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
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#include "synkit_mapper/mces/mces.h"
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#include "../solvers/seed.h"
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#include "synkit_mapper/core/runtime.h"
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namespace synkit_mapper {
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namespace {
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struct Vertex {
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int32_t source, target;
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};
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struct Metadata {
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int64_t vertices = 0, edges = 0, graph_bytes = 0;
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};
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thread_local Metadata metadata;
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struct PhaseTimer {
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double &total;
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Clock::time_point start = Clock::now();
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~PhaseTimer() { total += elapsed(start); }
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};
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class CliqueSearch {
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const Problem &p;
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const Request &r;
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Callback callback;
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void *userdata;
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Statistics &s;
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Budget budget;
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std::vector<Vertex> vertices;
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std::vector<int64_t> pair_upper;
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std::vector<int> clique;
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int64_t constant = 0, best_overlap = -1, target_overlap = 0, base_bytes = 0,
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live_bytes = 0;
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bool optimize = false, at_most = false;
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bool adjacent(int a, int b) const {
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return (adjacency[a][b / 64] >> (b % 64)) & 1ULL;
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}
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int64_t weight(int a, int b) const {
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const auto &u = vertices[a], &v = vertices[b];
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return std::min(p.a2[u.source * p.n + v.source],
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p.b2[u.target * p.n + v.target]);
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}
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void memory(int64_t extra) {
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int64_t proposed = live_bytes + extra;
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if (r.memory_limit_bytes >= 0 &&
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base_bytes + proposed > r.memory_limit_bytes)
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throw Stop{SYNKIT_STOP_MEMORY};
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live_bytes = proposed;
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s.peak_memory_bytes =
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std::max(s.peak_memory_bytes, base_bytes + live_bytes);
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}
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void visit(const std::vector<int> &candidates, int64_t overlap) {
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budget.check();
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if (r.max_states >= 0 && s.nodes >= r.max_states)
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throw Stop{SYNKIT_STOP_STATES};
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++s.nodes;
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if (static_cast<int>(clique.size()) == p.n) {
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++s.leaves;
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std::vector<int32_t> mapping(p.n, -1);
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for (int v : clique)
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mapping[vertices[v].source] = vertices[v].target;
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int64_t cost = mapping_cost2(p, mapping);
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if (cost != constant - 2 * overlap)
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throw std::runtime_error(
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"Weighted MCES overlap disagrees with chemical rescoring");
|
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68
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if (s.incumbent2 < 0 || cost < s.incumbent2)
|
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s.incumbent2 = cost;
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if (optimize) {
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best_overlap = std::max(best_overlap, overlap);
|
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return;
|
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}
|
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74
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if ((at_most && overlap < target_overlap) ||
|
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(!at_most && overlap != target_overlap))
|
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return;
|
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77
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++s.candidate_count;
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s.labeled_count = s.candidate_count;
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int stop = 0;
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{
|
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81
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PhaseTimer timer{s.callback_seconds};
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82
|
+
if (callback)
|
|
83
|
+
stop = callback(mapping.data(), cost, userdata);
|
|
84
|
+
}
|
|
85
|
+
if (stop)
|
|
86
|
+
throw Stop{SYNKIT_STOP_CALLBACK};
|
|
87
|
+
budget.check();
|
|
88
|
+
if (r.max_candidates >= 0 && s.candidate_count >= r.max_candidates)
|
|
89
|
+
throw Stop{SYNKIT_STOP_CANDIDATES};
|
|
90
|
+
return;
|
|
91
|
+
}
|
|
92
|
+
// Source rows form a proper coloring of the association graph: no clique
|
|
93
|
+
// contains two vertices with the same source. A full clique needs every
|
|
94
|
+
// remaining color, giving both a size bound and safe weighted bounds.
