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/Stereo/matching.py +899 -0
- synkit/Graph/Stereo/native.py +154 -0
- synkit/Graph/Stereo/orbits.py +668 -0
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- synkit/Graph/Stereo/pairwise.py +350 -0
- synkit/Graph/Stereo/rdkit_adapter.py +662 -0
- synkit/Graph/Stereo/rdkit_identity.py +118 -0
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- 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
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- 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
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#pragma once
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// Exact sparse typed-assignment model in doubled chemical-distance units.
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// Every true typed bijection embeds into these x/y/total variables. The
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#include "synkit_mapper/core/runtime.h"
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#include <memory>
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#include <utility>
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#include <vector>
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namespace synkit_mapper {
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namespace sparse_root_lp {
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constexpr int max_variables = 100000, max_constraints = 300000,
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max_nonzeros = 2000000;
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struct Term {
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int column;
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int coefficient;
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};
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struct Row {
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int rhs;
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bool equality;
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struct ModelEdge {
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struct ModelProduct {
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};
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struct PreparedModel {
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int n = 0;
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int64_t constant = 0, mass = 0, gcd = 0, assignment_variables = 0,
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auxiliary_variables = 0, nonzeros = 0;
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std::vector<int64_t> costs;
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std::vector<int> fixed, variable_rows, columns, assignment, source_totals,
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target_totals;
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std::vector<std::vector<int>> domains;
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std::vector<ModelEdge> source_edges, target_edges;
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std::vector<ModelProduct> products;
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};
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struct ModelLimit {};
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template <class Check>
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std::unique_ptr<PreparedModel> build_model(const Problem &p, Check check) {
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if (p.n < 1 || p.n > 256 || !p.a2 || !p.b2 || !p.types_r || !p.types_p)
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return nullptr;
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auto model = std::make_unique<PreparedModel>();
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model->n = p.n;
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check();
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const int n = p.n;
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std::map<int32_t, int> counts, other, target_position;
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target_position[p.types_p[i]] = i;
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}
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if (counts != other)
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return nullptr;
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std::vector<int> fixed(n, -1), rows, cols;
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fixed[i] = target_position[p.types_r[i]];
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else
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rows.push_back(i);
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cols.push_back(j);
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int64_t mass = 0, gcd = 0;
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check();
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const int64_t a = p.a2[i * n + k], b = p.b2[i * n + k];
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if (a < 0 || b < 0 || a > 1000000 || b > 1000000 ||
