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
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- synkit/Graph/utils.py +324 -0
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- 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
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- 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
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- 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
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- synkit/Synthesis/MSR/path_finder.py +239 -0
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"""Non-mutating pushout-style construction with explicit provenance."""
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NODE_CONFLICT = "FUSION_CONSTRUCTION_NODE_CONFLICT"
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STEREO_CONFLICT = "FUSION_CONSTRUCTION_STEREO_CONFLICT"
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SOURCE_MUTATED = "FUSION_CONSTRUCTION_SOURCE_MUTATED"
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virtual = parse_virtual_reference(reference)
|
|
92
|
+
if virtual is not None and virtual.center in reference_mapping:
|
|
93
|
+
mapping[reference] = virtual_reference(
|
|
94
|
+
virtual.kind,
|
|
95
|
+
reference_mapping[virtual.center],
|
|
96
|
+
)
|
|
97
|
+
return mapping
|
|
98
|
+
|
|
99
|
+
|
|
100
|
+
def _configuration_payload(configuration: StereoConfiguration) -> dict[str, Any]:
|
|
101
|
+
return {
|
|
102
|
+
"shape": configuration.shape,
|
|
103
|
+
"frame": stable_value(configuration.frame),
|
|
104
|
+
"specification": configuration.specification.value,
|
|
105
|
+
"canonical_frame": stable_value(configuration.canonical_frame),
|
|
106
|
+
}
|
|
107
|
+
|
|
108
|
+
|
|
109
|
+
def _relation_payload(relation: StereoRelation) -> dict[str, Any]:
|
|
110
|
+
return {
|
|
111
|
+
"kind": relation.kind.value,
|
|
112
|
+
"shape": relation.shape,
|
|
113
|
+
"class_id": (
|
|
114
|
+
list(relation.class_id) if relation.class_id is not None else None
|
|
115
|
+
),
|
|
116
|
+
"witness": (
|
|
117
|
+
list(relation.witness.permutation.image)
|
|
118
|
+
if relation.witness is not None
|
|
119
|
+
else None
|
|
120
|
+
),
|
|
121
|
+
"source_canonical": stable_value(relation.source_canonical),
|
|
122
|
+
"target_canonical": stable_value(relation.target_canonical),
|
|
123
|
+
}
|
|
124
|
+
|
|
125
|
+
|
|
126
|
+
@dataclass(frozen=True)
|
|
127
|
+
class FusionStereoEvidence:
|
|
128
|
+
"""Replayable local orbit evidence for one transported descriptor."""
|
|
129
|
+
|
|
130
|
+
side: str
|
|
131
|
+
layer: str
|
|
132
|
+
source_descriptor_id: str
|
|
133
|
+
target_descriptor_id: str
|
|
134
|
+
effect: StereoEffect
|
|
135
|
+
source_configuration: StereoConfiguration
|
|
136
|
+
interface_configuration: StereoConfiguration
|
|
137
|
+
target_configuration: StereoConfiguration
|
|
138
|
+
reference_mapping: tuple[tuple[int, int], ...]
|
|
139
|
+
source_to_interface: StereoRelation
|
|
140
|
+
interface_to_candidate: StereoRelation
|
|
141
|
+
direct_relation: StereoRelation
|
|
142
|
+
composed_witness: PermutationWitness | None
|
|
143
|
+
endpoint_orbit: tuple[Any, ...]
|
|
144
|
+
|
|
145
|
+
@classmethod
|
|
146
|
+
def create(
|
|
147
|
+
cls,
|
|
148
|
+
*,
|
|
149
|
+
side: str,
|
|
150
|
+
layer: str,
|
|
151
|
+
source_descriptor_id: str,
|
|
152
|
+
target_descriptor_id: str,
|
|
153
|
+
effect: StereoEffect,
|
|
154
|
+
source_configuration: StereoConfiguration,
|
|
155
|
+
interface_configuration: StereoConfiguration,
|
|
156
|
+
target_configuration: StereoConfiguration,
|
|
157
|
+
reference_mapping: Mapping[int, int],
|
|
158
|
+
) -> "FusionStereoEvidence":
|
|
159
|
+
rebased = source_configuration.relabel(
|
|
160
|
+
_configuration_mapping(source_configuration, reference_mapping)
|
|
161
|
+
)
|
|
162
|
+
source_relation = rebased.relation_to(interface_configuration)
|
|
163
|
+
target_relation = interface_configuration.relation_to(target_configuration)
|
|
164
|
+
direct_relation = rebased.relation_to(target_configuration)
|
|
165
|
+
composed = (
|
|
166
|
+
source_relation.witness.then(target_relation.witness)
|
|
167
|
+
if source_relation.witness is not None
|
|
168
|
+
and target_relation.witness is not None
|
|
169
|
+
else None
|
|
170
|
+
)
|
|
171
|
+
evidence = cls(
|
|
172
|
+
side,
|
|
173
|
+
layer,
|
|
174
|
+
source_descriptor_id,
|
|
175
|
+
target_descriptor_id,
|
|
176
|
+
StereoEffect(effect),
|
|
177
|
+
source_configuration,
|
|
178
|
+
interface_configuration,
|
|
179
|
+
target_configuration,
|
|
180
|
+
tuple(sorted(reference_mapping.items())),
|
|
181
|
+
source_relation,
|
|
182
|
+
target_relation,
|
|
183
|
+
direct_relation,
|
|
184
|
+
composed,
|
|
185
|
+
target_configuration.canonical_frame,
|
|
186
|
+
)
|
|
187
|
+
replay = evidence.replay()
|
|
188
|
+
if not replay.valid:
|
|
189
|
+
raise FusionConstructionError(