|
|
95
|
+
std::vector<uint8_t> selected(p.n, 0);
|
|
96
|
+
for (int v : clique)
|
|
97
|
+
selected[vertices[v].source] = 1;
|
|
98
|
+
std::vector<int64_t> maximum(p.n, -1),
|
|
99
|
+
minimum(p.n, std::numeric_limits<int64_t>::max());
|
|
100
|
+
size_t checked = 0;
|
|
101
|
+
for (int v : candidates) {
|
|
102
|
+
if (!(++checked % 1024))
|
|
103
|
+
budget.check();
|
|
104
|
+
int row = vertices[v].source;
|
|
105
|
+
int64_t increment = 0;
|
|
106
|
+
for (int q : clique)
|
|
107
|
+
increment += weight(v, q);
|
|
108
|
+
maximum[row] = std::max(maximum[row], increment);
|
|
109
|
+
minimum[row] = std::min(minimum[row], increment);
|
|
110
|
+
}
|
|
111
|
+
int64_t upper = overlap, lower = overlap;
|
|
112
|
+
for (int i = 0; i < p.n; ++i)
|
|
113
|
+
if (!selected[i]) {
|
|
114
|
+
if (maximum[i] < 0)
|
|
115
|
+
return;
|
|
116
|
+
upper += maximum[i];
|
|
117
|
+
lower += minimum[i];
|
|
118
|
+
for (int k = i + 1; k < p.n; ++k)
|
|
119
|
+
if (!selected[k])
|
|
120
|
+
upper += pair_upper[i * p.n + k];
|
|
121
|
+
}
|
|
122
|
+
if (optimize
|
|
123
|
+
? upper <= best_overlap
|
|
124
|
+
: upper < target_overlap || (!at_most && lower > target_overlap))
|
|
125
|
+
return;
|
|
126
|
+
for (size_t i = 0; i < candidates.size(); ++i) {
|
|
127
|
+
budget.check();
|
|
128
|
+
int v = candidates[i];
|
|
129
|
+
std::vector<int> next;
|
|
130
|
+
next.reserve(candidates.size() - i - 1);
|
|
131
|
+
for (size_t j = i + 1; j < candidates.size(); ++j)
|
|
132
|
+
if (adjacent(v, candidates[j]))
|
|
133
|
+
next.push_back(candidates[j]);
|
|
134
|
+
if (next.size() + clique.size() + 1 < static_cast<size_t>(p.n))
|
|
135
|
+
continue;
|
|
136
|
+
int64_t increment = 0;
|
|
137
|
+
for (int q : clique)
|
|
138
|
+
increment += weight(v, q);
|
|
139
|
+
clique.push_back(v);
|
|
140
|
+
int64_t bytes = next.capacity() * sizeof(int);
|
|
141
|
+
memory(bytes);
|
|
142
|
+
try {
|
|
143
|
+
visit(next, overlap + increment);
|
|
144
|
+
} catch (...) {
|
|
145
|
+
live_bytes -= bytes;
|
|
146
|
+
clique.pop_back();
|
|
147
|
+
throw;
|
|
148
|
+
}
|
|
149
|
+
live_bytes -= bytes;
|
|
150
|
+
clique.pop_back();
|
|
151
|
+
}
|
|
152
|
+
}
|
|
153
|
+
|
|
154
|
+
public:
|
|
155
|
+
CliqueSearch(const Problem &problem, const Request &request, Callback cb,
|
|
156
|
+
void *data, Statistics &stats)
|
|
157
|
+
: p(problem), r(request), callback(cb), userdata(data), s(stats),
|
|
158
|
+
budget(request) {}
|
|
159
|
+
void solve() {
|
|
160
|
+
struct Finish {
|
|
161
|
+
Statistics &s;
|
|
162
|
+
Budget &b;
|
|
163
|
+
~Finish() { s.elapsed_seconds = b.seconds(); }
|
|
164
|
+
} finish{s, budget};
|
|
165
|
+
try {
|
|
166
|
+
budget.check();
|
|
167
|
+
std::vector<int32_t> seed;
|
|
168
|
+
{
|
|
169
|
+
PhaseTimer timer{s.model_seconds};
|
|
170
|
+
for (int i = 0; i < p.n; ++i) {
|
|
171
|
+
budget.check();
|
|
172
|
+
for (int j = 0; j < p.n; ++j)
|
|
173
|
+
if (p.types_r[i] == p.types_p[j])
|
|
174
|
+
vertices.push_back({i, j});
|
|
175
|
+
for (int k = i + 1; k < p.n; ++k)
|
|
176
|
+
constant += p.a2[i * p.n + k] + p.b2[i * p.n + k];
|
|
177
|
+
}
|
|
178
|
+
if (vertices.size() > 8192) {
|
