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/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
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- synkit/IO/debug.py +73 -0
- synkit/IO/gml_to_nx.py +150 -0
- synkit/IO/graph_to_mol.py +199 -0
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- 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
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- synkit/Mechanism/benchmark.py +638 -0
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- 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
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- synkit/Mechanism/stereo_state.py +416 -0
- synkit/Mechanism/symbols.py +91 -0
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- synkit/Rule/Apply/dpo.py +998 -0
- synkit/Rule/Apply/rule_matcher.py +218 -0
- synkit/Rule/Apply/validation.py +354 -0
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- synkit/Rule/generic_stereo.py +884 -0
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#pragma once
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namespace synkit_mapper::solvers::detail {
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constexpr int64_t kInfinity = std::numeric_limits<int64_t>::max() / 4;
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using Terms = std::vector<std::pair<int, int64_t>>;
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struct Row {
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Terms terms;
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struct Product {
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struct Formulation {
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int n = 0, cost = -1, variables = 0;
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int64_t maximum = 0;
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std::vector<int> x;
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std::vector<Row> rows;
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std::vector<Product> products;
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int64_t aggregate_constraints = 0;
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int64_t size = sizeof(*this) + x.capacity() * sizeof(int) +
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rows.capacity() * sizeof(Row) +
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products.capacity() * sizeof(Product);
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for (const auto &row : rows)
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size += row.terms.capacity() * sizeof(Terms::value_type);
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return size;
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}
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int variable() {
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if (variables == std::numeric_limits<int>::max())
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throw std::overflow_error(
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"Assignment model exceeds int variable indices");
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return variables++;
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}
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void add(Terms terms, int64_t lower, int64_t upper) {
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rows.push_back({std::move(terms), lower, upper});
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}
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};
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inline Formulation formulate(int n, const int64_t *a, const int64_t *b,
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const int32_t *left, const int32_t *right,
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const std::function<void()> &check,
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const uint8_t *allowed = nullptr) {
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Formulation f;
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check();
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Terms row;
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if (left[i] == right[j] && (!allowed || allowed[i * n + j])) {
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int x = f.variable();
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f.x[i * n + j] = x;
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row.emplace_back(x, 1);
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}
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f.add(std::move(row), 1, 1);
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}
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for (int j = 0; j < n; ++j) {
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check();
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Terms column;
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if (f.x[i * n + j] >= 0)
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column.emplace_back(f.x[i * n + j], 1);
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}
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struct Edge {
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};
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std::vector<Edge> left_edges, right_edges;
|
|
84
|
+
for (int i = 0; i < n; ++i) {
|
|
85
|
+
check();
|
|
86
|
+
for (int k = i + 1; k < n; ++k) {
|
|
87
|
+
if (a[i * n + k])
|
|
88
|
+
left_edges.push_back({i, k, a[i * n + k]});
|
|
89
|
+
if (b[i * n + k])
|
|
90
|
+
right_edges.push_back({i, k, b[i * n + k]});
|
|
91
|
+
int64_t increment = a[i * n + k] + b[i * n + k];
|
|
92
|
+
if (increment > kInfinity - f.maximum)
|
|
93
|
+
throw std::overflow_error(
|
|
94
|
+
"Assignment cost exceeds supported integer range");
|
|
95
|
+
f.maximum += increment;
|
|
96
|
+
}
|
|
97
|
+
}
|
|
98
|
+
Terms cost;
|
|
99
|
+
size_t checks = 0;
|
|
100
|
+
for (const auto &e : left_edges) {
|
|
101
|
+
check();
|
|
102
|
+
std::map<int, Terms> aggregate;
|
|
103
|
+
for (const auto &g : right_edges)
|
|
104
|
+
for (int direction = 0; direction != 2; ++direction) {
|
|
105
|
+
if (!(++checks % 1024))
|
|
106
|
+
check();
|
|
107
|
+
int j = direction ? g.k : g.i, l = direction ? g.i : g.k;
|
|
108
|
+
int u = f.x[e.i * n + j], v = f.x[e.k * n + l];
|
|
109
|
+
if (u < 0 || v < 0)
|
|
110
|
+
continue;
|
|
111
|
+
int y = f.variable();
|
|
112
|
+
f.add({{y, 1}, {u, -1}}, -kInfinity, 0);
|
|
113
|
+
f.add({{y, 1}, {v, -1}}, -kInfinity, 0);
|
|
114
|
+
f.add({{y, 1}, {u, -1}, {v, -1}}, -1, kInfinity);
|
|
115
|
+
int64_t benefit = 2 * std::min(e.weight, g.weight);
|
|
116
|
+
cost.emplace_back(y, benefit);
|
|
117
|
+
f.products.push_back({y, u, v, benefit});
|
|
118
|
+
aggregate[u].emplace_back(y, 1);
|
|
119
|
+
aggregate[v].emplace_back(y, 1);
|
|
120
|
+
}
|
|
121
|
+
// RLT strengthening: for a fixed source edge and one endpoint image,
|
|
122
|
+
// at most one product can be selected. In integral models this follows
|
|
123
|
+
// from bijectivity; the aggregate inequality strengthens the MILP LP.