|
|
190
|
+
FusionConstructionIssue(
|
|
191
|
+
FusionConstructionIssueCode.STEREO_CONFLICT,
|
|
192
|
+
"Fusion stereo evidence is not replayable.",
|
|
193
|
+
{
|
|
194
|
+
"side": side,
|
|
195
|
+
"layer": layer,
|
|
196
|
+
"descriptor_id": source_descriptor_id,
|
|
197
|
+
"issues": replay.issues,
|
|
198
|
+
},
|
|
199
|
+
)
|
|
200
|
+
)
|
|
201
|
+
return evidence
|
|
202
|
+
|
|
203
|
+
def replay(self) -> FusionStereoReplay:
|
|
204
|
+
issues: list[str] = []
|
|
205
|
+
relations = (
|
|
206
|
+
("source_to_interface", self.source_to_interface),
|
|
207
|
+
("interface_to_candidate", self.interface_to_candidate),
|
|
208
|
+
("direct_relation", self.direct_relation),
|
|
209
|
+
)
|
|
210
|
+
for name, relation in relations:
|
|
211
|
+
if relation.witness is None:
|
|
212
|
+
issues.append(f"{name}:missing_witness")
|
|
213
|
+
rebased = self.source_configuration.relabel(
|
|
214
|
+
_configuration_mapping(
|
|
215
|
+
self.source_configuration,
|
|
216
|
+
dict(self.reference_mapping),
|
|
217
|
+
)
|
|
218
|
+
)
|
|
219
|
+
if self.source_to_interface.witness is not None and (
|
|
220
|
+
self.source_to_interface.witness.apply(rebased.frame)
|
|
221
|
+
!= self.interface_configuration.frame
|
|
222
|
+
):
|
|
223
|
+
issues.append("source_to_interface:witness_replay")
|
|
224
|
+
if self.interface_to_candidate.witness is not None and (
|
|
225
|
+
self.interface_to_candidate.witness.apply(
|
|
226
|
+
self.interface_configuration.frame
|
|
227
|
+
)
|
|
228
|
+
!= self.target_configuration.frame
|
|
229
|
+
):
|
|
230
|
+
issues.append("interface_to_candidate:witness_replay")
|
|
231
|
+
if self.composed_witness is None:
|
|
232
|
+
issues.append("composition:missing_witness")
|
|
233
|
+
elif self.composed_witness.apply(rebased.frame) != (
|
|
234
|
+
self.target_configuration.frame
|
|
235
|
+
):
|
|
236
|
+
issues.append("composition:witness_replay")
|
|
237
|
+
classified = rebased.relation_to(self.target_configuration)
|
|
238
|
+
if (
|
|
239
|
+
classified.kind is not self.direct_relation.kind
|
|
240
|
+
or classified.class_id != self.direct_relation.class_id
|
|
241
|
+
):
|
|
242
|
+
issues.append("direct_relation:classification")
|
|
243
|
+
if self.endpoint_orbit != self.target_configuration.canonical_frame:
|
|
244
|
+
issues.append("endpoint:orbit")
|
|
245
|
+
return FusionStereoReplay(not issues, tuple(issues))
|
|
246
|
+
|
|
247
|
+
def canonical_signature(self) -> tuple[Any, ...]:
|
|
248
|
+
"""Return numbering- and operand-independent local proof identity."""
|
|
249
|
+
relation_signature = lambda relation: ( # noqa: E731
|
|
250
|
+
relation.kind.value,
|
|
251
|
+
relation.shape,
|
|
252
|
+
relation.class_id,
|
|
253
|
+
(
|
|
254
|
+
relation.witness.permutation.image
|
|
255
|
+
if relation.witness is not None
|
|
256
|
+
else None
|
|
257
|
+
),
|
|
258
|
+
)
|
|
259
|
+
return (
|
|
260
|
+
self.layer,
|
|
261
|
+
self.effect.value,
|
|
262
|
+
self.source_configuration.shape,
|
|
263
|
+
self.source_configuration.specification.value,
|
|
264
|
+
self.interface_configuration.specification.value,
|
|
265
|
+
self.target_configuration.specification.value,
|
|
266
|
+
len(self.reference_mapping),
|
|
267
|
+
relation_signature(self.source_to_interface),
|
|
268
|
+
relation_signature(self.interface_to_candidate),
|
|
269
|
+
relation_signature(self.direct_relation),
|
|
270
|
+
(
|
|
271
|
+
self.composed_witness.permutation.image
|
|
272
|
+
if self.composed_witness is not None
|
|
273
|
+
else None
|
|
274
|
+
),
|
|
275
|
+
)
|
|
276
|
+
|
|
277
|
+
def to_dict(self) -> dict[str, Any]:
|
|
278
|
+
return {
|
|
279
|
+
"side": self.side,
|
|
280
|
+
"layer": self.layer,
|
|
281
|
+
"source_descriptor_id": self.source_descriptor_id,
|
|
282
|
+
"target_descriptor_id": self.target_descriptor_id,
|
|
283
|
+
"effect": self.effect.value,
|
|
284
|
+
"source_configuration": _configuration_payload(self.source_configuration),
|
|
285
|
+
"reference_mapping": [list(pair) for pair in self.reference_mapping],
|
|
286
|
+
"interface_configuration": _configuration_payload(
|
|
287
|
+
self.interface_configuration
|
|
288
|
+
),
|
|
289
|
+
"source_to_interface": _relation_payload(self.source_to_interface),
|
|
290
|
+
"interface_to_candidate": _relation_payload(self.interface_to_candidate),
|
|
291
|
+
"target_configuration": _configuration_payload(self.target_configuration),
|
|
292
|
+
"direct_relation": _relation_payload(self.direct_relation),
|
|
293
|
+
"composed_witness": (
|
|
294
|
+
list(self.composed_witness.permutation.image)
|
|
295
|
+
if self.composed_witness is not None
|
|
296
|
+
else None
|
|
297
|
+
),
|
|
298
|
+
"endpoint_orbit": stable_value(self.endpoint_orbit),
|
|
299
|
+
}
|
|
300
|
+
|
|
301
|
+
|
|
302
|
+
@dataclass(frozen=True)
|
|
303
|
+
class FusionProvenance:
|
|
304
|
+
"""Origin records for every node, edge, and wildcard substitution."""
