
|
+
FusionInterfaceIssue(
|
|
408
|
+
FusionInterfaceIssueCode.WILDCARD_CONFLICT,
|
|
409
|
+
"Wildcard substitutions contradict across the interface.",
|
|
410
|
+
{"interface_node": repr(node)},
|
|
411
|
+
)
|
|
412
|
+
)
|
|
413
|
+
|
|
414
|
+
edge_pairs = {frozenset((left, right)) for left, right, _ in normalized_edges}
|
|
415
|
+
for node, constraint in self.substitutions.items():
|
|
416
|
+
if (
|
|
417
|
+
constraint.owner is not None
|
|
418
|
+
and frozenset((node, constraint.owner)) not in edge_pairs
|
|
419
|
+
):
|
|
420
|
+
raise FusionInterfaceError(
|
|
421
|
+
FusionInterfaceIssue(
|
|
422
|
+
FusionInterfaceIssueCode.OWNER_OUTSIDE_INTERFACE,
|
|
423
|
+
"Wildcard owner incidence is absent from K.",
|
|
424
|
+
{
|
|
425
|
+
"interface_node": repr(node),
|
|
426
|
+
"owner": repr(constraint.owner),
|
|
427
|
+
},
|
|
428
|
+
)
|
|
429
|
+
)
|
|
430
|
+
|
|
431
|
+
@property
|
|
432
|
+
def interface_nodes(self) -> frozenset[Hashable]:
|
|
433
|
+
return self.forward_morphism.source_nodes
|
|
434
|
+
|
|
435
|
+
@property
|
|
436
|
+
def substitutions(self) -> dict[Hashable, WildcardConstraint]:
|
|
437
|
+
"""Return the normalized cross-arm substitution environment."""
|
|
438
|
+
result: dict[Hashable, WildcardConstraint] = {}
|
|
439
|
+
forward = self.forward_morphism.substitutions
|
|
440
|
+
backward = self.backward_morphism.substitutions
|
|
441
|
+
for node in self.interface_nodes:
|
|
442
|
+
left = forward.get(node)
|
|
443
|
+
right = backward.get(node)
|
|
444
|
+
if left is None and right is None:
|
|
445
|
+
continue
|
|
446
|
+
if left is None:
|
|
447
|
+
result[node] = right # type: ignore[assignment]
|
|
448
|
+
elif right is None:
|
|
449
|
+
result[node] = left
|
|
450
|
+
else:
|
|
451
|
+
unified = left.intersect(right)
|
|
452
|
+
if unified.constraint is not None:
|
|
453
|
+
result[node] = unified.constraint
|
|
454
|
+
return result
|
|
455
|
+
|
|
456
|
+
def to_dict(self) -> dict[str, Any]:
|
|
457
|
+
"""Return the interface and both morphism arms as proof data."""
|
|
458
|
+
|
|
459
|
+
def morphism_payload(morphism: GraphMorphism) -> dict[str, Any]:
|
|
460
|
+
return {
|
|
461
|
+
"source": repr(morphism.source),
|
|
462
|
+
"target": repr(morphism.target),
|
|
463
|
+
"mapping": [(repr(left), repr(right)) for left, right in morphism.f],
|
|
464
|
+
"theta": [
|
|
465
|
+
{
|
|
466
|
+
"node": repr(node),
|
|
467
|
+
"constraint": constraint.normalized(),
|
|
468
|
+
}
|
|
469
|
+
for node, constraint in morphism.theta
|
|
470
|
+
],
|
|
471
|
+
"canonical_signature": morphism.canonical_signature(),
|
|
472
|
+
}
|
|
473
|
+
|
|
474
|
+
return {
|
|
475
|
+
"nodes": [repr(node) for node in sorted(self.interface_nodes, key=repr)],
|
|
476
|
+
"node_labels": [(repr(node), label) for node, label in self.node_labels],
|
|
477
|
+
"edges": [
|
|
478
|
+
(repr(left), repr(right), label) for left, right, label in self.edges
|
|
479
|
+
],
|
|
480
|
+
"stereo_effects": [
|
|
481
|
+
{
|
|
482
|
+
"side": side,
|
|
483
|
+
"layer": layer,
|
|
484
|
+
"descriptor_id": descriptor_id,
|
|
485
|
+
"effect": effect.value,
|
|
486
|
+
}
|
|
487
|
+
for side, layer, descriptor_id, effect in self.stereo_effects
|
|
488
|
+
],
|
|
489
|
+
"forward_morphism": morphism_payload(self.forward_morphism),
|
|
490
|
+
"backward_morphism": morphism_payload(self.backward_morphism),
|
|
491
|
+
"canonical_signature": self.canonical_signature(),
|
|
492
|
+
}
|
|
493
|
+
|
|
494
|
+
def canonical_signature(self) -> tuple[Any, ...]:
|
|
495
|
+
"""Return a relabeling-invariant signature of K and both arms."""