|
179
|
+
unsupported(s);
|
|
180
|
+
return;
|
|
181
|
+
}
|
|
182
|
+
metadata.vertices = vertices.size();
|
|
183
|
+
int64_t words = (vertices.size() + 63) / 64;
|
|
184
|
+
base_bytes = sizeof(*this) + vertices.capacity() * sizeof(Vertex) +
|
|
185
|
+
vertices.size() * (sizeof(std::vector<uint64_t>) +
|
|
186
|
+
words * sizeof(uint64_t)) +
|
|
187
|
+
static_cast<int64_t>(p.n) * p.n * sizeof(int64_t) +
|
|
188
|
+
p.n * sizeof(int);
|
|
189
|
+
metadata.graph_bytes = base_bytes;
|
|
190
|
+
memory(0);
|
|
191
|
+
adjacency.resize(vertices.size(), std::vector<uint64_t>(words, 0));
|
|
192
|
+
pair_upper.assign(p.n * p.n, 0);
|
|
193
|
+
size_t checks = 0;
|
|
194
|
+
for (size_t i = 0; i < vertices.size(); ++i) {
|
|
195
|
+
budget.check();
|
|
196
|
+
for (size_t j = i + 1; j < vertices.size(); ++j) {
|
|
197
|
+
if (!(++checks % 1024))
|
|
198
|
+
budget.check();
|
|
199
|
+
const auto &u = vertices[i], &v = vertices[j];
|
|
200
|
+
if (u.source == v.source || u.target == v.target)
|
|
201
|
+
continue;
|
|
202
|
+
adjacency[i][j / 64] |= uint64_t{1} << (j % 64);
|
|
203
|
+
adjacency[j][i / 64] |= uint64_t{1} << (i % 64);
|
|
204
|
+
++metadata.edges;
|
|
205
|
+
int64_t w = weight(i, j);
|
|
206
|
+
auto &bound = pair_upper[u.source * p.n + v.source];
|
|
207
|
+
bound = std::max(bound, w);
|
|
208
|
+
pair_upper[v.source * p.n + u.source] = bound;
|
|
209
|
+
}
|
|
210
|
+
}
|
|
211
|
+
seed = solvers::detail::feasible_seed(p, budget);
|
|
212
|
+
if (!seed.empty())
|
|
213
|
+
s.incumbent2 = mapping_cost2(p, seed);
|
|
214
|
+
}
|
|
215
|
+
std::vector<int> root(vertices.size());
|
|
216
|
+
std::iota(root.begin(), root.end(), 0);
|
|
217
|
+
int64_t root_bytes = root.capacity() * sizeof(int);
|
|
218
|
+
memory(root_bytes);
|
|
219
|
+
if (r.query == SYNKIT_MINIMUM_CLASSES ||
|
|
220
|
+
r.query == SYNKIT_MINIMUM_PROOF) {
|
|
221
|
+
optimize = true;
|
|
222
|
+
if (s.incumbent2 >= 0)
|
|
223
|
+
best_overlap = (constant - s.incumbent2) / 2;
|
|
224
|
+
{
|
|
225
|
+
PhaseTimer timer{s.optimization_seconds};
|
|
226
|
+
visit(root, 0);
|
|
227
|
+
}
|
|
228
|
+
if (best_overlap < 0) {
|
|
229
|
+
s.search_complete = 1;
|
|
230
|
+
return;
|
|
231
|
+
}
|
|
232
|
+
s.minimum_proven = 1;
|
|
233
|
+
s.minimum2 = s.lower_bound2 = constant - 2 * best_overlap;
|
|
234
|
+
if (r.query == SYNKIT_MINIMUM_PROOF) {
|
|
235
|
+
s.search_complete = 1;
|
|
236
|
+
return;
|
|
237
|
+
}
|
|
238
|
+
target_overlap = best_overlap;
|
|
239
|
+
} else {
|
|
240
|
+
int64_t threshold = constant - r.target2;
|
|
241
|
+
if (r.query == SYNKIT_EXACT_DISTANCE &&
|
|
242
|
+
(threshold < 0 || threshold % 2)) {
|
|
243
|
+
s.search_complete = 1;
|
|
244
|
+
return;
|
|
245
|
+
}
|
|
246
|
+
at_most = r.query == SYNKIT_AT_MOST_DISTANCE;
|
|
247
|
+
target_overlap = threshold <= 0 ? 0 : (threshold + 1) / 2;
|
|
248
|
+
}
|
|
249
|
+
optimize = false;
|
|
250
|
+
{
|
|
251
|
+
PhaseTimer timer{s.enumeration_seconds};
|
|
252
|
+
visit(root, 0);
|
|
253
|
+
}
|
|
254
|
+
s.search_complete = 1;
|
|
255
|
+
} catch (const Stop &stop) {
|
|
256
|
+
stopped(s, stop.reason);
|
|
257
|
+
}
|
|
258
|
+