|
|
305
|
+
|
|
306
|
+
node_sources: tuple[tuple[int, tuple[tuple[str, Hashable], ...]], ...]
|
|
307
|
+
edge_sources: tuple[
|
|
308
|
+
tuple[tuple[int, int], tuple[tuple[str, Hashable, Hashable], ...]], ...
|
|
309
|
+
]
|
|
310
|
+
wildcard_substitutions: tuple[tuple[Hashable, tuple[Any, ...]], ...] = ()
|
|
311
|
+
stereo_evidence: tuple[FusionStereoEvidence, ...] = ()
|
|
312
|
+
stereo_comparisons: tuple[StereoSemanticComparison, ...] = ()
|
|
313
|
+
|
|
314
|
+
def to_dict(self) -> dict[str, Any]:
|
|
315
|
+
return {
|
|
316
|
+
"node_sources": [
|
|
317
|
+
{
|
|
318
|
+
"fused_node": fused,
|
|
319
|
+
"sources": [
|
|
320
|
+
{"side": side, "node": repr(node)} for side, node in sources
|
|
321
|
+
],
|
|
322
|
+
}
|
|
323
|
+
for fused, sources in self.node_sources
|
|
324
|
+
],
|
|
325
|
+
"edge_sources": [
|
|
326
|
+
{
|
|
327
|
+
"fused_edge": edge,
|
|
328
|
+
"sources": [
|
|
329
|
+
{"side": side, "edge": (repr(left), repr(right))}
|
|
330
|
+
for side, left, right in sources
|
|
331
|
+
],
|
|
332
|
+
}
|
|
333
|
+
for edge, sources in self.edge_sources
|
|
334
|
+
],
|
|
335
|
+
"wildcard_substitutions": [
|
|
336
|
+
{"interface_node": repr(node), "constraint": stable_value(value)}
|
|
337
|
+
for node, value in self.wildcard_substitutions
|
|
338
|
+
],
|
|
339
|
+
"stereo_evidence": [
|
|
340
|
+
evidence.to_dict() for evidence in self.stereo_evidence
|
|
341
|
+
],
|
|
342
|
+
"stereo_comparisons": [
|
|
343
|
+
comparison.to_dict() for comparison in self.stereo_comparisons
|
|
344
|
+
],
|
|
345
|
+
}
|
|
346
|
+
|
|
347
|
+
|
|
348
|
+
@dataclass(frozen=True)
|
|
349
|
+
class EndpointCertificate:
|
|
350
|
+
"""Commuting inclusion evidence for both source graphs."""
|
|
351
|
+
|
|
352
|
+
forward_inclusion: tuple[tuple[Hashable, int], ...]
|
|
353
|
+
backward_inclusion: tuple[tuple[Hashable, int], ...]
|
|
354
|
+
forward_nodes_verified: int
|
|
355
|
+
backward_nodes_verified: int
|
|
356
|
+
forward_edges_verified: int
|
|
357
|
+
backward_edges_verified: int
|
|
358
|
+
replay_status: str = "not_requested"
|
|
359
|
+
replay_reason: str | None = None
|
|
360
|
+
|
|
361
|
+
def digest_payload(self) -> dict[str, Any]:
|
|
362
|
+
return {
|
|
363
|
+
"forward_nodes_verified": self.forward_nodes_verified,
|
|
364
|
+
"backward_nodes_verified": self.backward_nodes_verified,
|
|
365
|
+
"forward_edges_verified": self.forward_edges_verified,
|
|
366
|
+
"backward_edges_verified": self.backward_edges_verified,
|
|
367
|
+
"replay_status": self.replay_status,
|
|
368
|
+
"replay_reason": self.replay_reason,
|
|
369
|
+
}
|
|
370
|
+
|
|
371
|
+
def to_dict(self) -> dict[str, Any]:
|
|
372
|
+
return {
|
|
373
|
+
**self.digest_payload(),
|
|
374
|
+
"forward_inclusion": [
|
|
375
|
+
(repr(source), target) for source, target in self.forward_inclusion
|
|
376
|
+
],
|
|
377
|
+
"backward_inclusion": [
|
|
378
|
+
(repr(source), target) for source, target in self.backward_inclusion
|
|
379
|
+
],
|
|
380
|
+
}
|
|
381
|
+
|
|
382
|
+
|
|
383
|
+
@dataclass(frozen=True)
|
|
384
|
+
class FusionConstruction:
|
|
385
|
+
graph: nx.Graph = field(compare=False, repr=False)
|
|
386
|
+
interface: FusionInterface
|
|
387
|
+
provenance: FusionProvenance
|
|
388
|
+
endpoint_certificate: EndpointCertificate
|
|
389
|
+
|
|
390
|
+
|
|
391
|
+
def _legacy_transport_stereo_descriptor(
|
|
392
|
+
descriptor: Any,
|
|
393
|
+
mapping: Mapping[int, int],
|
|
394
|
+
effect: StereoEffect,
|
|
395
|
+
) -> Any:
|
|
396
|
+
"""Reproduce proof-v1 descriptor transport without orbit operations."""