|
|
496
|
+
graph = nx.Graph()
|
|
497
|
+
labels = dict(self.node_labels)
|
|
498
|
+
substitutions = self.substitutions
|
|
499
|
+
for node in self.interface_nodes:
|
|
500
|
+
constraint = substitutions.get(node)
|
|
501
|
+
graph.add_node(
|
|
502
|
+
node,
|
|
503
|
+
signature=repr(
|
|
504
|
+
(
|
|
505
|
+
labels.get(node, ()),
|
|
506
|
+
constraint.normalized() if constraint is not None else None,
|
|
507
|
+
)
|
|
508
|
+
),
|
|
509
|
+
)
|
|
510
|
+
for left, right, label in self.edges:
|
|
511
|
+
graph.add_edge(left, right, signature=repr(label))
|
|
512
|
+
digest = nx.weisfeiler_lehman_graph_hash(
|
|
513
|
+
graph,
|
|
514
|
+
node_attr="signature",
|
|
515
|
+
edge_attr="signature",
|
|
516
|
+
iterations=FUSION_WL_ITERATIONS,
|
|
517
|
+
digest_size=16,
|
|
518
|
+
)
|
|
519
|
+
arms = tuple(
|
|
520
|
+
sorted(
|
|
521
|
+
(
|
|
522
|
+
self.forward_morphism.canonical_signature(),
|
|
523
|
+
self.backward_morphism.canonical_signature(),
|
|
524
|
+
),
|
|
525
|
+
key=repr,
|
|
526
|
+
)
|
|
527
|
+
)
|
|
528
|
+
effects = tuple(
|
|
529
|
+
(side, layer, descriptor_id, effect.value)
|
|
530
|
+
for side, layer, descriptor_id, effect in self.stereo_effects
|
|
531
|
+
)
|
|
532
|
+
return (digest, arms, effects)
|
|
533
|
+
|
|
534
|
+
def with_stereo_effects(
|
|
535
|
+
self,
|
|
536
|
+
effects: Mapping[tuple[str, str, str], StereoEffect | str],
|
|
537
|
+
) -> "FusionInterface":
|
|
538
|
+
"""Return a copy carrying explicit rule-authoritative stereo effects."""
|
|
539
|
+
return replace(
|
|
540
|
+
self,
|
|
541
|
+
stereo_effects=tuple(
|
|
542
|
+
(side, layer, descriptor_id, StereoEffect(effect))
|
|
543
|
+
for (side, layer, descriptor_id), effect in effects.items()
|
|
544
|
+
),
|
|
545
|
+
)
|
|
546
|
+
|
|
547
|
+
@classmethod
|
|
548
|
+
def from_mapping(
|
|
549
|
+
cls,
|
|
550
|
+
forward_graph: nx.Graph,
|
|
551
|
+
backward_graph: nx.Graph,
|
|
552
|
+
mapping: Mapping[Hashable, Hashable],
|
|
553
|
+
*,
|
|
554
|
+
node_keys: Sequence[str] = DEFAULT_INTERFACE_NODE_KEYS,
|
|
555
|
+
edge_keys: Sequence[str] = DEFAULT_INTERFACE_EDGE_KEYS,
|
|
556
|
+
element_key: str = "element",
|
|
557
|
+
role_key: str = "wildcard_role",
|
|
558
|
+
wildcard_element: Any = "*",
|
|
559
|
+
) -> "FusionInterface":
|
|
560
|
+
"""Validate a proposed forward-to-backward overlap and build K."""