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a != p.a2[k * n + i] || b != p.b2[k * n + i])
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return nullptr;
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|
81
|
+
if (k < i) {
|
|
82
|
+
mass += a + b;
|
|
83
|
+
gcd = std::gcd(gcd, a);
|
|
84
|
+
gcd = std::gcd(gcd, b);
|
|
85
|
+
}
|
|
86
|
+
}
|
|
87
|
+
}
|
|
88
|
+
model->constant = mass;
|
|
89
|
+
for (int i = 0; i < n; ++i)
|
|
90
|
+
if (fixed[i] >= 0)
|
|
91
|
+
for (int k = 0; k < i; ++k)
|
|
92
|
+
if (fixed[k] >= 0)
|
|
93
|
+
model->constant -=
|
|
94
|
+
2 * std::min(p.a2[i * n + k], p.b2[fixed[i] * n + fixed[k]]);
|
|
95
|
+
std::vector<int> x(n * n, -1);
|
|
96
|
+
std::vector<std::vector<int>> domains(n);
|
|
97
|
+
auto variable = [&](int64_t cost) {
|
|
98
|
+
if (model->costs.size() >= max_variables)
|
|
99
|
+
throw ModelLimit{};
|
|
100
|
+
int index = model->costs.size();
|
|
101
|
+
model->costs.push_back(cost);
|
|
102
|
+
return index;
|
|
103
|
+
};
|
|
104
|
+
int nonzeros = 0;
|
|
105
|
+
auto constraint = [&](std::vector<Term> terms, int rhs,
|
|
106
|
+
bool equality = false) {
|
|
107
|
+
if (model->rows.size() >= max_constraints ||
|
|
108
|
+
nonzeros + terms.size() > max_nonzeros)
|
|
109
|
+
throw ModelLimit{};
|
|
110
|
+
nonzeros += terms.size();
|
|
111
|
+
model->rows.push_back({std::move(terms), rhs, equality});
|
|
112
|
+
};
|
|
113
|
+
for (int i : rows) {
|
|
114
|
+
check();
|
|
115
|
+
for (int j : cols)
|
|
116
|
+
if (p.types_r[i] == p.types_p[j]) {
|
|
117
|
+
int64_t unary = 0;
|
|
118
|
+
for (int k = 0; k < n; ++k)
|
|
119
|
+
if (fixed[k] >= 0)
|
|
120
|
+
unary -= 2 * std::min(p.a2[i * n + k], p.b2[j * n + fixed[k]]);
|
|
121
|
+
x[i * n + j] = variable(unary);
|
|
122
|
+
domains[i].push_back(j);
|
|
123
|
+
}
|
|
124
|
+
}
|
|
125
|
+
model->assignment_variables = model->costs.size();
|
|
126
|
+
for (int i : rows) {
|
|
127
|
+
std::vector<Term> terms;
|
|
128
|
+
for (int j : domains[i])
|
|
129
|
+
terms.push_back({x[i * n + j], 1});
|
|
130
|
+
constraint(std::move(terms), 1, true);
|
|
131
|
+
}
|
|
132
|
+
for (int j : cols) {
|
|
133
|
+
std::vector<Term> terms;
|
|
134
|
+
for (int i : rows)
|
|
135
|
+
if (x[i * n + j] >= 0)
|
|
136
|
+
terms.push_back({x[i * n + j], 1});
|
|
137
|
+
constraint(std::move(terms), 1, true);
|
|
138
|
+
}
|
|
139
|
+
using Edge = ModelEdge;
|
|
140
|
+
std::vector<Edge> source, target;
|
|
141
|
+
for (size_t r = 0; r < rows.size(); ++r)
|
|
142
|
+
for (size_t s = r + 1; s < rows.size(); ++s) {
|
|
143
|
+
const int i = rows[r], k = rows[s];
|
|
144
|
+
if (p.a2[i * n + k])
|
|
145
|
+
source.push_back({i, k, p.a2[i * n + k]});
|
|
146
|
+
}
|
|
147
|
+
for (size_t r = 0; r < cols.size(); ++r)
|
|
148
|
+
for (size_t s = r + 1; s < cols.size(); ++s) {
|
|
149
|
+
const int j = cols[r], l = cols[s];
|
|
150
|
+
if (p.b2[j * n + l])
|
|
151
|
+
target.push_back({j, l, p.b2[j * n + l]});
|
|
152
|
+
}
|
|
153
|
+
using Product = ModelProduct;
|
|
154
|
+
std::vector<Product> products;
|
|
155
|
+
std::vector<std::vector<int>> sy(source.size()), ty(target.size());
|
|
156
|
+
std::vector<int> source_totals(source.size(), -1),
|
|
157
|
+
target_totals(target.size(), -1);
|
|
158
|
+
std::vector<std::vector<int>> so(source.size() * n), si(source.size() * n),
|
|
159
|
+
to(target.size() * n), ti(target.size() * n);
|
|
160
|
+
for (size_t e = 0; e < source.size(); ++e) {
|
|
161
|
+
check();
|
|
162
|
+
const auto &s = source[e];
|
|
163
|
+
for (size_t f = 0; f < target.size(); ++f) {
|
|
164
|
+
if (!(f % 64))
|
|
165
|
+
check();
|
|
166
|
+
const auto &t = target[f];
|
|
167
|
+
for (int direction = 0; direction < 2; ++direction) {
|
|
168
|
+
const int j = direction ? t.k : t.i, l = direction ? t.i : t.k;
|
|
169
|
+
if (x[s.i * n + j] < 0 || x[s.k * n + l] < 0)
|
|
170
|
+
continue;
|
|
171
|
+
const int index = variable(-2 * std::min(s.weight, t.weight));
|
|
172
|
+
const int product = products.size();
|
|
173
|
+
products.push_back({index, int(e), int(f), j, l});
|
|
174
|
+
sy[e].push_back(product);
|
|
175
|
+
ty[f].push_back(product);
|
|
176
|
+
so[e * n + j].push_back(index);
|
|
177
|
+
si[e * n + l].push_back(index);
|
|
178
|
+
to[f * n + (direction ? s.k : s.i)].push_back(index);
|
|
179
|
+
ti[f * n + (direction ? s.i : s.k)].push_back(index);
|
|
180
|
+
}
|
|
181
|
+
}
|
|
182
|
+
}
|
|
183
|
+
auto marginal = [&](const std::vector<int> &indices, int assignment) {
|
|
184
|
+
if (indices.empty())
|
|
185
|
+
return;
|
|
186
|
+
std::vector<Term> terms;
|
|
187
|
+
terms.reserve(indices.size() + 1);
|
|
188
|
+
for (int index : indices)
|
|
189
|
+
terms.push_back({index, 1});
|
|
190
|
+
terms.push_back({assignment, -1});
|
|
191
|
+
constraint(std::move(terms), 0);
|
|
192
|
+
};
|
|
193
|
+
for (size_t e = 0; e < source.size(); ++e) {
|
|
194
|
+
check();
|
|
195
|
+
const auto &s = source[e];
|
|
196
|
+
// Existing marginals and sum_j x[i,j]=1 imply 0<=sum_e y<=1.
|
|
197
|
+
// A zero-cost total in [0,1] therefore preserves the exact LP projection.