|
|
397
|
+
aligned = transport_stereo_descriptor(
|
|
398
|
+
descriptor,
|
|
399
|
+
mapping,
|
|
400
|
+
StereoReferenceDelta(effect=StereoEffect.RETAIN),
|
|
401
|
+
)
|
|
402
|
+
if effect is StereoEffect.RETAIN:
|
|
403
|
+
return aligned
|
|
404
|
+
if effect is StereoEffect.UNSPECIFIED:
|
|
405
|
+
return type(aligned)(aligned.atoms, None, aligned.provenance)
|
|
406
|
+
if aligned.parity is None or aligned.descriptor_class == "square_planar":
|
|
407
|
+
return aligned
|
|
408
|
+
if aligned.descriptor_class == "planar_bond":
|
|
409
|
+
atoms = (aligned.atoms[1], aligned.atoms[0], *aligned.atoms[2:])
|
|
410
|
+
return type(aligned)(atoms, 0, aligned.provenance)
|
|
411
|
+
return type(aligned)(aligned.atoms, -aligned.parity, aligned.provenance)
|
|
412
|
+
|
|
413
|
+
|
|
414
|
+
def _attribute_signature(
|
|
415
|
+
attributes: Mapping[str, Any], keys: Sequence[str]
|
|
416
|
+
) -> tuple[Any, ...]:
|
|
417
|
+
return tuple((key, stable_value(attributes.get(key))) for key in keys)
|
|
418
|
+
|
|
419
|
+
|
|
420
|
+
def _is_wildcard(
|
|
421
|
+
attributes: Mapping[str, Any], element_key: str, wildcard_element: Any
|
|
422
|
+
) -> bool:
|
|
423
|
+
scalar = (
|
|
424
|
+
wildcard_element[0]
|
|
425
|
+
if isinstance(wildcard_element, (tuple, list))
|
|
426
|
+
else wildcard_element
|
|
427
|
+
)
|
|
428
|
+
return attributes.get(element_key) in (wildcard_element, scalar)
|
|
429
|
+
|
|
430
|
+
|
|
431
|
+
def _merge_node_attributes(
|
|
432
|
+
forward: Mapping[str, Any],
|
|
433
|
+
backward: Mapping[str, Any],
|
|
434
|
+
*,
|
|
435
|
+
node_keys: Sequence[str],
|
|
436
|
+
element_key: str,
|
|
437
|
+
wildcard_element: Any,
|
|
438
|
+
) -> dict[str, Any]:
|
|
439
|
+
forward_wc = _is_wildcard(forward, element_key, wildcard_element)
|
|
440
|
+
backward_wc = _is_wildcard(backward, element_key, wildcard_element)
|
|
441
|
+
if not forward_wc and not backward_wc:
|
|
442
|
+
if _attribute_signature(forward, node_keys) != _attribute_signature(
|
|
443
|
+
backward, node_keys
|
|
444
|
+
):
|
|
445
|
+
raise FusionConstructionError(
|
|
446
|
+
FusionConstructionIssue(
|
|
447
|
+
FusionConstructionIssueCode.NODE_CONFLICT,
|
|
448
|
+
"Concrete quotient nodes have incompatible attributes.",
|
|
449
|
+
)
|
|
450
|
+
)
|
|
451
|
+
preferred = forward
|
|
452
|
+
elif forward_wc and not backward_wc:
|
|
453
|
+
preferred = backward
|
|
454
|
+
elif backward_wc and not forward_wc:
|
|
455
|
+
preferred = forward
|
|
456
|
+
else:
|
|
457
|
+
preferred = forward
|
|
458
|
+
merged = copy.deepcopy(dict(preferred))
|
|
459
|
+
wildcard_only_keys = {
|
|
460
|
+
"wildcard_role",
|
|
461
|
+
"owner",
|
|
462
|
+
"elements",
|
|
463
|
+
"charges",
|
|
464
|
+
"radicals",
|
|
465
|
+
"bond_orders",
|
|
466
|
+
"side",
|
|
467
|
+
"capacity",
|
|
468
|
+
"resource_budget",
|
|
469
|
+
"stereo_slot",
|
|
470
|
+
"virtual_kind",
|
|
471
|
+
"mapped_identity",
|
|
472
|
+
"materialization",
|
|
473
|
+
}
|
|
474
|
+
resolving_to_concrete = forward_wc != backward_wc
|
|
475
|
+
for key, value in backward.items():
|
|
476
|
+
# The constraint is retained in the interface/provenance proof. Once
|
|
477
|
+
# its wildcard node is identified with a concrete atom, wildcard-only
|
|
478
|
+
# metadata must not leak onto that concrete quotient node.
|
|
479
|
+
if resolving_to_concrete and key in wildcard_only_keys:
|
|
480
|
+
continue
|
|
481
|
+
merged.setdefault(key, copy.deepcopy(value))
|
|
482
|
+
return merged
|
|
483
|
+
|
|
484
|
+
|
|
485
|
+
def _merge_graph_stereo(
|
|
486
|
+
fused: nx.Graph,
|
|
487
|
+
forward: nx.Graph,
|
|
488
|
+
backward: nx.Graph,
|
|
489
|
+
interface: FusionInterface,
|
|
490
|
+
forward_inclusion: Mapping[Hashable, int],
|
|
491
|
+
backward_inclusion: Mapping[Hashable, int],
|
|
492
|
+
*,
|
|
493
|
+
semantics: str = "orbit",
|
|
494
|
+
) -> tuple[
|
|
495
|
+
tuple[FusionStereoEvidence, ...],
|
|
496
|
+
tuple[StereoSemanticComparison, ...],
|
|
497
|
+
]:
|
|
498
|
+
"""Merge already map-stable descriptor registries without inference."""