|
|
561
|
+
pairs = _validated_mapping_pairs(forward_graph, backward_graph, mapping)
|
|
562
|
+
|
|
563
|
+
interface_nodes = frozenset(range(len(pairs)))
|
|
564
|
+
forward_arm = {index: left for index, (left, _) in enumerate(pairs)}
|
|
565
|
+
backward_arm = {index: right for index, (_, right) in enumerate(pairs)}
|
|
566
|
+
inverse_forward = {value: key for key, value in forward_arm.items()}
|
|
567
|
+
inverse_backward = {value: key for key, value in backward_arm.items()}
|
|
568
|
+
forward_theta: dict[Hashable, WildcardConstraint] = {}
|
|
569
|
+
backward_theta: dict[Hashable, WildcardConstraint] = {}
|
|
570
|
+
labels: list[tuple[Hashable, tuple[Any, ...]]] = []
|
|
571
|
+
wildcard_values = _wildcard_values(wildcard_element)
|
|
572
|
+
|
|
573
|
+
for interface_node, (forward_node, backward_node) in enumerate(pairs):
|
|
574
|
+
forward_attrs = forward_graph.nodes[forward_node]
|
|
575
|
+
backward_attrs = backward_graph.nodes[backward_node]
|
|
576
|
+
forward_wildcard = forward_attrs.get(element_key) in wildcard_values
|
|
577
|
+
backward_wildcard = backward_attrs.get(element_key) in wildcard_values
|
|
578
|
+
labels.append(
|
|
579
|
+
(
|
|
580
|
+
interface_node,
|
|
581
|
+
_compatible_node_label(
|
|
582
|
+
forward_attrs,
|
|
583
|
+
backward_attrs,
|
|
584
|
+
node_keys=node_keys,
|
|
585
|
+
element_key=element_key,
|
|
586
|
+
wildcard_values=wildcard_values,
|
|
587
|
+
forward_node=forward_node,
|
|
588
|
+
backward_node=backward_node,
|
|
589
|
+
allow_hcount_resolution=(
|
|
590
|
+
_owns_completion_port(
|
|
591
|
+
forward_graph,
|
|
592
|
+
forward_node,
|
|
593
|
+
element_key=element_key,
|
|
594
|
+
role_key=role_key,
|
|
595
|
+
wildcard_values=wildcard_values,
|
|
596
|
+
)
|
|
597
|
+
or _owns_completion_port(
|
|
598
|
+
backward_graph,
|
|
599
|
+
backward_node,
|
|
600
|
+
element_key=element_key,
|
|
601
|
+
role_key=role_key,
|
|
602
|
+
wildcard_values=wildcard_values,
|
|
603
|
+
)
|
|
604
|
+
),
|
|
605
|
+
),
|
|
606
|
+
)
|
|
607
|
+
)
|
|
608
|
+
|
|
609
|
+
if forward_wildcard:
|
|
610
|
+
constraint = _constraint_for_interface(
|
|
611
|
+
forward_graph,
|
|
612
|
+
forward_node,
|
|
613
|
+
inverse_forward,
|
|
614
|
+
element_key=element_key,
|
|
615
|
+
role_key=role_key,
|
|
616
|
+
wildcard_element=wildcard_element,
|
|
617
|
+
)
|
|
618
|
+
if constraint is not None:
|
|
619
|
+
forward_theta[interface_node] = constraint
|
|
620
|
+
if backward_wildcard:
|
|
621
|
+
constraint = _constraint_for_interface(
|
|
622
|
+
backward_graph,
|
|
623
|
+
backward_node,
|
|
624
|
+
inverse_backward,