|
|
198
|
+
int total = -1;
|
|
199
|
+
if (p.types_r[s.i] == p.types_r[s.k]) {
|
|
200
|
+
total = variable(0);
|
|
201
|
+
source_totals[e] = total;
|
|
202
|
+
++model->auxiliary_variables;
|
|
203
|
+
std::vector<Term> definition;
|
|
204
|
+
definition.reserve(sy[e].size() + 1);
|
|
205
|
+
definition.push_back({total, 1});
|
|
206
|
+
for (int h : sy[e])
|
|
207
|
+
definition.push_back({products[h].index, -1});
|
|
208
|
+
constraint(std::move(definition), 0, true);
|
|
209
|
+
}
|
|
210
|
+
for (int j : domains[s.i])
|
|
211
|
+
marginal(so[e * n + j], x[s.i * n + j]);
|
|
212
|
+
for (int j : domains[s.k])
|
|
213
|
+
marginal(si[e * n + j], x[s.k * n + j]);
|
|
214
|
+
for (int j : domains[s.i])
|
|
215
|
+
if (x[s.k * n + j] >= 0) {
|
|
216
|
+
std::vector<Term> terms;
|
|
217
|
+
// sum(nonincident y)=total-sum(incident y); the positive
|
|
218
|
+
// target edges are loop-free, so these incident lists are disjoint.
|
|
219
|
+
terms.push_back({total, 1});
|
|
220
|
+
for (int index : so[e * n + j])
|
|
221
|
+
terms.push_back({index, -1});
|
|
222
|
+
for (int index : si[e * n + j])
|
|
223
|
+
terms.push_back({index, -1});
|
|
224
|
+
terms.push_back({x[s.i * n + j], 1});
|
|
225
|
+
terms.push_back({x[s.k * n + j], 1});
|
|
226
|
+
constraint(std::move(terms), 1);
|
|
227
|
+
}
|
|
228
|
+
}
|
|
229
|
+
for (size_t f = 0; f < target.size(); ++f) {
|
|
230
|
+
check();
|
|
231
|
+
const auto &t = target[f];
|
|
232
|
+
int total = -1;
|
|
233
|
+
if (p.types_p[t.i] == p.types_p[t.k]) {
|
|
234
|
+
total = variable(0);
|
|
235
|
+
target_totals[f] = total;
|
|
236
|
+
++model->auxiliary_variables;
|
|
237
|
+
std::vector<Term> definition;
|
|
238
|
+
definition.reserve(ty[f].size() + 1);
|
|
239
|
+
definition.push_back({total, 1});
|
|
240
|
+
for (int h : ty[f])
|
|
241
|
+
definition.push_back({products[h].index, -1});
|
|
242
|
+
constraint(std::move(definition), 0, true);
|
|
243
|
+
}
|
|
244
|
+
for (int i : rows) {
|
|
245
|
+
if (x[i * n + t.i] >= 0)
|
|
246
|
+
marginal(to[f * n + i], x[i * n + t.i]);
|
|
247
|
+
if (x[i * n + t.k] >= 0)
|
|
248
|
+
marginal(ti[f * n + i], x[i * n + t.k]);
|
|
249
|
+
if (x[i * n + t.i] >= 0 && x[i * n + t.k] >= 0) {
|
|
250
|
+
std::vector<Term> terms;
|
|
251
|
+
terms.push_back({total, 1});
|
|
252
|
+
for (int index : to[f * n + i])
|
|
253
|
+
terms.push_back({index, -1});
|
|
254
|
+
for (int index : ti[f * n + i])
|
|
255
|
+
terms.push_back({index, -1});
|
|
256
|
+
terms.push_back({x[i * n + t.i], 1});
|
|
257
|
+
terms.push_back({x[i * n + t.k], 1});
|
|
258
|
+
constraint(std::move(terms), 1);
|
|
259
|
+
}
|
|
260
|
+
}
|
|
261
|
+
}
|
|
262
|
+
model->mass = mass;
|
|
263
|
+
model->gcd = gcd;
|
|
264
|
+
model->nonzeros = nonzeros;
|
|
265
|
+
model->fixed = std::move(fixed);
|
|
266
|
+
model->variable_rows = std::move(rows);
|
|
267
|
+
model->columns = std::move(cols);
|
|
268
|
+
model->assignment = std::move(x);
|
|
269
|
+
model->domains = std::move(domains);
|
|
270
|
+
model->source_edges = std::move(source);
|
|
271
|
+
model->target_edges = std::move(target);
|
|
272
|
+
model->products = std::move(products);
|
|
273
|
+
model->source_totals = std::move(source_totals);
|
|
274
|
+
model->target_totals = std::move(target_totals);
|
|
275
|
+
return model;
|
|
276
|
+
}
|
|
277
|
+
|
|
278
|
+
#if defined(__SIZEOF_INT128__)
|
|
279
|
+
// A freshly computed typed map supplies a feasible numerical starting point
|
|
280
|
+
// only. Check its complete original-index embedding independently before PDLP
|
|
281
|
+
// sees it; the exact dual checker remains the sole source of LP lower bounds.