|
|
499
|
+
combined: dict[str, dict[str, Any]] = {}
|
|
500
|
+
proof: list[FusionStereoEvidence] = []
|
|
501
|
+
consumed_effects: set[tuple[str, str, str]] = set()
|
|
502
|
+
comparisons: list[StereoSemanticComparison] = []
|
|
503
|
+
semantics_mode = StereoSemanticsMode(semantics)
|
|
504
|
+
effects = {
|
|
505
|
+
(side, layer, descriptor_id): effect
|
|
506
|
+
for side, layer, descriptor_id, effect in interface.stereo_effects
|
|
507
|
+
}
|
|
508
|
+
for side, graph, inclusion in (
|
|
509
|
+
("forward", forward, forward_inclusion),
|
|
510
|
+
("backward", backward, backward_inclusion),
|
|
511
|
+
):
|
|
512
|
+
for layer, registry in stereo_registry_layers(graph).items():
|
|
513
|
+
reference_mapping = _stereo_reference_mapping(
|
|
514
|
+
graph, fused, inclusion, layer
|
|
515
|
+
)
|
|
516
|
+
deltas = {
|
|
517
|
+
descriptor_key: StereoReferenceDelta(
|
|
518
|
+
effect=effects.get(
|
|
519
|
+
(side, layer, descriptor_key), StereoEffect.RETAIN
|
|
520
|
+
)
|
|
521
|
+
)
|
|
522
|
+
for descriptor_key in registry
|
|
523
|
+
}
|
|
524
|
+
try:
|
|
525
|
+
transport_stereo_registry(registry, reference_mapping, deltas)
|
|
526
|
+
except StereoTransportError as exc:
|
|
527
|
+
raise FusionConstructionError(
|
|
528
|
+
FusionConstructionIssue(
|
|
529
|
+
FusionConstructionIssueCode.STEREO_CONFLICT,
|
|
530
|
+
"A source stereo frame cannot be transported into the quotient.",
|
|
531
|
+
{"side": side, "layer": layer, "reason": str(exc)},
|
|
532
|
+
)
|
|
533
|
+
) from exc
|
|
534
|
+
target = combined.setdefault(layer, {})
|
|
535
|
+
for source_key in sorted(registry):
|
|
536
|
+
source_descriptor = registry[source_key]
|
|
537
|
+
delta = deltas[source_key]
|
|
538
|
+
interface_descriptor = transport_stereo_descriptor(
|
|
539
|
+
source_descriptor,
|
|
540
|
+
reference_mapping,
|
|
541
|
+
StereoReferenceDelta(effect=StereoEffect.RETAIN),
|
|
542
|
+
)
|
|
543
|
+
orbit_descriptor = transport_stereo_descriptor(
|
|
544
|
+
source_descriptor,
|
|
545
|
+
reference_mapping,
|
|
546
|
+
delta,
|
|
547
|
+
)
|
|
548
|
+
legacy_descriptor = _legacy_transport_stereo_descriptor(
|
|
549
|
+
source_descriptor,
|
|
550
|
+
reference_mapping,
|
|
551
|
+
delta.effect,
|
|
552
|
+
)
|
|
553
|
+
descriptor = (
|
|
554
|
+
legacy_descriptor
|
|
555
|
+
if semantics_mode is StereoSemanticsMode.LEGACY
|
|
556
|
+
else orbit_descriptor
|
|
557
|
+
)
|
|
558
|
+
descriptor_key = descriptor_id(descriptor)
|
|
559
|
+
if (side, layer, source_key) in effects:
|
|
560
|
+
consumed_effects.add((side, layer, source_key))
|
|
561
|
+
previous = target.get(descriptor_key)
|
|
562
|
+
if previous is not None and previous != descriptor:
|
|
563
|
+
raise FusionConstructionError(
|
|
564
|
+
FusionConstructionIssue(
|
|
565
|
+
FusionConstructionIssueCode.STEREO_CONFLICT,
|
|
566
|
+
"Source stereo descriptors disagree in the quotient.",
|
|
567
|
+
{"descriptor_id": descriptor_key, "layer": layer},
|
|
568
|
+
)
|
|
569
|
+
)
|
|
570
|
+
target[descriptor_key] = descriptor
|
|
571
|
+
evidence = FusionStereoEvidence.create(
|
|
572
|
+
side=side,
|
|
573
|
+
layer=layer,
|
|
574
|
+
source_descriptor_id=source_key,
|
|
575
|
+
target_descriptor_id=descriptor_key,
|
|
576
|
+
effect=delta.effect,
|
|
577
|
+
source_configuration=source_descriptor.configuration,
|
|
578
|
+
interface_configuration=interface_descriptor.configuration,
|
|
579
|
+
target_configuration=descriptor.configuration,
|
|
580
|
+
reference_mapping=reference_mapping,
|
|
581
|
+
)
|
|
582
|
+
proof.append(evidence)
|
|
583
|
+
if semantics_mode is StereoSemanticsMode.COMPARE:
|
|
584
|
+
comparisons.append(
|
|
585
|
+
StereoSemanticComparison.create(
|
|
586
|
+
"fusion_stereo_transport",
|
|
587
|
+
legacy_canonical_form(orbit_descriptor),
|
|
588
|
+
legacy_canonical_form(legacy_descriptor),
|
|
589
|
+
)
|
|
590
|
+
)
|
|
591
|
+