|
|
124
|
+
for (auto &[assignment, terms] : aggregate) {
|
|
125
|
+
check();
|
|
126
|
+
if (terms.size() < 2)
|
|
127
|
+
continue;
|
|
128
|
+
terms.emplace_back(assignment, -1);
|
|
129
|
+
f.add(std::move(terms), -kInfinity, 0);
|
|
130
|
+
++f.aggregate_constraints;
|
|
131
|
+
}
|
|
132
|
+
}
|
|
133
|
+
f.cost = f.variable();
|
|
134
|
+
cost.emplace_back(f.cost, 1);
|
|
135
|
+
f.add(std::move(cost), f.maximum, f.maximum);
|
|
136
|
+
return f;
|
|
137
|
+
}
|
|
138
|
+
} // namespace synkit_mapper::solvers::detail
|
|
@@ -0,0 +1,526 @@
|
|
|
1
|
+
#include "formulation.h"
|
|
2
|
+
#include "seed.h"
|
|
3
|
+
#include "synkit_mapper/core/runtime.h"
|
|
4
|
+
#include "synkit_mapper/solvers/solvers.h"
|
|
5
|
+
#include "weighted_cnf.h"
|
|
6
|
+
|
|
7
|
+
#include <cerrno>
|
|
8
|
+
#include <cstdio>
|
|
9
|
+
#include <cstdlib>
|
|
10
|
+
#include <cstring>
|
|
11
|
+
#include <filesystem>
|
|
12
|
+
#include <fstream>
|
|
13
|
+
#include <memory>
|
|
14
|
+
#include <sstream>
|
|
15
|
+
#include <stdexcept>
|
|
16
|
+
#include <string>
|
|
17
|
+
#include <vector>
|
|
18
|
+
|
|
19
|
+
#if defined(__unix__) || defined(__APPLE__)
|
|
20
|
+
#include <fcntl.h>
|
|
21
|
+
#include <poll.h>
|
|
22
|
+
#include <signal.h>
|
|
23
|
+
#include <sys/resource.h>
|
|
24
|
+
#include <sys/types.h>
|
|
25
|
+
#include <sys/wait.h>
|
|
26
|
+
#include <unistd.h>
|
|
27
|
+
#endif
|
|
28
|
+
|
|
29
|
+
#ifndef SYNKIT_MAPPER_OPENWBO_EXECUTABLE
|
|
30
|
+
#define SYNKIT_MAPPER_OPENWBO_EXECUTABLE ""
|
|
31
|
+
#endif
|
|
32
|
+
|
|
33
|
+
#ifndef SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE
|
|
34
|
+
#define SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE ""
|
|
35
|
+
#endif
|
|
36
|
+
|
|
37
|
+
namespace synkit_mapper {
|
|
38
|
+
namespace {
|
|
39
|
+
struct RunMetadata {
|
|
40
|
+
int64_t products = 0, constraints = 0, formulation_bytes = 0, cnf_bytes = 0,
|
|
41
|
+
cnf_variables = 0, cnf_clauses = 0, seed_cost = -1,
|
|
42
|
+
engine_peak_rss = -1;
|
|
43
|
+
double seed_seconds = 0;
|
|
44
|
+
};
|
|
45
|
+
thread_local RunMetadata metadata;
|
|
46
|
+
bool modern_engine() {
|
|
47
|
+
return std::strlen(SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE) != 0;
|
|
48
|
+
}
|
|
49
|
+
const char *engine_path() {
|
|
50
|
+
return modern_engine() ? SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE
|
|
51
|
+
: SYNKIT_MAPPER_OPENWBO_EXECUTABLE;
|
|
52
|
+
}
|
|
53
|
+
using solvers::detail::Formulation;
|
|
54
|
+
using solvers::detail::kInfinity;
|
|
55
|
+
using solvers::detail::Terms;
|
|
56
|
+
struct PhaseTimer {
|
|
57
|
+
double &total;
|
|
58
|
+
Clock::time_point start = Clock::now();
|
|
59
|
+
~PhaseTimer() { total += elapsed(start); }
|
|
60
|
+
};
|
|
61
|
+
#if defined(__unix__) || defined(__APPLE__)
|
|
62
|
+
struct TemporaryFiles {
|
|
63
|
+
std::string directory, input, output;
|
|
64
|
+
TemporaryFiles() {
|
|
65
|
+
auto pattern =
|
|
66
|
+
(std::filesystem::temp_directory_path() / "synkit-maxsat-XXXXXX")
|
|
67
|
+
.string();
|
|
68
|
+
std::vector<char> name(pattern.begin(), pattern.end());
|
|
69
|
+
name.push_back('\0');
|
|
70
|
+
char *created = ::mkdtemp(name.data());
|
|
71
|
+
if (!created)
|
|
72
|
+
throw std::runtime_error("Cannot create MaxSAT temporary directory");
|
|
73
|