|
|
282
|
+
template <class Check>
|
|
283
|
+
bool embed_incumbent(const Problem &p, const PreparedModel &model,
|
|
284
|
+
const std::vector<int32_t> &mapping, int64_t expected_cost,
|
|
285
|
+
std::vector<int64_t> &point, Check check) {
|
|
286
|
+
__extension__ typedef __int128 SeedWide;
|
|
287
|
+
const int n = model.n;
|
|
288
|
+
point.clear();
|
|
289
|
+
if (p.n != n || n < 1 || mapping.size() != size_t(n) ||
|
|
290
|
+
expected_cost < 0)
|
|
291
|
+
return false;
|
|
292
|
+
std::vector<bool> used(n, false);
|
|
293
|
+
SeedWide original_cost = 0;
|
|
294
|
+
for (int i = 0; i < n; ++i) {
|
|
295
|
+
check();
|
|
296
|
+
const int j = mapping[i];
|
|
297
|
+
if (j < 0 || j >= n || used[j] ||
|
|
298
|
+
p.types_r[i] != p.types_p[j] ||
|
|
299
|
+
(model.fixed[i] >= 0 && model.fixed[i] != j))
|
|
300
|
+
return false;
|
|
301
|
+
used[j] = true;
|
|
302
|
+
}
|
|
303
|
+
for (int i = 0; i < n; ++i) {
|
|
304
|
+
check();
|
|
305
|
+
for (int k = i + 1; k < n; ++k)
|
|
306
|
+
original_cost +=
|
|
307
|
+
std::abs(p.a2[i * n + k] -
|
|
308
|
+
p.b2[mapping[i] * n + mapping[k]]);
|
|
309
|
+
}
|
|
310
|
+
if (original_cost != expected_cost)
|
|
311
|
+
return false;
|
|
312
|
+
point.assign(model.costs.size(), 0);
|
|
313
|
+
for (int i : model.variable_rows) {
|
|
314
|
+
const int x = model.assignment[i * n + mapping[i]];
|
|
315
|
+
if (x < 0 || size_t(x) >= point.size())
|
|
316
|
+
return false;
|
|
317
|
+
point[x] = 1;
|
|
318
|
+
}
|
|
319
|
+
size_t visited = 0;
|
|
320
|
+
for (const auto &product : model.products) {
|
|
321
|
+
if (!(visited++ % 128))
|
|
322
|
+
check();
|
|
323
|
+
const auto &edge = model.source_edges[product.e];
|
|
324
|
+
if (mapping[edge.i] != product.left ||
|
|
325
|
+
mapping[edge.k] != product.right)
|
|
326
|
+
continue;
|
|
327
|
+
point[product.index] = 1;
|
|
328
|
+
for (int total : {model.source_totals[product.e],
|
|
329
|
+
model.target_totals[product.f]}) {
|
|
330
|
+
if (total < 0)
|
|
331
|
+
continue;
|
|
332
|
+
if (point[total] != 0)
|
|
333
|
+
return false;
|
|
334
|
+
point[total] = 1;
|
|
335
|
+
}
|
|
336
|
+
}
|
|
337
|
+
SeedWide objective = model.constant;
|
|
338
|
+
for (size_t j = 0; j < point.size(); ++j) {
|
|
339
|
+
if (!(j % 128))
|
|
340
|
+
check();
|
|
341
|
+
if (point[j] != 0 && point[j] != 1)
|
|
342
|
+
return false;
|
|
343
|
+
objective += SeedWide(model.costs[j]) * point[j];
|
|
344
|
+
}
|
|
345
|
+
if (objective != original_cost)
|
|
346
|
+
return false;
|
|
347
|
+
visited = 0;
|
|
348
|
+
for (const auto &row : model.rows) {
|
|
349
|
+
SeedWide sum = 0;
|
|
350
|
+
for (const auto &term : row.terms) {
|
|
351
|
+
if (!(visited++ % 1024))
|
|
352
|
+
check();
|
|
353
|
+
if (term.column < 0 || size_t(term.column) >= point.size())
|
|
354
|
+
return false;
|
|
355
|
+
sum += SeedWide(term.coefficient) * point[term.column];
|
|
356
|
+
}
|
|
357
|
+
if (row.equality ? sum != row.rhs : sum > row.rhs)
|
|
358
|
+
return false;
|
|
359
|
+
}
|
|
360
|
+
check();
|
|
361
|
+
return true;
|
|
362
|
+
}
|
|
363
|
+
#endif
|
|
364
|
+
} // namespace sparse_root_lp
|
|
365
|
+
} // namespace synkit_mapper
|
|
@@ -0,0 +1,319 @@
|
|
|
1
|
+
// Included inside sparse_root_lp only with OR-Tools and exact wide arithmetic.