legacy_projection = legacy_classify_stereo_change(
|
|
592
|
+
interface_descriptor,
|
|
593
|
+
legacy_descriptor,
|
|
594
|
+
)
|
|
595
|
+
legacy_relation = {
|
|
596
|
+
"RETAINED": "equivalent",
|
|
597
|
+
"INVERTED": "opposite",
|
|
598
|
+
}.get(legacy_projection, "unspecified")
|
|
599
|
+
expected_divergence = None
|
|
600
|
+
if (
|
|
601
|
+
evidence.interface_to_candidate.kind.value == "reconfigured"
|
|
602
|
+
and evidence.interface_to_candidate.shape
|
|
603
|
+
in {"trigonal_bipyramidal", "octahedral"}
|
|
604
|
+
and delta.effect is StereoEffect.INVERT
|
|
605
|
+
):
|
|
606
|
+
expected_divergence = "nonbinary_orbit_reconfiguration"
|
|
607
|
+
comparisons.append(
|
|
608
|
+
StereoSemanticComparison.create(
|
|
609
|
+
"fusion_stereo_relation",
|
|
610
|
+
evidence.interface_to_candidate.kind.value,
|
|
611
|
+
legacy_relation,
|
|
612
|
+
expected_divergence=expected_divergence,
|
|
613
|
+
)
|
|
614
|
+
)
|
|
615
|
+
if combined:
|
|
616
|
+
fused.graph["stereo_descriptors"] = combined
|
|
617
|
+
unknown_effects = set(effects) - consumed_effects
|
|
618
|
+
if unknown_effects:
|
|
619
|
+
raise FusionConstructionError(
|
|
620
|
+
FusionConstructionIssue(
|
|
621
|
+
FusionConstructionIssueCode.STEREO_CONFLICT,
|
|
622
|
+
"A declared fusion stereo effect has no source descriptor.",
|
|
623
|
+
{"effects": tuple(sorted(unknown_effects))},
|
|
624
|
+
)
|
|
625
|
+
)
|
|
626
|
+
return (
|
|
627
|
+
tuple(
|
|
628
|
+
sorted(
|
|
629
|
+
proof,
|
|
630
|
+
key=lambda evidence: (
|
|
631
|
+
evidence.canonical_signature(),
|
|
632
|
+
evidence.side,
|
|
633
|
+
evidence.layer,
|
|
634
|
+
evidence.source_descriptor_id,
|
|
635
|
+
),
|
|
636
|
+
)
|
|
637
|
+
),
|
|
638
|
+
tuple(comparisons),
|
|
639
|
+
)
|
|
640
|
+
|
|
641
|
+
|
|
642
|
+
def _layer_reference(
|
|
643
|
+
graph: nx.Graph,
|
|
644
|
+
node: Hashable,
|
|
645
|
+
layer: str,
|
|
646
|
+
) -> Hashable:
|
|
647
|
+
atom_map = graph.nodes[node].get("atom_map")
|
|
648
|
+
if isinstance(atom_map, (tuple, list)) and len(atom_map) == 2:
|
|
649
|
+
index = {"reactant": 0, "product": 1}.get(layer)
|
|
650
|
+
if index is not None and type(atom_map[index]) is int:
|
|
651
|
+
return atom_map[index]
|
|
652
|
+
if type(atom_map) is int:
|
|
653
|
+
return atom_map
|
|
654
|
+
return node
|
|
655
|
+
|
|
656
|
+
|
|
657
|
+
def _stereo_reference_mapping(
|
|
658
|
+
source: nx.Graph,
|
|
659
|
+
fused: nx.Graph,
|
|
660
|
+
inclusion: Mapping[Hashable, int],
|
|
661
|
+
layer: str,
|
|
662
|
+
) -> dict[int, int]:
|
|
663
|
+
mapping: dict[int, int] = {}
|
|
664
|
+
for source_node, fused_node in inclusion.items():
|
|
665
|
+
source_reference = _layer_reference(source, source_node, layer)
|
|
666
|
+
target_reference = _layer_reference(fused, fused_node, layer)
|
|
667
|
+
if type(source_reference) is not int or type(target_reference) is not int:
|
|
668
|
+
continue
|
|
669
|
+
previous = mapping.get(source_reference)
|
|
670
|
+
if previous is not None and previous != target_reference:
|
|
671
|
+
raise FusionConstructionError(
|
|
672
|
+
FusionConstructionIssue(
|
|
673
|
+
FusionConstructionIssueCode.STEREO_CONFLICT,
|
|
674
|
+
"A stereo reference has ambiguous quotient images.",
|
|
675
|
+
{"reference": source_reference},
|
|
676
|
+
)
|
|
677
|
+
)
|
|
678
|
+
mapping[source_reference] = target_reference
|
|
679
|
+
return mapping
|
|
680
|
+
|
|
681
|
+
|
|
682
|
+
def _verify_endpoint(
|
|
683
|
+
source: nx.Graph,
|
|
684
|
+
fused: nx.Graph,
|
|
685
|
+
inclusion: Mapping[Hashable, int],
|
|
686
|
+
) -> tuple[int, int]:
|
|
687
|
+
if set(inclusion) != set(source.nodes):
|
|
688
|
+
raise FusionConstructionError(
|
|
689
|
+
FusionConstructionIssue(
|
|
690
|
+
FusionConstructionIssueCode.ENDPOINT_NONCOMMUTATIVE,
|
|
691
|
+
"Endpoint inclusion is not total.",
|
|
692
|
+
)
|
|
693
|
+
)
|
|
694
|
+
for left, right in source.edges:
|
|
695
|
+
