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/combinatorial/gml_to_graph.py +223 -0
- synkit/IO/combinatorial/graph_to_gml.py +280 -0
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- synkit/IO/combinatorial/smarts_expander.py +147 -0
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- synkit/IO/combinatorial/smarts_to_graph.py +179 -0
- synkit/IO/conversion.py +42 -0
- synkit/IO/data_io.py +269 -0
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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
- 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
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- 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
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- 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
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- synkit/Rule/Apply/conditions.py +45 -0
- synkit/Rule/Apply/dpo.py +998 -0
- synkit/Rule/Apply/rule_matcher.py +218 -0
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- synkit/Rule/Compose/composition.py +976 -0
- synkit/Rule/Compose/laws.py +439 -0
- synkit/Rule/Compose/search.py +771 -0
- synkit/Rule/Compose/synrule.py +170 -0
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- synkit/Synthesis/Metrics/_plot.py +129 -0
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+
if (!ISELEMENT(pgp,posp)) return FALSE;
|
|
84
|
+
}
|
|
85
|
+
}
|
|
86
|
+
return TRUE;
|
|
87
|
+
}
|
|
88
|
+
|
|
89
|
+
/*****************************************************************************
|
|
90
|
+
* *
|
|
91
|
+
* testcanlab(g,canong,lab,samerows,m,n) compares g^lab to canong, *
|
|
92
|
+
* using an ordering which is immaterial since it's only used here. The *
|
|
93
|
+
* value returned is -1,0,1 if g^lab <,=,> canong. *samerows is set to *
|
|
94
|
+
* the number of rows (0..n) of canong which are the same as those of g^lab. *
|
|
95
|
+
* *
|
|
96
|
+
* GLOBALS ACCESSED: workset<rw>,permset(),workperm<rw> *
|
|
97
|
+
* *
|
|
98
|
+
*****************************************************************************/
|
|
99
|
+
|
|
100
|
+
int
|
|
101
|
+
testcanlab(graph *g, graph *canong, int *lab, int *samerows, int m, int n)
|
|
102
|
+
{
|
|
103
|
+
int i,j;
|
|
104
|
+
set *ph;
|
|
105
|
+
|
|
106
|
+
#if !MAXN
|
|
107
|
+
DYNALLOC1(int,workperm,workperm_sz,n,"testcanlab");
|
|
108
|
+
DYNALLOC1(set,workset,workset_sz,m,"testcanlab");
|
|
109
|
+
#endif
|
|
110
|
+
|
|
111
|
+
for (i = 0; i < n; ++i) workperm[lab[i]] = i;
|
|
112
|
+
|
|
113
|
+
for (i = 0, ph = canong; i < n; ++i, ph += M)
|
|
114
|
+
{
|
|
115
|
+
permset(GRAPHROW(g,lab[i],M),workset,M,workperm);
|
|
116
|
+
for (j = 0; j < M; ++j)
|
|
117
|
+
if (workset[j] < ph[j])
|
|
118
|
+
{
|
|
119
|
+
*samerows = i;
|
|
120
|
+
return -1;
|
|
121
|
+
}
|
|
122
|
+
else if (workset[j] > ph[j])
|
|
123
|
+
{
|
|
124
|
+
*samerows = i;
|
|
125
|
+
return 1;
|
|
126
|
+
}
|
|
127
|
+
}
|
|
128
|
+
|
|
129
|
+
*samerows = n;
|
|
130
|
+
return 0;
|
|
131
|
+
}
|
|
132
|
+
|
|
133
|
+
/*****************************************************************************
|
|
134
|
+
* *
|
|
135
|
+