s.elapsed_seconds = budget.seconds();
|
|
259
|
+
}
|
|
260
|
+
};
|
|
261
|
+
} // namespace
|
|
262
|
+
const char *mces_run_metadata() {
|
|
263
|
+
static thread_local std::string value;
|
|
264
|
+
std::ostringstream out;
|
|
265
|
+
out << "{\"architecture\":\"weighted_association_graph_size_n_clique\","
|
|
266
|
+
"\"association_vertices\":"
|
|
267
|
+
<< metadata.vertices << ",\"association_edges\":" << metadata.edges
|
|
268
|
+
<< ",\"accounted_graph_bytes\":" << metadata.graph_bytes
|
|
269
|
+
<< ",\"memory_scope\":\"accounted_native_graph_and_clique_candidates\","
|
|
270
|
+
"\"objective_equivalence\":\"D2=C-2*weighted_common_edge_overlap\"}";
|
|
271
|
+
value = out.str();
|
|
272
|
+
return value.c_str();
|
|
273
|
+
}
|
|
274
|
+
int solve_mces(const Problem &p, const Request &r, Callback callback,
|
|
275
|
+
void *userdata, Statistics &s) {
|
|
276
|
+
initialize(s, r);
|
|
277
|
+
metadata = {};
|
|
278
|
+
s.labeled_count = 0;
|
|
279
|
+
s.peak_frontier = s.peak_frontier_bytes = -1;
|
|
280
|
+
if (r.symmetry || r.classify || r.max_classes != -1 || r.max_frontier != -1 ||
|
|
281
|
+
p.n > 256)
|
|
282
|
+
return unsupported(s);
|
|
283
|
+
CliqueSearch search(p, r, callback, userdata, s);
|
|
284
|
+
search.solve();
|
|
285
|
+
return 0;
|
|
286
|
+
}
|
|
287
|
+
} // namespace synkit_mapper
|
|
@@ -0,0 +1,334 @@
|
|
|
1
|
+
// Compile the common exact kernel once, preserving its ABI3 exports.
|
|
2
|
+
// The shared-core bridge owns preparation, optional bounds and phase
|
|
3
|
+
// accounting.
|
|
4
|
+
#include "../../../../exact/native/native_distance.cpp"
|
|
5
|
+
#include "exact_helpers.h"
|
|
6
|
+
#include "sparse_root_lp.h"
|
|
7
|
+
#include "synkit_mapper/core/pmcd_witness.h"
|
|
8
|
+
#include "synkit_mapper/core/runtime.h"
|
|
9
|
+
#include "synkit_mapper/pabs/seed.h"
|
|
10
|
+
#include "synkit_mapper/slap.h"
|
|
11
|
+
#include <set>
|
|
12
|
+
static thread_local int64_t bridge_embedding_statistics[14] = {};
|
|
13
|
+
static thread_local int64_t bridge_deck_statistics[14] = {};
|
|
14
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
15
|
+
static thread_local int64_t lp_assignment_statistics[6] = {};
|
|
16
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
17
|
+
|
|
18
|
+
namespace synkit_mapper {
|
|
19
|
+
namespace {
|
|
20
|
+
|
|
21
|
+
#include "chemical_floor.inc"
|
|
22
|
+
#include "endpoint_symmetry.inc"
|
|
23
|
+
#include "seed_heuristics.inc"
|
|
24
|
+
|
|
25
|
+
struct Receiver {
|
|
26
|
+
const Problem &p;
|
|
27
|
+
const Request &r;
|
|
28
|
+
Callback callback;
|
|
29
|
+
void *userdata;
|
|
30
|
+
Statistics &s;
|
|
31
|
+
Budget &budget;
|
|
32
|
+
static int receive(const int *map, int cost4, void *pointer) {
|
|
33
|
+
auto &self = *static_cast<Receiver *>(pointer);
|
|
34
|
+
std::vector<int32_t> mapping(map, map + self.p.n);
|
|
35
|
+
int64_t cost = mapping_cost2(self.p, mapping);
|
|
36
|
+
if (cost4 != 2 * cost)
|
|
37
|
+
throw std::runtime_error(
|
|
38
|
+
"PABS quarter-CD witness does not match rescoring");
|
|
39
|
+
const auto start = Clock::now();
|
|
40
|
+
int stop =
|
|
41
|
+
self.callback ? self.callback(mapping.data(), cost, self.userdata) : 0;