+
directory = created;
|
|
74
|
+
input = directory + (modern_engine() ? "/mapping.wcnf" : "/mapping.opb");
|
|
75
|
+
output = directory + "/solver.log";
|
|
76
|
+
}
|
|
77
|
+
~TemporaryFiles() {
|
|
78
|
+
::unlink(input.c_str());
|
|
79
|
+
::unlink(output.c_str());
|
|
80
|
+
::rmdir(directory.c_str());
|
|
81
|
+
}
|
|
82
|
+
};
|
|
83
|
+
pid_t wait_child(pid_t pid, int *status, int options) {
|
|
84
|
+
#if defined(__linux__) || defined(__APPLE__)
|
|
85
|
+
struct rusage usage{};
|
|
86
|
+
pid_t observed = ::wait4(pid, status, options, &usage);
|
|
87
|
+
if (observed == pid) {
|
|
88
|
+
#if defined(__APPLE__)
|
|
89
|
+
int64_t bytes = usage.ru_maxrss;
|
|
90
|
+
#else
|
|
91
|
+
int64_t bytes = static_cast<int64_t>(usage.ru_maxrss) * 1024;
|
|
92
|
+
#endif
|
|
93
|
+
metadata.engine_peak_rss = std::max(metadata.engine_peak_rss, bytes);
|
|
94
|
+
}
|
|
95
|
+
return observed;
|
|
96
|
+
#else
|
|
97
|
+
return ::waitpid(pid, status, options);
|
|
98
|
+
#endif
|
|
99
|
+
}
|
|
100
|
+
struct Child {
|
|
101
|
+
pid_t pid = -1;
|
|
102
|
+
~Child() {
|
|
103
|
+
if (pid > 0) {
|
|
104
|
+
::kill(pid, SIGKILL);
|
|
105
|
+
int status;
|
|
106
|
+
while (wait_child(pid, &status, 0) < 0 && errno == EINTR) {
|
|
107
|
+
}
|
|
108
|
+
}
|
|
109
|
+
}
|
|
110
|
+
};
|
|
111
|
+
struct Response {
|
|
112
|
+
enum State { Unknown, Feasible, Optimum, Infeasible } state = Unknown;
|
|
113
|
+
std::vector<int8_t> values;
|
|
114
|
+
};
|
|
115
|
+
|
|
116
|
+
Response run_openwbo(const TemporaryFiles &files, int variables,
|
|
117
|
+
Budget &budget) {
|
|
118
|
+
budget.check();
|
|
119
|
+
int output = ::open(files.output.c_str(), O_WRONLY | O_CREAT | O_TRUNC, 0600);
|
|
120
|
+
if (output < 0)
|
|
121
|
+
throw std::runtime_error("Cannot open MaxSAT output file");
|
|
122
|
+
const char *executable = engine_path();
|
|
123
|
+
const bool modern = modern_engine();
|
|
124
|
+
Child child;
|
|
125
|
+
child.pid = ::fork();
|
|
126
|
+
if (child.pid == 0) {
|
|
127
|
+
// Only async-signal-safe calls between fork and exec (Python may have
|
|
128
|
+
// other threads). No shell, interpolation, or inherited solver state.
|
|
129
|
+
if (::dup2(output, STDOUT_FILENO) < 0 || ::dup2(output, STDERR_FILENO) < 0)
|
|
130
|
+
::_exit(126);
|
|
131
|
+
::close(output);
|
|
132
|
+
if (modern)
|
|
133
|
+
::execl(executable, executable, "--old", files.input.c_str(),
|
|
134
|
+
static_cast<char *>(nullptr));
|
|
135
|
+
else
|
|
136
|
+
::execl(executable, executable, "-formula=1", "-algorithm=4",
|
|
137
|
+
"-verbosity=0", "-print-model", files.input.c_str(),
|
|
138
|
+
static_cast<char *>(nullptr));
|
|
139
|
+
::_exit(127);
|
|
140
|
+
}
|
|
141
|
+
::close(output);
|
|
142
|
+
if (child.pid < 0)
|
|
143
|
+
throw std::runtime_error("Cannot start native Open-WBO engine");
|
|
144
|
+
int status = 0;
|
|
145
|
+
while (true) {
|
|
146
|
+
budget.check();
|
|
147
|
+
pid_t observed = wait_child(child.pid, &status, WNOHANG);
|
|
148
|
+
if (observed == child.pid) {
|
|
149
|
+
child.pid = -1;
|
|
150
|
+
break;
|
|
151
|
+
}
|
|
152
|
+
if (observed < 0 && errno != EINTR)
|
|
153
|
+
throw std::runtime_error("Cannot wait for native Open-WBO engine");
|
|
154
|
+
::poll(nullptr, 0,
|
|
155
|
+
5); // Cancellation/deadline polling; not a solver worker.