|
|
2
|
+
// This numerical module returns untrusted ORIGINAL-index vectors. It has no
|
|
3
|
+
// authority to declare a lower bound, optimal map, or completed enumeration.
|
|
4
|
+
template <class Check>
|
|
5
|
+
bool make_initial_dual(const PreparedModel &model, std::vector<double> &proposal,
|
|
6
|
+
Check check) {
|
|
7
|
+
const int n = model.n, m = model.variable_rows.size();
|
|
8
|
+
proposal.clear();
|
|
9
|
+
if (m != int(model.columns.size()) || model.rows.size() < size_t(2 * m))
|
|
10
|
+
return false;
|
|
11
|
+
std::vector<int64_t> twice_dual(model.rows.size(), 0);
|
|
12
|
+
// Each overlap variable appears in four marginal inequalities. A multiplier
|
|
13
|
+
// -max(overlap)/2 on each makes its original reduced cost nonnegative.
|
|
14
|
+
for (size_t r = 0; r < model.rows.size(); ++r) {
|
|
15
|
+
if (!(r % 128))
|
|
16
|
+
check();
|
|
17
|
+
const auto &row = model.rows[r];
|
|
18
|
+
if (row.equality || row.rhs || row.terms.size() < 2)
|
|
19
|
+
continue;
|
|
20
|
+
const auto &last = row.terms.back();
|
|
21
|
+
if (last.coefficient != -1 || last.column < 0 ||
|
|
22
|
+
last.column >= model.assignment_variables)
|
|
23
|
+
continue;
|
|
24
|
+
int64_t largest = 0;
|
|
25
|
+
bool marginal = true;
|
|
26
|
+
for (size_t k = 0; k + 1 < row.terms.size(); ++k) {
|
|
27
|
+
const auto &term = row.terms[k];
|
|
28
|
+
if (term.coefficient != 1 || term.column < model.assignment_variables ||
|
|
29
|
+
size_t(term.column) >= model.costs.size() ||
|
|
30
|
+
model.costs[term.column] > 0 || model.costs[term.column] % 2) {
|
|
31
|
+
marginal = false;
|
|
32
|
+
break;
|
|
33
|
+
}
|
|
34
|
+
largest = std::max(largest, -model.costs[term.column] / 2);
|
|
35
|
+
}
|
|
36
|
+
if (marginal)
|
|
37
|
+
twice_dual[r] = -largest;
|
|
38
|
+
}
|
|
39
|
+
auto reduced_costs = [&]() {
|
|
40
|
+
std::vector<Wide> reduced;
|
|
41
|
+
reduced.reserve(model.costs.size());
|
|
42
|
+
for (int64_t value : model.costs)
|
|
43
|
+
reduced.push_back(Wide(2) * value);
|
|
44
|
+
size_t visited = 0;
|
|
45
|
+
for (size_t r = 0; r < model.rows.size(); ++r)
|
|
46
|
+
if (twice_dual[r])
|
|
47
|
+
for (const auto &term : model.rows[r].terms) {
|
|
48
|
+
if (!(visited++ % 1024))
|
|
49
|
+
check();
|
|
50
|
+
reduced[term.column] -= Wide(term.coefficient) * twice_dual[r];
|
|
51
|
+
}
|
|
52
|
+
return reduced;
|
|
53
|
+
};
|
|
54
|
+
auto reduced = reduced_costs();
|
|
55
|
+
if (m) {
|
|
56
|
+
const int safe_entry = INF / (8 * m) - 1;
|
|
57
|
+
if (safe_entry < 1)
|
|
58
|
+
return false;
|
|
59
|
+
std::vector<Wide> shifts(m);
|
|
60
|
+
Wide largest = 0;
|
|
61
|
+
std::vector<int> position(n, -1);
|
|
62
|
+
for (int j = 0; j < m; ++j)
|
|
63
|
+
position[model.columns[j]] = j;
|
|
64
|
+
for (int i = 0; i < m; ++i) {
|
|
65
|
+
check();
|
|
66
|
+
const int row = model.variable_rows[i];
|
|
67
|
+
if (model.domains[row].empty())
|
|
68
|
+
return false;
|
|
69
|
+
shifts[i] = reduced[model.assignment[row * n + model.domains[row][0]]];
|
|
70
|
+
for (int image : model.domains[row])
|
|
71
|
+
shifts[i] = std::min(shifts[i], reduced[model.assignment[row * n + image]]);
|
|
72
|
+
for (int image : model.domains[row])
|
|
73
|
+
largest = std::max(largest, reduced[model.assignment[row * n + image]] - shifts[i]);