if not fused.has_edge(inclusion[left], inclusion[right]):
|
|
696
|
+
raise FusionConstructionError(
|
|
697
|
+
FusionConstructionIssue(
|
|
698
|
+
FusionConstructionIssueCode.ENDPOINT_NONCOMMUTATIVE,
|
|
699
|
+
"A source edge is absent from the fused quotient.",
|
|
700
|
+
{"edge": (repr(left), repr(right))},
|
|
701
|
+
)
|
|
702
|
+
)
|
|
703
|
+
return source.number_of_nodes(), source.number_of_edges()
|
|
704
|
+
|
|
705
|
+
|
|
706
|
+
def _publish_stereo_diagnostics(
|
|
707
|
+
target: list[StereoSemanticComparison] | None,
|
|
708
|
+
values: tuple[StereoSemanticComparison, ...],
|
|
709
|
+
) -> None:
|
|
710
|
+
if target is not None:
|
|
711
|
+
target.extend(values)
|
|
712
|
+
|
|
713
|
+
|
|
714
|
+
def construct_pushout(
|
|
715
|
+
forward_graph: nx.Graph,
|
|
716
|
+
backward_graph: nx.Graph,
|
|
717
|
+
interface: FusionInterface,
|
|
718
|
+
*,
|
|
719
|
+
node_keys: Sequence[str] = DEFAULT_INTERFACE_NODE_KEYS,
|
|
720
|
+
edge_keys: Sequence[str] = DEFAULT_INTERFACE_EDGE_KEYS,
|
|
721
|
+
element_key: str = "element",
|
|
722
|
+
wildcard_element: Any = "*",
|
|
723
|
+
replay_status: str = "not_requested",
|
|
724
|
+
replay_reason: str | None = None,
|
|
725
|
+
stereo_semantics: str = "orbit",
|
|
726
|
+
stereo_diagnostics: list[StereoSemanticComparison] | None = None,
|
|
727
|
+
) -> FusionConstruction:
|
|
728
|
+
"""Construct a pushout-like quotient after all interface checks pass."""
|
|
729
|
+
if any(
|
|
730
|
+
isinstance(graph, (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
|
|
731
|
+
for graph in (forward_graph, backward_graph)
|
|
732
|
+
):
|
|
733
|
+
raise FusionConstructionError(
|
|
734
|
+
FusionConstructionIssue(
|
|
735
|
+
FusionConstructionIssueCode.UNSUPPORTED_GRAPH,
|
|
736
|
+
"Sprint 15 verified fusion currently requires simple undirected graphs.",
|
|
737
|
+
)
|
|
738
|
+
)
|
|
739
|
+
if interface.forward_morphism.target_nodes != frozenset(forward_graph.nodes) or (
|
|
740
|
+
interface.backward_morphism.target_nodes != frozenset(backward_graph.nodes)
|
|
741
|
+
):
|
|
742
|
+
raise FusionConstructionError(
|
|
743
|
+
FusionConstructionIssue(
|
|
744
|
+
FusionConstructionIssueCode.TARGET_MISMATCH,
|
|
745
|
+
"Interface arms do not target the supplied source graphs.",
|
|
746
|
+
)
|
|
747
|
+
)
|
|
748
|
+
|
|
749
|
+
forward_snapshot = copy.deepcopy(forward_graph)
|
|
750
|
+
backward_snapshot = copy.deepcopy(backward_graph)
|
|
751
|
+
forward_arm = interface.forward_morphism.mapping
|
|
752
|
+
backward_arm = interface.backward_morphism.mapping
|
|
753
|
+
fused = nx.Graph()
|
|
754
|
+
forward_inclusion: dict[Hashable, int] = {}
|
|
755
|
+
backward_inclusion: dict[Hashable, int] = {}
|
|
756
|
+
node_sources: dict[int, list[tuple[str, Hashable]]] = {}
|
|
757
|
+
next_node = 1
|
|
758
|
+
|
|
759
|
+
for interface_node in sorted(interface.interface_nodes, key=repr):
|
|
760
|
+
forward_node = forward_arm[interface_node]
|
|
761
|
+
backward_node = backward_arm[interface_node]
|
|
762
|
+
attributes = _merge_node_attributes(
|
|
763
|
+
forward_graph.nodes[forward_node],
|
|
764
|
+
backward_graph.nodes[backward_node],
|
|
765
|
+
node_keys=node_keys,
|
|
766
|
+
element_key=element_key,
|
|
767
|
+
wildcard_element=wildcard_element,
|
|
768
|
+
)
|
|
769
|
+
fused.add_node(next_node, **attributes)
|
|
770
|
+
forward_inclusion[forward_node] = next_node
|
|
771
|
+
backward_inclusion[backward_node] = next_node
|
|
772
|
+
node_sources[next_node] = [
|
|
773
|
+
("forward", forward_node),
|
|
774
|
+
("backward", backward_node),
|
|
775
|
+
]
|
|
776
|
+
next_node += 1
|
|
777
|
+
|
|
778
|
+
for side, graph, inclusion in (
|
|
779
|
+
("forward", forward_graph, forward_inclusion),
|
|
780
|
+
("backward", backward_graph, backward_inclusion),
|
|
781
|
+
):
|
|
782
|
+
for source_node in sorted(graph.nodes, key=repr):
|
|
783
|
+
if source_node in inclusion:
|
|