|
|
156
|
+
}
|
|
157
|
+
if (!WIFEXITED(status) ||
|
|
158
|
+
(WEXITSTATUS(status) != 0 && WEXITSTATUS(status) != 10 &&
|
|
159
|
+
WEXITSTATUS(status) != 20 && WEXITSTATUS(status) != 30)) {
|
|
160
|
+
std::ifstream failed(files.output);
|
|
161
|
+
std::string diagnostic((std::istreambuf_iterator<char>(failed)), {});
|
|
162
|
+
if (diagnostic.size() > 2000)
|
|
163
|
+
diagnostic = diagnostic.substr(diagnostic.size() - 2000);
|
|
164
|
+
throw std::runtime_error("Native Open-WBO failed (wait status " +
|
|
165
|
+
std::to_string(status) + "): " + diagnostic);
|
|
166
|
+
}
|
|
167
|
+
Response response;
|
|
168
|
+
response.values.resize(variables, -1);
|
|
169
|
+
std::ifstream stream(files.output);
|
|
170
|
+
std::string line;
|
|
171
|
+
while (std::getline(stream, line)) {
|
|
172
|
+
if (line == "s OPTIMUM FOUND")
|
|
173
|
+
response.state = Response::Optimum;
|
|
174
|
+
else if (line == "s UNSATISFIABLE")
|
|
175
|
+
response.state = Response::Infeasible;
|
|
176
|
+
else if (line == "s SATISFIABLE")
|
|
177
|
+
response.state = Response::Feasible;
|
|
178
|
+
else if (line.rfind("v ", 0) == 0) {
|
|
179
|
+
std::istringstream literals(line.substr(2));
|
|
180
|
+
std::string literal;
|
|
181
|
+
size_t parsed = 0;
|
|
182
|
+
while (literals >> literal) {
|
|
183
|
+
if (!(++parsed % 1024))
|
|
184
|
+
budget.check();
|
|
185
|
+
bool positive = literal[0] != '-';
|
|
186
|
+
size_t offset = positive ? 0 : 1;
|
|
187
|
+
if (offset >= literal.size() || (!modern && literal[offset] != 'x'))
|
|
188
|
+
throw std::runtime_error("Unexpected Open-WBO PB model literal");
|
|
189
|
+
size_t prefix = offset + (modern ? 0 : 1), used = 0;
|
|
190
|
+
long long variable = std::stoll(literal.substr(prefix), &used);
|
|
191
|
+
if (used != literal.size() - prefix || variable < 1 ||
|
|
192
|
+
variable > variables)
|
|
193
|
+
throw std::runtime_error("Invalid Open-WBO PB variable identifier");
|
|
194
|
+
response.values[variable - 1] = positive;
|
|
195
|
+
}
|
|
196
|
+
}
|
|
197
|
+
}
|
|
198
|
+
if (!stream.eof())
|
|
199
|
+
throw std::runtime_error("Cannot read Open-WBO output");
|
|
200
|
+
if (response.state == Response::Unknown)
|
|
201
|
+
throw std::runtime_error(
|
|
202
|
+
"Open-WBO terminated without a certified solver status");
|
|
203
|
+
budget.check();
|
|
204
|
+
return response;
|
|
205
|
+
}
|
|
206
|
+
|
|
207
|
+
void expression(std::ostream &out, const Terms &terms, Budget &budget) {
|
|
208
|
+
size_t written = 0;
|
|
209
|
+
for (auto [variable, coefficient] : terms) {
|
|
210
|
+
if (!(++written % 1024))
|
|
211
|
+
budget.check();
|
|
212
|
+
out << (coefficient >= 0 ? " +" : " ") << coefficient << " x"
|
|
213
|
+
<< variable + 1;
|
|
214
|
+
}
|
|
215
|
+
}
|
|
216
|
+
void row(std::ostream &out, const Terms &terms, int64_t lower, int64_t upper,
|
|
217
|
+
Budget &budget) {
|
|
218
|
+
if (lower == upper) {
|
|
219
|
+
expression(out, terms, budget);
|
|
220
|
+
out << " = " << lower << " ;\n";
|
|
221
|
+
} else {
|
|
222
|
+
if (lower > -kInfinity) {
|
|
223
|
+
expression(out, terms, budget);
|
|
224
|
+
out << " >= " << lower << " ;\n";
|
|
225
|
+
}
|
|
226
|
+
if (upper < kInfinity) {
|
|
227
|
+
expression(out, terms, budget);
|
|
228
|
+
out << " <= " << upper << " ;\n";
|
|
229
|
+
}
|
|
230
|
+
}
|
|
231
|
+
}
|
|
232
|
+
|
|
233
|
+
// The shared sparse product model is reused, except the integer cost variable
|
|
234
|
+
// becomes one forced Boolean z. The chemical objective is C*z - sum(w*y)
|
|
235
|
+
// with z=1. In the satisfaction phase z=0 and actual cost is constrained by
|
|
236
|
+
// sum(w*y)+z == C-target (or >= for a ball). Each y is an exact conjunction.