|
|
74
|
+
}
|
|
75
|
+
const Wide quantum = std::max(Wide(1), (largest + safe_entry - 1) / safe_entry);
|
|
76
|
+
std::vector<int> cost(m * m, INF);
|
|
77
|
+
for (int i = 0; i < m; ++i) {
|
|
78
|
+
check();
|
|
79
|
+
const int row = model.variable_rows[i];
|
|
80
|
+
for (int image : model.domains[row]) {
|
|
81
|
+
const Wide value = (reduced[model.assignment[row * n + image]] - shifts[i]) / quantum;
|
|
82
|
+
if (value < 0 || value > safe_entry || position[image] < 0)
|
|
83
|
+
return false;
|
|
84
|
+
cost[i * m + position[image]] = int(value);
|
|
85
|
+
}
|
|
86
|
+
}
|
|
87
|
+
Perm mapping, u, v;
|
|
88
|
+
check();
|
|
89
|
+
const int optimum = Solver::assignment(cost, m, mapping, u, v);
|
|
90
|
+
check();
|
|
91
|
+
if (optimum >= INF / 2 || mapping.size() != size_t(m) ||
|
|
92
|
+
u.size() != size_t(m + 1) || v.size() != size_t(m + 1))
|
|
93
|
+
return false;
|
|
94
|
+
std::vector<bool> used(m, false);
|
|
95
|
+
int64_t primal = 0, dual = 0;
|
|
96
|
+
for (int i = 0; i < m; ++i) {
|
|
97
|
+
const int j = mapping[i];
|
|
98
|
+
if (j < 0 || j >= m || used[j] || cost[i * m + j] >= INF / 2)
|
|
99
|
+
return false;
|
|
100
|
+
used[j] = true;
|
|
101
|
+
primal += cost[i * m + j];
|
|
102
|
+
dual += int64_t(u[i + 1]) + v[i + 1];
|
|
103
|
+
for (int k = 0; k < m; ++k)
|
|
104
|
+
if (cost[i * m + k] < INF / 2 &&
|
|
105
|
+
int64_t(cost[i * m + k]) - u[i + 1] - v[k + 1] < 0)
|
|
106
|
+
return false;
|
|
107
|
+
const Wide row_value = shifts[i] + quantum * u[i + 1];
|
|
108
|
+
const Wide column_value = quantum * v[i + 1];
|
|
109
|
+
// Stay inside the existing numerical-proposal clipping range.
|
|
110
|
+
if (row_value < -2000000 || row_value > 2000000 ||
|
|
111
|
+
column_value < -2000000 || column_value > 2000000)
|
|
112
|
+
return false;
|
|
113
|
+
twice_dual[i] = int64_t(row_value);
|
|
114
|
+
twice_dual[m + i] = int64_t(column_value);
|
|
115
|
+
}
|
|
116
|
+
if (primal != optimum || dual != optimum)
|
|
117
|
+
return false;
|
|
118
|
+
}
|
|
119
|
+
reduced = reduced_costs();
|
|
120
|
+
for (Wide value : reduced)
|
|
121
|
+
if (value < 0)
|
|
122
|
+
return false;
|
|
123
|
+
proposal.resize(twice_dual.size());
|
|
124
|
+
for (size_t r = 0; r < twice_dual.size(); ++r) {
|
|
125
|
+
if (!(r % 128))
|
|
126
|
+
check();
|
|
127
|
+
if ((!model.rows[r].equality && twice_dual[r] > 0) ||
|
|
128
|
+
twice_dual[r] < -2000000 || twice_dual[r] > 2000000)
|
|
129
|
+
return false;
|
|
130
|
+
proposal[r] = 0.5 * twice_dual[r];
|
|
131
|
+
}
|
|
132
|
+
check();
|
|
133
|
+
return true;
|
|
134
|
+
}
|
|
135
|
+
|
|
136
|
+
class PDLPProvider {
|
|
137
|
+
std::unique_ptr<operations_research::pdlp::QuadraticProgram> qp_;
|
|
138
|
+
std::vector<double> primal_, dual_;
|
|
139
|
+
std::optional<operations_research::pdlp::PrimalAndDualSolution> initial_;
|
|
140
|
+
|
|
141
|
+
public:
|
|
142
|
+
int reason = 0;
|
|
143
|
+
int64_t iterations = 0;
|
|
144
|
+
template <class Check>
|
|
145
|
+
PDLPProvider(const std::vector<int64_t> &costs, const std::vector<Row> &rows,
|
|
146
|
+
int64_t constant, Check check) {
|
|
147
|
+
|
|
148
|
+
qp_ = std::make_unique<operations_research::pdlp::QuadraticProgram>(
|
|
149
|
+
costs.size(), rows.size());
|
|
150
|
+