|
|
625
|
+
element_key=element_key,
|
|
626
|
+
role_key=role_key,
|
|
627
|
+
wildcard_element=wildcard_element,
|
|
628
|
+
)
|
|
629
|
+
if constraint is not None:
|
|
630
|
+
backward_theta[interface_node] = constraint
|
|
631
|
+
if forward_wildcard and not backward_wildcard:
|
|
632
|
+
constraint = forward_theta.get(interface_node)
|
|
633
|
+
if constraint is not None and not _constraint_accepts_concrete(
|
|
634
|
+
constraint,
|
|
635
|
+
backward_attrs,
|
|
636
|
+
graph=backward_graph,
|
|
637
|
+
node=backward_node,
|
|
638
|
+
arm=backward_arm,
|
|
639
|
+
element_key=element_key,
|
|
640
|
+
):
|
|
641
|
+
raise FusionInterfaceError(
|
|
642
|
+
FusionInterfaceIssue(
|
|
643
|
+
FusionInterfaceIssueCode.WILDCARD_CONFLICT,
|
|
644
|
+
"Backward concrete state violates the forward wildcard domain.",
|
|
645
|
+
{"interface_node": repr(interface_node)},
|
|
646
|
+
)
|
|
647
|
+
)
|
|
648
|
+
if backward_wildcard and not forward_wildcard:
|
|
649
|
+
constraint = backward_theta.get(interface_node)
|
|
650
|
+
if constraint is not None and not _constraint_accepts_concrete(
|
|
651
|
+
constraint,
|
|
652
|
+
forward_attrs,
|
|
653
|
+
graph=forward_graph,
|
|
654
|
+
node=forward_node,
|
|
655
|
+
arm=forward_arm,
|
|
656
|
+
element_key=element_key,
|
|
657
|
+
):
|
|
658
|
+
raise FusionInterfaceError(
|
|
659
|
+
FusionInterfaceIssue(
|
|
660
|
+
FusionInterfaceIssueCode.WILDCARD_CONFLICT,
|
|
661
|
+
"Forward concrete state violates the backward wildcard domain.",
|
|
662
|
+
{"interface_node": repr(interface_node)},
|
|
663
|
+
)
|
|
664
|
+
)
|
|
665
|
+
|
|
666
|
+
edges = _common_interface_edges(
|
|
667
|
+
forward_graph,
|
|
668
|
+
backward_graph,
|
|
669
|
+
forward_arm,
|
|
670
|
+
backward_arm,
|
|
671
|
+
edge_keys,
|
|
672
|
+
)
|
|
673
|
+
|
|
674
|
+
forward = GraphMorphism(
|
|
675
|
+
"K",
|
|
676
|
+
"forward",
|
|
677
|
+
interface_nodes,
|
|
678
|
+
frozenset(forward_graph.nodes),
|
|
679
|
+
forward_arm,
|
|
680
|
+
forward_theta,
|
|
681
|
+
)
|
|
682
|
+
backward = GraphMorphism(
|
|
683
|
+
"K",
|
|
684
|
+
"backward",
|
|
685
|
+
interface_nodes,
|
|
686
|
+
frozenset(backward_graph.nodes),
|
|
687
|
+
backward_arm,
|
|
688
|
+
backward_theta,
|
|
689
|
+
)
|
|
690
|
+
return cls(forward, backward, tuple(labels), edges)
|
|
691
|
+
|
|
692
|
+
|
|
693
|
+
__all__ = [
|
|
694
|
+
"DEFAULT_INTERFACE_EDGE_KEYS",
|
|
695
|
+
"DEFAULT_INTERFACE_NODE_KEYS",
|
|
696
|
+
"FusionInterface",
|
|
697
|
+
"FusionInterfaceError",
|
|
698
|
+
"FusionInterfaceIssue",
|
|
699
|
+
"FusionInterfaceIssueCode",
|
|
700
|
+
]
|