|
|
237
|
+
void write_problem(const TemporaryFiles &files, const Formulation &f,
|
|
238
|
+
bool optimize, int query, int64_t target,
|
|
239
|
+
const std::vector<std::vector<int32_t>> &blocked,
|
|
240
|
+
int64_t seed_cost, Budget &budget) {
|
|
241
|
+
std::ofstream stream(files.input, std::ios::binary | std::ios::trunc);
|
|
242
|
+
if (!stream)
|
|
243
|
+
throw std::runtime_error("Cannot write native MaxSAT input");
|
|
244
|
+
stream << "* Native sparse full-space atom assignment, doubled CD\nmin:";
|
|
245
|
+
const auto &cost_terms = f.rows.back().terms;
|
|
246
|
+
if (optimize && f.maximum) {
|
|
247
|
+
stream << " +" << f.maximum << " x" << f.cost + 1;
|
|
248
|
+
size_t written = 0;
|
|
249
|
+
for (auto [variable, coefficient] : cost_terms) {
|
|
250
|
+
if (!(++written % 1024))
|
|
251
|
+
budget.check();
|
|
252
|
+
if (variable != f.cost)
|
|
253
|
+
stream << " -" << coefficient << " x" << variable + 1;
|
|
254
|
+
}
|
|
255
|
+
} else
|
|
256
|
+
stream << " +1 x" << f.cost + 1;
|
|
257
|
+
stream << " ;\n";
|
|
258
|
+
row(stream, {{f.cost, 1}}, optimize && f.maximum ? 1 : 0,
|
|
259
|
+
optimize && f.maximum ? 1 : 0, budget);
|
|
260
|
+
for (size_t i = 0; i + 1 < f.rows.size(); ++i) {
|
|
261
|
+
if (!(i % 1024))
|
|
262
|
+
budget.check();
|
|
263
|
+
row(stream, f.rows[i].terms, f.rows[i].lower, f.rows[i].upper, budget);
|
|
264
|
+
}
|
|
265
|
+
if (optimize && seed_cost >= 0 && f.maximum > seed_cost) {
|
|
266
|
+
Terms overlap;
|
|
267
|
+
for (auto term : cost_terms)
|
|
268
|
+
if (term.first != f.cost)
|
|
269
|
+
overlap.push_back(term);
|
|
270
|
+
row(stream, overlap, f.maximum - seed_cost, kInfinity, budget);
|
|
271
|
+
}
|
|
272
|
+
if (!optimize) {
|
|
273
|
+
int64_t bound = f.maximum - std::min(target, f.maximum);
|
|
274
|
+
row(stream, cost_terms, bound,
|
|
275
|
+
query == SYNKIT_AT_MOST_DISTANCE ? kInfinity : bound, budget);
|
|
276
|
+
}
|
|
277
|
+
for (size_t b = 0; b < blocked.size(); ++b) {
|
|
278
|
+
if (!(b % 256))
|
|
279
|
+
budget.check();
|
|
280
|
+
Terms nogood;
|
|
281
|
+
for (int i = 0; i < f.n; ++i)
|
|
282
|
+
nogood.emplace_back(f.x[i * f.n + blocked[b][i]], 1);
|
|
283
|
+
row(stream, nogood, -kInfinity, f.n - 1, budget);
|
|
284
|
+
}
|
|
285
|
+
// Upstream maps the file read-only, uses strlen(), and incorrectly attempts
|
|
286
|
+
// to write if its length differs from st_size. Keep no interior NUL and
|
|
287
|
+
// ensure kernel zero-padding exists in the final mmap page.