|
|
42
|
+
self.s.callback_seconds += elapsed(start);
|
|
43
|
+
++self.s.candidate_count;
|
|
44
|
+
if (stop) {
|
|
45
|
+
self.s.reason = SYNKIT_STOP_CALLBACK;
|
|
46
|
+
return 1;
|
|
47
|
+
}
|
|
48
|
+
if (self.budget.reason()) {
|
|
49
|
+
self.s.reason = self.budget.reason();
|
|
50
|
+
return 1;
|
|
51
|
+
}
|
|
52
|
+
return 0;
|
|
53
|
+
}
|
|
54
|
+
};
|
|
55
|
+
} // namespace
|
|
56
|
+
|
|
57
|
+
#include "overlap_dual.inc"
|
|
58
|
+
|
|
59
|
+
#include "profile_seed.inc"
|
|
60
|
+
|
|
61
|
+
int solve_pabs_original(const Problem &p, const Request &r, Callback callback,
|
|
62
|
+
void *userdata, Statistics &s) {
|
|
63
|
+
synkit_mapper_clear_pmcd_witness();
|
|
64
|
+
sparse_root_lp::clear();
|
|
65
|
+
std::fill(bridge_embedding_statistics, bridge_embedding_statistics + 14, 0);
|
|
66
|
+
std::fill(coherent_seed_statistics, coherent_seed_statistics + 20, 0);
|
|
67
|
+
coherent_seed_mapping.clear();
|
|
68
|
+
std::fill(conditioned_factor_cache_statistics,
|
|
69
|
+
conditioned_factor_cache_statistics + 8, 0);
|
|
70
|
+
|
|
71
|
+
std::fill(bridge_deck_statistics, bridge_deck_statistics + 14, 0);
|
|
72
|
+
bridge_deck_statistics[13] = -1;
|
|
73
|
+
Budget budget(r);
|
|
74
|
+
budget.check();
|
|
75
|
+
if (p.n > SYNKIT_PABS_MAX_VERTICES || r.classify || r.max_states != -1 ||
|
|
76
|
+
r.max_classes != -1 || r.max_frontier != -1 ||
|
|
77
|
+
r.memory_limit_bytes != -1 || r.cancel_token)
|
|
78
|
+
return unsupported(s);
|
|
79
|
+
const int n = p.n;
|
|
80
|
+
auto stage = Clock::now();
|
|
81
|
+
std::vector<int> a(n * n), b(n * n), cr(n), cp(n), order(n), pred(n * n, 0);
|
|
82
|
+
std::map<int32_t, int> types;
|
|
83
|
+
std::set<int> levels;
|
|
84
|
+
int64_t maximum2 = 0;
|
|
85
|
+
for (int i = 0; i < n; ++i) {
|
|
86
|
+
cr[i] = types.emplace(p.types_r[i], types.size()).first->second;
|
|
87
|
+
cp[i] = types.emplace(p.types_p[i], types.size()).first->second;
|
|
88
|
+
order[i] = i;
|
|
89
|
+
for (int j = 0; j < n; ++j) {
|
|
90
|
+
if (p.a2[i * n + j] > 1024 || p.b2[i * n + j] > 1024)
|
|
91
|
+
return unsupported(s);
|
|
92
|
+
a[i * n + j] = static_cast<int>(p.a2[i * n + j]);
|
|
93
|
+
b[i * n + j] = static_cast<int>(p.b2[i * n + j]);
|
|
94
|
+
levels.insert(a[i * n + j]);
|
|
95
|
+
levels.insert(b[i * n + j]);
|
|
96
|
+
if (j > i)
|
|
97
|
+
maximum2 += a[i * n + j] + b[i * n + j];
|
|
98
|
+
}
|
|
99
|
+
}
|
|
100
|
+
if (levels.size() > 16 || maximum2 > 500000)
|
|
101
|
+
return unsupported(s);
|
|
102
|
+
std::vector<int> rg, pg;
|
|
103
|
+
if (r.symmetry) {
|
|
104
|
+
rg = endpoint_generators(p, false, budget);
|
|
105
|
+
pg = endpoint_generators(p, true, budget);
|
|
106
|
+
}
|
|
107
|
+
std::stable_sort(order.begin(), order.end(), [&](int i, int j) {
|
|
108
|
+
int di = 0, dj = 0;
|
|
109
|
+
for (int k = 0; k < n; ++k) {
|
|
110
|
+
di += a[i * n + k] != 0;
|
|
111
|
+
dj += a[j * n + k] != 0;
|
|
112
|
+
}
|
|
113
|
+
return di > dj;
|
|
114
|
+
});
|
|
115
|
+
Perm seed;
|
|
116
|
+
RootDualBranchCertificate root_certificate;
|
|
117
|
+
sparse_root_lp::AssignmentCertificate assignment_certificate;
|
|