* updatecan(g,canong,lab,samerows,m,n) sets canong = g^lab, assuming *
|
|
136
|
+
* the first samerows of canong are ok already. *
|
|
137
|
+
* *
|
|
138
|
+
* GLOBALS ACCESSED: permset(),workperm<rw> *
|
|
139
|
+
* *
|
|
140
|
+
*****************************************************************************/
|
|
141
|
+
|
|
142
|
+
void
|
|
143
|
+
updatecan(graph *g, graph *canong, int *lab, int samerows, int m, int n)
|
|
144
|
+
{
|
|
145
|
+
int i;
|
|
146
|
+
set *ph;
|
|
147
|
+
|
|
148
|
+
#if !MAXN
|
|
149
|
+
DYNALLOC1(int,workperm,workperm_sz,n,"updatecan");
|
|
150
|
+
#endif
|
|
151
|
+
|
|
152
|
+
for (i = 0; i < n; ++i) workperm[lab[i]] = i;
|
|
153
|
+
|
|
154
|
+
for (i = samerows, ph = GRAPHROW(canong,samerows,M);
|
|
155
|
+
i < n; ++i, ph += M)
|
|
156
|
+
permset(GRAPHROW(g,lab[i],M),ph,M,workperm);
|
|
157
|
+
}
|
|
158
|
+
|
|
159
|
+
/*****************************************************************************
|
|
160
|
+
* *
|
|
161
|
+
* refine(g,lab,ptn,level,numcells,count,active,code,m,n) performs a *
|
|
162
|
+
* refinement operation on the partition at the specified level of the *
|
|
163
|
+
* partition nest (lab,ptn). *numcells is assumed to contain the number of *
|
|
164
|
+
* cells on input, and is updated. The initial set of active cells (alpha *
|
|
165
|
+
* in the paper) is specified in the set active. Precisely, x is in active *
|
|
166
|
+
* iff the cell starting at index x in lab is active. *
|
|
167
|
+
* The resulting partition is equitable if active is correct (see the paper *
|
|
168
|
+
* and the Guide). *
|
|
169
|
+
* *code is set to a value which depends on the fine detail of the *
|
|
170
|
+
* algorithm, but which is independent of the labelling of the graph. *
|
|
171
|
+
* count is used for work space. *
|
|
172
|
+
* *
|
|
173
|
+
* GLOBALS ACCESSED: workset<w>,bit<r>,nextelement(),bucket<w>,workperm<w> *
|
|
174
|
+
* *
|
|
175
|
+
*****************************************************************************/
|
|
176
|
+
|
|
177
|
+
void
|
|
178
|
+
refine(graph *g, int *lab, int *ptn, int level, int *numcells,
|
|
179
|
+
int *count, set *active, int *code, int m, int n)
|
|
180
|
+
{
|
|
181
|
+
|
|
182
|
+
#if MAXM==1
|
|
183
|
+
refine1(g,lab,ptn,level,numcells,count,active,code,m,n);
|
|
184
|
+
}
|
|
185
|
+
#else
|
|
186
|
+
|
|
187
|
+
int i,c1,c2,labc1;
|
|
188
|
+
setword x;
|
|
189
|
+
set *set1,*set2;
|
|
190
|
+
int split1,split2,cell1,cell2;
|
|
191
|
+
int cnt,bmin,bmax;
|
|
192
|
+
long longcode;
|
|
193
|
+
set *gptr;
|
|
194
|
+
int maxcell,maxpos,hint;
|
|
195
|
+
|
|
196
|
+
#if !MAXN
|
|
197
|
+
DYNALLOC1(int,workperm,workperm_sz,n,"refine");
|
|
198
|
+
DYNALLOC1(set,workset,workset_sz,m,"refine");
|
|
199
|
+
DYNALLOC1(int,bucket,bucket_sz,n+2,"refine");
|
|
200
|
+
#endif
|
|
201
|
+
|
|
202
|
+
longcode = *numcells;
|
|
203
|
+
split1 = -1;
|
|
204
|
+
hint = 0;
|
|
205
|
+
maxpos = 0;
|
|
206
|
+
while (*numcells < n && ((split1 = hint, ISELEMENT(active,split1))
|
|
207
|
+
|| (split1 = nextelement(active,M,split1)) >= 0
|
|
208
|
+
|| (split1 = nextelement(active,M,-1)) >= 0))
|
|
209
|
+
{
|
|
210
|
+
DELELEMENT(active,split1);