|
|
288
|
+
const auto page_size = ::sysconf(_SC_PAGESIZE);
|
|
289
|
+
if (page_size > 0 && static_cast<int64_t>(stream.tellp()) % page_size == 0)
|
|
290
|
+
stream.put('\n');
|
|
291
|
+
stream.close();
|
|
292
|
+
if (!stream)
|
|
293
|
+
throw std::runtime_error("Failed to complete MaxSAT input file");
|
|
294
|
+
}
|
|
295
|
+
|
|
296
|
+
std::pair<std::vector<int32_t>, int64_t> project(const Problem &problem,
|
|
297
|
+
const Formulation &f,
|
|
298
|
+
const Response &response,
|
|
299
|
+
Budget &budget) {
|
|
300
|
+
std::vector<int32_t> mapping(problem.n, -1);
|
|
301
|
+
for (int i = 0; i < problem.n; ++i)
|
|
302
|
+
for (int j = 0; j < problem.n; ++j) {
|
|
303
|
+
int x = f.x[i * problem.n + j];
|
|
304
|
+
if (x >= 0) {
|
|
305
|
+
if (response.values[x] < 0)
|
|
306
|
+
throw std::runtime_error("Open-WBO omitted an atom variable");
|
|
307
|
+
if (response.values[x])
|
|
308
|
+
mapping[i] = j;
|
|
309
|
+
}
|
|
310
|
+
}
|
|
311
|
+
int64_t cost = mapping_cost2(problem, mapping);
|
|
312
|
+
int64_t actual = f.maximum;
|
|
313
|
+
size_t checked = 0;
|
|
314
|
+
for (auto [variable, coefficient] : f.rows.back().terms)
|
|
315
|
+
if (variable != f.cost) {
|
|
316
|
+
if (!(++checked % 1024))
|
|
317
|
+
budget.check();
|
|
318
|
+
if (response.values[variable] < 0)
|
|
319
|
+
throw std::runtime_error("Open-WBO omitted a product variable");
|
|
320
|
+
actual -= coefficient * response.values[variable];
|
|
321
|
+
}
|
|
322
|
+
if (cost != actual)
|
|
323
|
+
throw std::runtime_error(
|
|
324
|
+
"Open-WBO cost disagrees with independent rescoring");
|
|
325
|
+
return {std::move(mapping), cost};
|
|
326
|
+
}
|
|
327
|
+
#endif
|
|
328
|
+
} // namespace
|
|
329
|
+
|
|
330
|
+
const char *maxsat_solver_version() {
|
|
331
|
+
return modern_engine()
|
|
332
|
+
? "EvalMaxSAT CLI, OLL/CaDiCaL, external native process"
|
|
333
|
+
: "Open-WBO 2.1, OLL/Glucose4.1, external native process";
|
|
334
|
+
}
|
|
335
|
+
const char *maxsat_run_metadata() {
|
|
336
|
+
static thread_local std::string value;
|
|
337
|
+
std::ostringstream out;
|
|
338
|
+
out << "{\"formulation\":\""
|
|
339
|
+
<< (modern_engine() ? "exact_weighted_cnf_seed_v2"
|
|
340
|
+
: "sparse_pb_rlt_seed_v2")
|
|
341
|
+
<< "\",\"engine\":\"" << (modern_engine() ? "EvalMaxSAT" : "Open-WBO")
|
|
342
|
+
<< "\",\"product_variables\":" << metadata.products
|
|
343
|
+
<< ",\"model_constraints\":" << metadata.constraints
|
|
344
|
+
<< ",\"accounted_formulation_bytes\":" << metadata.formulation_bytes
|
|
345
|
+
<< ",\"accounted_cnf_bytes\":" << metadata.cnf_bytes
|
|
346
|
+
<< ",\"cnf_variables\":" << metadata.cnf_variables
|
|
347
|
+
<< ",\"cnf_clauses\":" << metadata.cnf_clauses
|
|
348
|
+
<< ",\"seed_cost2\":" << metadata.seed_cost
|
|
349
|
+
<< ",\"seed_seconds\":" << metadata.seed_seconds
|
|
350
|
+
<< ",\"engine_peak_rss_bytes\":" << metadata.engine_peak_rss
|
|
351
|
+
<< ",\"engine_peak_rss_scope\":\"child_process_lifetime_including_fork_"
|
|
352
|
+
"exec\""
|
|
353
|
+
<< ",\"cnf_reused_for_enumeration\":"
|
|
354
|
+
<< (modern_engine() ? "true" : "false")
|
|
355
|
+
<< ",\"seed_scope\":\"input_only_feasible_incumbent_bound\"}";
|
|
356
|
+
value = out.str();
|
|
357
|
+
return value.c_str();
|
|
358
|
+
}
|
|
359
|
+
|
|
360
|
+
int solve_maxsat(const Problem &problem, const Request &request,
|
|
361
|
+
Callback callback, void *userdata, Statistics &stats) {
|
|
362
|
+
initialize(stats, request);
|
|