118
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
119
|
+
std::fill(lp_assignment_statistics, lp_assignment_statistics + 6, 0);
|
|
120
|
+
struct SaveAssignmentStatistics {
|
|
121
|
+
sparse_root_lp::AssignmentCertificate &certificate;
|
|
122
|
+
~SaveAssignmentStatistics() {
|
|
123
|
+
lp_assignment_statistics[0] = certificate.ready;
|
|
124
|
+
lp_assignment_statistics[1] = certificate.m;
|
|
125
|
+
lp_assignment_statistics[2] = certificate.root_bound2;
|
|
126
|
+
lp_assignment_statistics[3] = certificate.calls;
|
|
127
|
+
lp_assignment_statistics[4] = certificate.prunes;
|
|
128
|
+
lp_assignment_statistics[5] = certificate.ready && certificate.m > 64;
|
|
129
|
+
}
|
|
130
|
+
} save_assignment_statistics{assignment_certificate};
|
|
131
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
132
|
+
|
|
133
|
+
std::fill(conditioned_dual_statistics, conditioned_dual_statistics + 6, 0);
|
|
134
|
+
bool original_profile_zero = false;
|
|
135
|
+
try {
|
|
136
|
+
const bool polish =
|
|
137
|
+
r.query == SYNKIT_MINIMUM_CLASSES || r.query == SYNKIT_MINIMUM_PROOF;
|
|
138
|
+
if (!pabs::prepare_seed(p, budget, polish, seed, s.incumbent2,
|
|
139
|
+
s.lower_bound2, &original_profile_zero)) {
|
|
140
|
+
s.model_seconds += elapsed(stage);
|
|
141
|
+
return unsupported(s);
|
|
142
|
+
}
|
|
143
|
+
|
|
144
|
+
if (r.query == SYNKIT_MINIMUM_PROOF &&
|
|
145
|
+
(!original_profile_zero || s.incumbent2 > 8) &&
|
|
146
|
+
s.incumbent2 > s.lower_bound2 && budget.remaining() > 0.2) {
|
|
147
|
+
const int64_t dual = conditioned_overlap_dual_floor(
|
|
148
|
+
p, budget, std::min(0.03, budget.remaining() * 0.05),
|
|
149
|
+
root_certificate);
|
|
150
|
+
if (dual > s.incumbent2)
|
|
151
|
+
throw std::runtime_error("Invalid overlap dual bound");
|
|
152
|
+
s.lower_bound2 = std::max(s.lower_bound2, dual);
|
|
153
|
+
}
|
|
154
|
+
if (r.query == SYNKIT_MINIMUM_PROOF && n <= 256 &&
|
|
155
|
+
s.incumbent2 > s.lower_bound2 && budget.remaining() > 0.05) {
|
|
156
|
+
const int64_t lp_floor = sparse_root_lp::run(
|
|
157
|
+
p, budget, std::min(20.0, budget.remaining() * 0.7), s.incumbent2,
|
|
158
|
+
&seed, &s.incumbent2, &assignment_certificate);
|
|
159
|
+
budget.check();
|
|
160
|
+
if (lp_floor > s.incumbent2)
|
|
161
|
+
throw std::runtime_error("Invalid exact sparse LP bound");
|
|
162
|
+
s.lower_bound2 = std::max(s.lower_bound2, lp_floor);
|
|
163
|
+
}
|
|
164
|
+
|
|
165
|
+
if (r.query == SYNKIT_MINIMUM_PROOF && s.incumbent2 == s.lower_bound2) {
|
|
166
|
+
budget.check();
|
|
167
|
+
synkit_mapper_store_pmcd_witness(n, seed.data(), s.incumbent2, 1);
|
|
168
|
+
s.minimum_proven = 1;
|
|
169
|
+
s.minimum2 = s.incumbent2;
|
|
170
|
+
s.search_complete = 1;
|
|
171
|
+
s.model_seconds += elapsed(stage);
|
|
172
|
+
return 0;
|
|
173
|
+
}
|
|
174
|
+
} catch (...) {
|
|
175
|
+
s.model_seconds += elapsed(stage);
|
|
176
|
+
throw;
|
|
177
|
+
}
|
|
178
|
+
s.model_seconds += elapsed(stage);
|
|
179
|
+
|
|
180
|
+
// Eligibility uses the initial profile relaxation, before subsequent exact
|
|
181
|
+
// bounds strengthen it. This schedules an additional edge-deck proof only.