qp_->objective_offset = constant;
|
|
151
|
+
qp_->objective_scaling_factor = 1;
|
|
152
|
+
qp_->variable_lower_bounds.setZero();
|
|
153
|
+
qp_->variable_upper_bounds.setOnes();
|
|
154
|
+
for (size_t j = 0; j < costs.size(); ++j) {
|
|
155
|
+
if (!(j % 128))
|
|
156
|
+
check();
|
|
157
|
+
qp_->objective_vector[j] = costs[j];
|
|
158
|
+
}
|
|
159
|
+
std::vector<Eigen::Triplet<double, int64_t>> coefficients;
|
|
160
|
+
size_t nonzeros = 0;
|
|
161
|
+
for (const auto &row : rows)
|
|
162
|
+
nonzeros += row.terms.size();
|
|
163
|
+
coefficients.reserve(nonzeros);
|
|
164
|
+
for (size_t r = 0; r < rows.size(); ++r) {
|
|
165
|
+
if (!(r % 128))
|
|
166
|
+
check();
|
|
167
|
+
const auto &row = rows[r];
|
|
168
|
+
qp_->constraint_lower_bounds[r] =
|
|
169
|
+
row.equality ? row.rhs : -std::numeric_limits<double>::infinity();
|
|
170
|
+
qp_->constraint_upper_bounds[r] = row.rhs;
|
|
171
|
+
for (const auto &term : row.terms)
|
|
172
|
+
coefficients.emplace_back(r, term.column, term.coefficient);
|
|
173
|
+
}
|
|
174
|
+
qp_->constraint_matrix.setFromTriplets(coefficients.begin(),
|
|
175
|
+
coefficients.end());
|
|
176
|
+
check();
|
|
177
|
+
}
|
|
178
|
+
|
|
179
|
+
template <class Check>
|
|
180
|
+
void set_initial_primal(const std::vector<int64_t> &point, Check check,
|
|
181
|
+
const std::vector<double> *dual = nullptr) {
|
|
182
|
+
if (!qp_ || point.size() != size_t(qp_->objective_vector.size()))
|
|
183
|
+
return;
|
|
184
|
+
operations_research::pdlp::PrimalAndDualSolution candidate;
|
|
185
|
+
candidate.primal_solution.resize(point.size());
|
|
186
|
+
candidate.dual_solution =
|
|
187
|
+
Eigen::VectorXd::Zero(qp_->constraint_lower_bounds.size());
|
|
188
|
+
for (size_t j = 0; j < point.size(); ++j) {
|
|
189
|
+
if (!(j % 128))
|
|
190
|
+
check();
|
|
191
|
+
if (point[j] != 0 && point[j] != 1)
|
|
192
|
+
return;
|
|
193
|
+
candidate.primal_solution[j] = point[j];
|
|
194
|
+
}
|
|
195
|
+
if (dual && dual->size() == size_t(candidate.dual_solution.size()))
|
|
196
|
+
for (size_t r = 0; r < dual->size(); ++r) {
|
|
197
|
+
if (!(r % 128))
|
|
198
|
+
check();
|
|
199
|
+
if (!std::isfinite((*dual)[r]))
|
|
200
|
+
return;
|
|
201
|
+
candidate.dual_solution[r] = (*dual)[r];
|
|
202
|
+
}
|
|
203
|
+
check();
|
|
204
|
+
initial_ = std::move(candidate);
|
|
205
|
+
}
|
|
206
|
+
|
|
207
|
+
void solve(double seconds,
|
|
208
|
+
int64_t stop_target = std::numeric_limits<int64_t>::max(),
|
|
209
|
+
int64_t cost_step = 0) {
|
|
210
|
+
if (!qp_)
|
|
211
|
+
return;
|
|
212
|
+
operations_research::pdlp::PrimalDualHybridGradientParams parameters;
|
|
213
|
+
parameters.set_num_threads(1);
|
|
214
|
+
parameters.set_verbosity_level(0);
|
|
215
|
+
parameters.set_record_iteration_stats(false);
|
|
216
|
+
parameters.mutable_termination_criteria()->set_time_sec_limit(
|
|
217
|
+
std::max(0.0, seconds));
|
|
218
|
+
auto *optimality = parameters.mutable_termination_criteria()
|
|
219
|
+
->mutable_simple_optimality_criteria();
|
|
220
|
+
optimality->set_eps_optimal_absolute(1e-6);
|
|
221
|
+
optimality->set_eps_optimal_relative(1e-6);
|
|
222
|
+
// This scalar controls WHEN to request a vector, never WHAT is proved.
|
|
223
|
+
// The returned original-index vector still passes certify_proposal.