363
|
+
metadata = {};
|
|
364
|
+
Budget budget(request);
|
|
365
|
+
struct Finish {
|
|
366
|
+
Statistics &s;
|
|
367
|
+
Budget &b;
|
|
368
|
+
~Finish() { s.elapsed_seconds = b.seconds(); }
|
|
369
|
+
} finish{stats, budget};
|
|
370
|
+
if (request.max_states != -1 || request.max_classes != -1 ||
|
|
371
|
+
request.max_frontier != -1 || request.memory_limit_bytes != -1 ||
|
|
372
|
+
request.symmetry || request.classify)
|
|
373
|
+
return unsupported(stats);
|
|
374
|
+
#if defined(__unix__) || defined(__APPLE__)
|
|
375
|
+
if (!std::strlen(engine_path()))
|
|
376
|
+
return unsupported(stats);
|
|
377
|
+
if (::access(engine_path(), X_OK))
|
|
378
|
+
throw std::runtime_error("Configured Open-WBO executable is unavailable");
|
|
379
|
+
stats.labeled_count = 0;
|
|
380
|
+
stats.peak_frontier = stats.peak_frontier_bytes = -1;
|
|
381
|
+
try {
|
|
382
|
+
budget.check();
|
|
383
|
+
Formulation f;
|
|
384
|
+
{
|
|
385
|
+
PhaseTimer timer{stats.model_seconds};
|
|
386
|
+
f = solvers::detail::formulate(problem.n, problem.a2, problem.b2,
|
|
387
|
+
problem.types_r, problem.types_p,
|
|
388
|
+
[&] { budget.check(); });
|
|
389
|
+
}
|
|
390
|
+
if (request.query == SYNKIT_EXACT_DISTANCE && request.target2 > f.maximum) {
|
|
391
|
+
stats.search_complete = 1;
|
|
392
|
+
return 0;
|
|
393
|
+
}
|
|
394
|
+
metadata.products = f.products.size();
|
|
395
|
+
metadata.constraints = f.rows.size();
|
|
396
|
+
metadata.formulation_bytes = f.accounted_bytes();
|
|
397
|
+
{
|
|
398
|
+
PhaseTimer timer{stats.model_seconds};
|
|
399
|
+
PhaseTimer seed_timer{metadata.seed_seconds};
|
|
400
|
+
auto seed = solvers::detail::feasible_seed(problem, budget);
|
|
401
|
+
if (!seed.empty())
|
|
402
|
+
metadata.seed_cost = stats.incumbent2 = mapping_cost2(problem, seed);
|
|
403
|
+
}
|
|
404
|
+
TemporaryFiles files;
|
|
405
|
+
std::vector<std::vector<int32_t>> blocked;
|
|
406
|
+
std::unique_ptr<solvers::detail::WeightedCnf> satisfaction_cnf;
|
|
407
|
+
size_t encoded_blocks = 0;
|
|
408
|
+
auto run = [&](bool optimize, int64_t target) {
|
|
409
|
+
int variables = f.variables;
|
|
410
|
+
{
|
|
411
|
+
PhaseTimer timer{stats.model_seconds};
|
|
412
|
+
if (modern_engine()) {
|
|
413
|
+
std::unique_ptr<solvers::detail::WeightedCnf> optimization_cnf;
|
|
414
|
+
if (optimize)
|
|
415
|
+
optimization_cnf =
|
|
416
|
+
std::make_unique<solvers::detail::WeightedCnf>(f, budget);
|
|
417
|
+
bool fresh = !satisfaction_cnf;
|
|
418
|
+
if (!optimize && fresh)
|
|
419
|
+
satisfaction_cnf =
|
|
420
|
+
std::make_unique<solvers::detail::WeightedCnf>(f, budget);
|
|
421
|
+
auto &cnf = optimize ? *optimization_cnf : *satisfaction_cnf;
|
|
422
|
+
if (optimize) {
|
|
423
|
+
for (const auto &product : f.products)
|
|
424
|
+
cnf.soft.emplace_back(product.benefit, product.variable + 1);
|
|
425
|
+
if (metadata.seed_cost >= 0 && f.maximum > metadata.seed_cost) {
|
|
426
|
+
cnf.build_sum(f);
|
|
427
|
+
cnf.bound(f.maximum - metadata.seed_cost, true);
|
|
428
|
+
}
|
|
429
|
+
} else if (fresh) {
|
|
430
|
+
cnf.build_sum(f);
|
|
431
|
+
cnf.bound(f.maximum - std::min(target, f.maximum), true);
|
|
432
|
+
if (request.query != SYNKIT_AT_MOST_DISTANCE)
|
|
433
|
+
cnf.bound(f.maximum - target, false);
|
|
434
|
+
}
|
|
435
|
+
while (!optimize && encoded_blocks < blocked.size()) {
|
|
436
|
+
budget.check();
|
|
437
|
+
const auto &mapping = blocked[encoded_blocks++];
|
|
438
|
+
std::vector<int> nogood;
|
|
439