|
|
182
|
+
if ((r.query == SYNKIT_MINIMUM_CLASSES || r.query == SYNKIT_MINIMUM_PROOF) &&
|
|
183
|
+
original_profile_zero && s.incumbent2 > s.lower_bound2 && n <= 512) {
|
|
184
|
+
stage = Clock::now();
|
|
185
|
+
int64_t mass_a = 0, mass_b = 0, g = 0, edge_a = 0, edge_b = 0;
|
|
186
|
+
for (int i = 0; i < n; ++i)
|
|
187
|
+
for (int j = 0; j < i; ++j) {
|
|
188
|
+
mass_a += p.a2[i * n + j];
|
|
189
|
+
mass_b += p.b2[i * n + j];
|
|
190
|
+
g = std::gcd(g, p.a2[i * n + j]);
|
|
191
|
+
g = std::gcd(g, p.b2[i * n + j]);
|
|
192
|
+
edge_a += p.a2[i * n + j] > 0;
|
|
193
|
+
edge_b += p.b2[i * n + j] > 0;
|
|
194
|
+
}
|
|
195
|
+
const int units = g == 1 ? 3 : 2;
|
|
196
|
+
int64_t families[6] = {};
|
|
197
|
+
const bool small_families =
|
|
198
|
+
g > 0 && mass_a == mass_b &&
|
|
199
|
+
pabs::edge_deck_sizes(n, p.a2, p.b2, p.types_r, p.types_p, units,
|
|
200
|
+
families) == 0 &&
|
|
201
|
+
families[units - 1] <= 60000 && families[units + 2] <= 60000;
|
|
202
|
+
budget.check();
|
|
203
|
+
if (g > 0 && mass_a == mass_b && s.incumbent2 <= 16 * g &&
|
|
204
|
+
s.lower_bound2 < 2LL * (units + 1) * g && small_families) {
|
|
205
|
+
const double allowance = std::min(0.65, budget.remaining() * 0.70);
|
|
206
|
+
Perm candidate(n);
|
|
207
|
+
int64_t lower2 = 0, witness2 = -1;
|
|
208
|
+
const int result =
|
|
209
|
+
pabs::edge_deck(n, p.a2, p.b2, p.types_r, p.types_p, units, allowance,
|
|
210
|
+
2000000, s.incumbent2, candidate.data(), &lower2,
|
|
211
|
+
&witness2, bridge_deck_statistics);
|
|
212
|
+
bridge_deck_statistics[12] = result;
|
|
213
|
+
budget.check();
|
|
214
|
+
if (result >= 0 && lower2 >= 0) {
|
|
215
|
+
if (lower2 > s.incumbent2)
|
|
216
|
+
throw std::runtime_error("Overlap bound exceeds feasible incumbent");
|
|
217
|
+
if (result == 1) {
|
|
218
|
+
const int64_t score = mapping_cost2(
|
|
219
|
+
p, std::vector<int32_t>(candidate.begin(), candidate.end()));
|
|
220
|
+
if (score != witness2 || score != lower2 || score < s.lower_bound2)
|
|
221
|
+
throw std::runtime_error("Invalid overlap minimum witness");
|
|
222
|
+
seed = std::move(candidate);
|
|
223
|
+
s.incumbent2 = score;
|
|
224
|
+
}
|
|
225
|
+
s.lower_bound2 = std::max(s.lower_bound2, lower2);
|
|
226
|
+
bridge_deck_statistics[13] = s.lower_bound2;
|
|
227
|
+
if (s.incumbent2 == s.lower_bound2) {
|
|
228
|
+
s.minimum_proven = 1;
|
|
229
|
+
s.minimum2 = s.incumbent2;
|
|
230
|
+
synkit_mapper_store_pmcd_witness(n, seed.data(), s.incumbent2, 1);
|
|
231
|
+
}
|
|
232
|
+
}
|
|
233
|
+
}
|
|
234
|
+
s.optimization_seconds += elapsed(stage);
|
|
235
|
+
}
|
|
236
|
+
|
|
237
|
+
int64_t raw[6] = {};
|
|
238
|
+
if (r.query == SYNKIT_MINIMUM_CLASSES || r.query == SYNKIT_MINIMUM_PROOF) {
|
|
239
|
+
if (!s.minimum_proven) {
|
|
240
|
+
int best4 = 0;
|
|
241
|
+
Perm best(n);
|
|
242
|
+
stage = Clock::now();
|
|
243
|
+
int status = native_minimum_impl(
|
|
244
|
+
n, types.size(), levels.size() - 1, budget.remaining(), a.data(),
|
|
245
|
+
b.data(), cr.data(), cp.data(), order.data(), pred.data(), pg.data(),
|
|
246
|
+
pg.size() / n, rg.data(), rg.size() / n, seed.data(), best.data(),
|
|
247
|
+
&best4, raw, 0, 0, false, static_cast<int>(2 * s.lower_bound2),
|
|
248
|
+
root_certificate.ready ? &root_certificate : nullptr,
|
|
249
|
+
conditioned_dual_statistics, nullptr,
|
|
250
|
+
assignment_certificate.ready
|
|
251
|
+
? +[](const int *mapping, const int *used, [[maybe_unused]] int target, void *data) {
|
|
252
|
+