784
|
+
continue
|
|
785
|
+
fused.add_node(next_node, **copy.deepcopy(graph.nodes[source_node]))
|
|
786
|
+
inclusion[source_node] = next_node
|
|
787
|
+
node_sources[next_node] = [(side, source_node)]
|
|
788
|
+
next_node += 1
|
|
789
|
+
|
|
790
|
+
edge_sources: dict[tuple[int, int], list[tuple[str, Hashable, Hashable]]] = {}
|
|
791
|
+
for side, graph, inclusion in (
|
|
792
|
+
("forward", forward_graph, forward_inclusion),
|
|
793
|
+
("backward", backward_graph, backward_inclusion),
|
|
794
|
+
):
|
|
795
|
+
for left, right, attributes in graph.edges(data=True):
|
|
796
|
+
fused_left, fused_right = inclusion[left], inclusion[right]
|
|
797
|
+
edge = tuple(sorted((fused_left, fused_right)))
|
|
798
|
+
if fused.has_edge(*edge):
|
|
799
|
+
existing = fused.edges[edge]
|
|
800
|
+
if _attribute_signature(existing, edge_keys) != _attribute_signature(
|
|
801
|
+
attributes, edge_keys
|
|
802
|
+
):
|
|
803
|
+
raise FusionConstructionError(
|
|
804
|
+
FusionConstructionIssue(
|
|
805
|
+
FusionConstructionIssueCode.EDGE_CONFLICT,
|
|
806
|
+
"Quotient edge attributes conflict across sources.",
|
|
807
|
+
{"edge": edge},
|
|
808
|
+
)
|
|
809
|
+
)
|
|
810
|
+
for key, value in attributes.items():
|
|
811
|
+
existing.setdefault(key, copy.deepcopy(value))
|
|
812
|
+
else:
|
|
813
|
+
fused.add_edge(*edge, **copy.deepcopy(attributes))
|
|
814
|
+
edge_sources.setdefault(edge, []).append((side, left, right))
|
|
815
|
+
|
|
816
|
+
stereo_evidence, stereo_comparisons = _merge_graph_stereo(
|
|
817
|
+
fused,
|
|
818
|
+
forward_graph,
|
|
819
|
+
backward_graph,
|
|
820
|
+
interface,
|
|
821
|
+
forward_inclusion,
|
|
822
|
+
backward_inclusion,
|
|
823
|
+
semantics=stereo_semantics,
|
|
824
|
+
)
|
|
825
|
+
_publish_stereo_diagnostics(stereo_diagnostics, stereo_comparisons)
|
|
826
|
+
forward_counts = _verify_endpoint(forward_graph, fused, forward_inclusion)
|
|
827
|
+
backward_counts = _verify_endpoint(backward_graph, fused, backward_inclusion)
|
|
828
|
+
if not nx.utils.graphs_equal(
|
|
829
|
+
forward_graph, forward_snapshot
|
|
830
|
+
) or not nx.utils.graphs_equal(backward_graph, backward_snapshot):
|
|
831
|
+
raise FusionConstructionError(
|
|
832
|
+
FusionConstructionIssue(
|
|
833
|
+
FusionConstructionIssueCode.SOURCE_MUTATED,
|
|
834
|
+
"Fusion construction mutated a source graph.",
|
|
835
|
+
)
|
|
836
|
+
)
|
|
837
|
+
|
|
838
|
+
substitutions = tuple(
|
|
839
|
+
sorted(
|
|
840
|
+
(
|
|
841
|
+
(node, constraint.normalized())
|
|
842
|
+
for node, constraint in interface.substitutions.items()
|
|
843
|
+
),
|
|
844
|
+
key=lambda item: repr(item[0]),
|
|
845
|
+
)
|
|
846
|
+
)
|
|
847
|
+
provenance = FusionProvenance(
|
|
848
|
+
tuple((node, tuple(sources)) for node, sources in sorted(node_sources.items())),
|
|
849
|
+
tuple((edge, tuple(sources)) for edge, sources in sorted(edge_sources.items())),
|
|
850
|
+
substitutions,
|
|
851
|
+
stereo_evidence,
|
|
852
|
+
stereo_comparisons,
|
|
853
|
+
)
|
|
854
|
+
certificate = EndpointCertificate(
|
|
855
|
+
tuple(sorted(forward_inclusion.items(), key=lambda item: repr(item[0]))),
|
|
856
|
+
tuple(sorted(backward_inclusion.items(), key=lambda item: repr(item[0]))),
|
|
857
|
+
forward_counts[0],
|
|
858
|
+
backward_counts[0],
|
|
859
|
+
forward_counts[1],
|
|
860
|
+
backward_counts[1],
|
|
861
|
+
replay_status,
|
|
862
|
+
replay_reason,
|
|
863
|
+
)
|
|
864
|
+
return FusionConstruction(fused, interface, provenance, certificate)
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
__all__ = [
|
|
868
|
+
"EndpointCertificate",
|
|
869
|
+
"FusionConstruction",
|
|
870
|
+
"FusionConstructionError",
|
|
871
|
+
"FusionConstructionIssue",
|
|
872
|
+
"FusionConstructionIssueCode",
|
|
873
|
+
"FusionProvenance",
|
|
874
|
+
"FusionStereoEvidence",
|
|
875
|
+
"FusionStereoReplay",
|
|
876
|
+
"construct_pushout",
|
|
877
|
+
]
|