|
|
224
|
+
const bool target_available =
|
|
225
|
+
cost_step > 0 && stop_target >= 0 &&
|
|
226
|
+
stop_target != std::numeric_limits<int64_t>::max();
|
|
227
|
+
const double trigger = double(stop_target) - double(cost_step) * 0.5;
|
|
228
|
+
std::atomic<bool> interrupt{false};
|
|
229
|
+
std::function<void(
|
|
230
|
+
const operations_research::pdlp::IterationCallbackInfo &)>
|
|
231
|
+
callback;
|
|
232
|
+
if (target_available) {
|
|
233
|
+
callback =
|
|
234
|
+
[&](const operations_research::pdlp::IterationCallbackInfo &info) {
|
|
235
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
236
|
+
++harvest_trace[1];
|
|
237
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
238
|
+
if (info.iteration_type !=
|
|
239
|
+
operations_research::pdlp::IterationType::kNormal)
|
|
240
|
+
return;
|
|
241
|
+
bool current_seen = false, average_seen = false, invalid = false;
|
|
242
|
+
double current = std::numeric_limits<double>::infinity();
|
|
243
|
+
double average = std::numeric_limits<double>::infinity();
|
|
244
|
+
for (const auto &point :
|
|
245
|
+
info.iteration_stats.convergence_information()) {
|
|
246
|
+
if (point.candidate_type() !=
|
|
247
|
+
operations_research::pdlp::POINT_TYPE_CURRENT_ITERATE &&
|
|
248
|
+
point.candidate_type() !=
|
|
249
|
+
operations_research::pdlp::POINT_TYPE_AVERAGE_ITERATE)
|
|
250
|
+
continue;
|
|
251
|
+
const bool is_current =
|
|
252
|
+
point.candidate_type() ==
|
|
253
|
+
operations_research::pdlp::POINT_TYPE_CURRENT_ITERATE;
|
|
254
|
+
if (is_current)
|
|
255
|
+
current_seen = true;
|
|
256
|
+
else
|
|
257
|
+
average_seen = true;
|
|
258
|
+
if (!point.has_corrected_dual_objective()) {
|
|
259
|
+
invalid = true;
|
|
260
|
+
continue;
|
|
261
|
+
}
|
|
262
|
+
const double value = point.corrected_dual_objective();
|
|
263
|
+
if (!std::isfinite(value)) {
|
|
264
|
+
invalid = true;
|
|
265
|
+
continue;
|
|
266
|
+
}
|
|
267
|
+
if (is_current)
|
|
268
|
+
current = std::min(current, value);
|
|
269
|
+
else
|
|
270
|
+
average = std::min(average, value);
|
|
271
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
272
|
+
const int64_t diagnostic = int64_t(
|
|
273
|
+
std::llround(std::max(-1e12, std::min(1e12, value)) * 1e6));
|
|
274
|
+
harvest_trace[14] = diagnostic;
|
|
275
|
+
harvest_trace[15] = std::max(harvest_trace[15], diagnostic);
|
|
276
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
277
|
+
}
|
|
278
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
279
|
+
harvest_trace[10] =
|
|
280
|
+
int(current_seen) + 2 * int(average_seen) + 4 * int(invalid);
|
|
281
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
282
|
+
// SAME callback iteration, both possible returned points.
|
|
283
|
+
// Historical scalar maxima are diagnostics only and never trigger
|
|
284
|
+
// interruption.
|
|
285
|
+
if (current_seen && average_seen && !invalid &&
|
|
286
|
+
current >= trigger && average >= trigger) {
|
|
287
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
288
|
+
harvest_trace[2] = 1;
|
|
289
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
290
|
+
interrupt.store(true, std::memory_order_relaxed);
|
|
291
|
+
}
|
|
292
|
+
};
|
|
293
|
+
}
|
|
294
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
295
|
+
const auto started = Clock::now();
|
|
296
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
297
|
+
auto result = operations_research::pdlp::PrimalDualHybridGradient(
|
|
298
|
+
std::move(*qp_), parameters, std::move(initial_),
|
|
299
|
+
target_available ? &interrupt : nullptr, nullptr, callback);
|
|
300
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
301
|
+
harvest_trace[5] = int64_t(elapsed(started) * 1e6);
|
|
302
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
303
|
+
qp_.reset();
|
|
304
|
+
reason = int(result.solve_log.termination_reason());
|
|
305
|
+
iterations = result.solve_log.iteration_count();
|
|
306
|
+
#ifdef SYNKIT_MAPPER_TEST_HOOKS
|
|
307
|
+
harvest_trace[3] = reason;
|
|
308
|
+
harvest_trace[4] = iterations;
|
|
309
|
+
#endif // SYNKIT_MAPPER_TEST_HOOKS
|
|
310
|
+
primal_.resize(result.primal_solution.size());
|
|
311
|
+
for (int64_t i = 0; i < result.primal_solution.size(); ++i)
|
|
312
|
+
primal_[i] = result.primal_solution[i];
|
|
313
|
+
dual_.resize(result.dual_solution.size());
|
|
314
|
+
for (int64_t i = 0; i < result.dual_solution.size(); ++i)
|
|
315
|
+
dual_[i] = result.dual_solution[i];
|
|
316
|
+
}
|
|
317
|
+
const std::vector<double> &primal() const { return primal_; }
|
|
318
|
+
const std::vector<double> &dual() const { return dual_; }
|
|
319
|
+
};
|