|
+
for (int i = 0; i < f.n; ++i)
|
|
440
|
+
nogood.push_back(-f.x[i * f.n + mapping[i]] - 1);
|
|
441
|
+
cnf.add(std::move(nogood));
|
|
442
|
+
}
|
|
443
|
+
variables = cnf.variables;
|
|
444
|
+
metadata.cnf_variables = variables;
|
|
445
|
+
metadata.cnf_clauses = cnf.hard.size() + cnf.soft.size();
|
|
446
|
+
metadata.cnf_bytes =
|
|
447
|
+
std::max(metadata.cnf_bytes, cnf.accounted_bytes());
|
|
448
|
+
cnf.write(files.input);
|
|
449
|
+
} else
|
|
450
|
+
write_problem(files, f, optimize, request.query, target, blocked,
|
|
451
|
+
metadata.seed_cost, budget);
|
|
452
|
+
}
|
|
453
|
+
PhaseTimer timer{optimize ? stats.optimization_seconds
|
|
454
|
+
: stats.enumeration_seconds};
|
|
455
|
+
return run_openwbo(files, variables, budget);
|
|
456
|
+
};
|
|
457
|
+
int64_t target = request.target2;
|
|
458
|
+
if (request.query == SYNKIT_MINIMUM_CLASSES ||
|
|
459
|
+
request.query == SYNKIT_MINIMUM_PROOF) {
|
|
460
|
+
auto response = run(true, 0);
|
|
461
|
+
if (response.state == Response::Infeasible) {
|
|
462
|
+
stats.search_complete = 1;
|
|
463
|
+
return 0;
|
|
464
|
+
}
|
|
465
|
+
auto [mapping, cost] = project(problem, f, response, budget);
|
|
466
|
+
stats.incumbent2 = cost;
|
|
467
|
+
if (response.state != Response::Optimum) {
|
|
468
|
+
stopped(stats,
|
|
469
|
+
cancelled(request) ? SYNKIT_STOP_CANCELLED : SYNKIT_STOP_TIME);
|
|
470
|
+
return 0;
|
|
471
|
+
}
|
|
472
|
+
stats.minimum_proven = 1;
|
|
473
|
+
target = stats.minimum2 = stats.lower_bound2 = cost;
|
|
474
|
+
if (request.query == SYNKIT_MINIMUM_PROOF) {
|
|
475
|
+
stats.search_complete = 1;
|
|
476
|
+
return 0;
|
|
477
|
+
}
|
|
478
|
+
}
|
|
479
|
+
while (true) {
|
|
480
|
+
auto response = run(false, target);
|
|
481
|
+
if (response.state == Response::Infeasible) {
|
|
482
|
+
stats.search_complete = 1;
|
|
483
|
+
return 0;
|
|
484
|
+
}
|
|
485
|
+
auto [mapping, cost] = project(problem, f, response, budget);
|
|
486
|
+
if ((request.query == SYNKIT_AT_MOST_DISTANCE && cost > target) ||
|
|
487
|
+
(request.query != SYNKIT_AT_MOST_DISTANCE && cost != target))
|
|
488
|
+
throw std::runtime_error(
|
|
489
|
+
"Open-WBO emitted a mapping outside the requested shell");
|
|
490
|
+
budget.check();
|
|
491
|
+
++stats.candidate_count;
|
|
492
|
+
if (stats.incumbent2 < 0 || cost < stats.incumbent2)
|
|
493
|
+
stats.incumbent2 = cost;
|
|
494
|
+
++stats.leaves;
|
|
495
|
+
stats.labeled_count = stats.candidate_count;
|
|
496
|
+
int stop = 0;
|
|
497
|
+
{
|
|
498
|
+
PhaseTimer callback_timer{stats.callback_seconds};
|
|
499
|
+
PhaseTimer enumeration_timer{stats.enumeration_seconds};
|
|
500
|
+
if (callback)
|
|
501
|
+
stop = callback(mapping.data(), cost, userdata);
|
|
502
|
+
}
|
|
503
|
+
if (stop) {
|
|
504
|
+
stopped(stats, SYNKIT_STOP_CALLBACK);
|
|
505
|
+
return 0;
|
|
506
|
+
}
|
|
507
|
+
budget.check();
|
|
508
|
+
if (request.max_candidates >= 0 &&
|
|
509
|
+
stats.candidate_count >= request.max_candidates) {
|
|
510
|
+
stopped(stats, SYNKIT_STOP_CANDIDATES);
|
|
511
|
+
return 0;
|
|
512
|
+
}
|
|
513
|
+
blocked.push_back(std::move(mapping));
|
|
514
|
+
}
|
|
515
|
+
} catch (const Stop &stop) {
|
|
516
|
+
stopped(stats, stop.reason);
|
|
517
|
+
}
|
|
518
|
+
#else
|
|
519
|
+
(void)problem;
|
|
520
|
+
(void)callback;
|
|
521
|
+
(void)userdata;
|
|
522
|
+
return unsupported(stats);
|
|
523
|
+
#endif
|
|
524
|
+
return 0;
|
|
525
|
+
}
|
|
526
|
+
} // namespace synkit_mapper
|