auto &certificate = *static_cast<
|
|
253
|
+
sparse_root_lp::AssignmentCertificate *>(data);
|
|
254
|
+
const int64_t bound = certificate.bound(mapping, used);
|
|
255
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
256
|
+
++certificate.calls;
|
|
257
|
+
certificate.prunes += 2 * bound > target;
|
|
258
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
259
|
+
return bound;
|
|
260
|
+
}
|
|
261
|
+
: nullptr,
|
|
262
|
+
&assignment_certificate);
|
|
263
|
+
s.optimization_seconds += elapsed(stage);
|
|
264
|
+
s.nodes += raw[0];
|
|
265
|
+
s.leaves += raw[1];
|
|
266
|
+
if (status < 0)
|
|
267
|
+
throw std::runtime_error("Legacy PABS minimum kernel error");
|
|
268
|
+
s.incumbent2 =
|
|
269
|
+
mapping_cost2(p, std::vector<int32_t>(best.begin(), best.end()));
|
|
270
|
+
if (best4 != 2 * s.incumbent2)
|
|
271
|
+
throw std::runtime_error("Invalid minimum witness units");
|
|
272
|
+
if (status) {
|
|
273
|
+
stopped(s, SYNKIT_STOP_TIME);
|
|
274
|
+
return 0;
|
|
275
|
+
}
|
|
276
|
+
synkit_mapper_store_pmcd_witness(n, best.data(), s.incumbent2, 1);
|
|
277
|
+
s.minimum_proven = 1;
|
|
278
|
+
s.minimum2 = s.incumbent2;
|
|
279
|
+
s.lower_bound2 = s.minimum2;
|
|
280
|
+
}
|
|
281
|
+
if (r.query == SYNKIT_MINIMUM_PROOF) {
|
|
282
|
+
s.search_complete = 1;
|
|
283
|
+
return 0;
|
|
284
|
+
}
|
|
285
|
+
}
|
|
286
|
+
budget.check();
|
|
287
|
+
int64_t target = (r.query == SYNKIT_MINIMUM_CLASSES ? s.minimum2 : r.target2);
|
|
288
|
+
if (r.query != SYNKIT_AT_MOST_DISTANCE && target > maximum2) {
|
|
289
|
+
s.search_complete = 1;
|
|
290
|
+
s.labeled_count = 0;
|
|
291
|
+
return 0;
|
|
292
|
+
}
|
|
293
|
+
target = std::min(target, maximum2);
|
|
294
|
+
Receiver receiver{p, r, callback, userdata, s, budget};
|
|
295
|
+
stage = Clock::now();
|
|
296
|
+
int status = synkit_distance_range(
|
|
297
|
+
n, types.size(), levels.size() - 1,
|
|
298
|
+
r.query == SYNKIT_AT_MOST_DISTANCE ? 0 : static_cast<int>(2 * target),
|
|
299
|
+
static_cast<int>(2 * target), budget.remaining(), r.max_candidates,
|
|
300
|
+
a.data(), b.data(), cr.data(), cp.data(), order.data(), pred.data(),
|
|
301
|
+
pg.data(), pg.size() / n, rg.data(), rg.size() / n, Receiver::receive,
|
|
302
|
+
&receiver, raw);
|
|
303
|
+
s.enumeration_seconds += elapsed(stage);
|
|
304
|
+
s.nodes += raw[0];
|
|
305
|
+
s.leaves += raw[1];
|
|
306
|
+
if (status < 0)
|
|
307
|
+
throw std::runtime_error("Legacy PABS range kernel error");
|
|
308
|
+
if (status) {
|
|
309
|
+
stopped(s, s.reason ? s.reason
|
|
310
|
+
: status == 2 ? SYNKIT_STOP_CANDIDATES
|
|
311
|
+
: status == 3 ? SYNKIT_STOP_CALLBACK
|
|
312
|
+
: SYNKIT_STOP_TIME);
|
|
313
|
+
} else
|
|
314
|
+
s.search_complete = 1;
|
|
315
|
+
s.labeled_count = rg.empty() && pg.empty() ? s.candidate_count : -1;
|
|
316
|
+
return 0;
|
|
317
|
+
}
|
|
318
|
+
} // namespace synkit_mapper
|
|
319
|
+
|
|
320
|
+
#include "objective_reduction.inc"
|
|
321
|
+
|
|
322
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
323
|
+
#include "test_hooks.inc"
|
|
324
|
+
#endif
|
|
325
|
+
|
|
326
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
327
|
+
extern "C" int synkit_private_lp_assignment_statistics(int64_t *out,
|
|
328
|
+
int capacity) {
|
|
329
|
+
if (!out || capacity < 6)
|
|
330
|
+
return -1;
|
|
331
|
+
std::copy(lp_assignment_statistics, lp_assignment_statistics + 6, out);
|
|
332
|
+
return 6;
|
|
333
|
+
}
|
|
334
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|