|
|
211
|
+
for (split2 = split1; ptn[split2] > level; ++split2) {}
|
|
212
|
+
longcode = MASH(longcode,split1+split2);
|
|
213
|
+
if (split1 == split2) /* trivial splitting cell */
|
|
214
|
+
{
|
|
215
|
+
gptr = GRAPHROW(g,lab[split1],M);
|
|
216
|
+
for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
|
|
217
|
+
{
|
|
218
|
+
for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
|
|
219
|
+
if (cell1 == cell2) continue;
|
|
220
|
+
c1 = cell1;
|
|
221
|
+
c2 = cell2;
|
|
222
|
+
while (c1 <= c2)
|
|
223
|
+
{
|
|
224
|
+
labc1 = lab[c1];
|
|
225
|
+
if (ISELEMENT(gptr,labc1))
|
|
226
|
+
++c1;
|
|
227
|
+
else
|
|
228
|
+
{
|
|
229
|
+
lab[c1] = lab[c2];
|
|
230
|
+
lab[c2] = labc1;
|
|
231
|
+
--c2;
|
|
232
|
+
}
|
|
233
|
+
}
|
|
234
|
+
if (c2 >= cell1 && c1 <= cell2)
|
|
235
|
+
{
|
|
236
|
+
ptn[c2] = level;
|
|
237
|
+
longcode = MASH(longcode,c2);
|
|
238
|
+
++*numcells;
|
|
239
|
+
if (ISELEMENT(active,cell1) || c2-cell1 >= cell2-c1)
|
|
240
|
+
{
|
|
241
|
+
ADDELEMENT(active,c1);
|
|
242
|
+
if (c1 == cell2) hint = c1;
|
|
243
|
+
}
|
|
244
|
+
else
|
|
245
|
+
{
|
|
246
|
+
ADDELEMENT(active,cell1);
|
|
247
|
+
if (c2 == cell1) hint = cell1;
|
|
248
|
+
}
|
|
249
|
+
}
|
|
250
|
+
}
|
|
251
|
+
}
|
|
252
|
+
|
|
253
|
+
else /* nontrivial splitting cell */
|
|
254
|
+
{
|
|
255
|
+
EMPTYSET(workset,m);
|
|
256
|
+
for (i = split1; i <= split2; ++i)
|
|
257
|
+
ADDELEMENT(workset,lab[i]);
|
|
258
|
+
longcode = MASH(longcode,split2-split1+1);
|
|
259
|
+
|
|
260
|
+
for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
|
|
261
|
+
{
|
|
262
|
+
for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
|
|
263
|
+
if (cell1 == cell2) continue;
|
|
264
|
+
i = cell1;
|
|
265
|
+
set1 = workset;
|
|
266
|
+
set2 = GRAPHROW(g,lab[i],m);
|
|
267
|
+
cnt = 0;
|
|
268
|
+
for (c1 = m; --c1 >= 0;)
|
|
269
|
+
if ((x = ((*set1++) & (*set2++))) != 0)
|
|
270
|
+
cnt += POPCOUNT(x);
|
|
271
|
+
|
|
272
|
+
count[i] = bmin = bmax = cnt;
|
|
273
|
+
bucket[cnt] = 1;
|
|
274
|
+
while (++i <= cell2)
|
|
275
|
+
{
|
|
276
|
+
set1 = workset;
|
|
277
|
+
set2 = GRAPHROW(g,lab[i],m);
|
|
278
|
+
cnt = 0;
|
|
279
|
+
for (c1 = m; --c1 >= 0;)
|
|
280
|
+
if ((x = ((*set1++) & (*set2++))) != 0)
|
|
281
|
+
cnt += POPCOUNT(x);
|
|
282
|
+
|
|
283
|
+
while (bmin > cnt) bucket[--bmin] = 0;
|
|
284
|
+
while (bmax < cnt) bucket[++bmax] = 0;
|
|
285
|
+
++bucket[cnt];
|
|
286
|
+
count[i] = cnt;
|
|
287
|
+
}
|
|
288
|
+
if (bmin == bmax)
|
|
289
|
+
{
|
|
290
|
+
longcode = MASH(longcode,bmin+cell1);
|
|
291
|
+
continue;
|
|
292
|
+
}
|
|
293
|
+
c1 = cell1;
|
|
294
|
+
maxcell = -1;
|
|
295
|
+
for (i = bmin; i <= bmax; ++i)
|
|
296
|
+
if (bucket[i])
|
|
297
|
+
{
|
|
298
|
+
c2 = c1 + bucket[i];
|
|
299
|
+
bucket[i] = c1;
|
|
300
|
+
longcode = MASH(longcode,i+c1);
|
|
301
|
+
if (c2-c1 > maxcell)
|
|
302
|
+
{
|
|
303
|
+
maxcell = c2-c1;
|
|
304
|
+
maxpos = c1;
|
|
305
|
+
}
|
|
306
|
+
if (c1 != cell1)
|
|
307
|
+
{
|
|
308
|
+
ADDELEMENT(active,c1);
|
|
309
|
+
if (c2-c1 == 1) hint = c1;
|
|
310
|
+
++*numcells;
|
|
311
|
+
}
|
|
312
|
+
if (c2 <= cell2) ptn[c2-1] = level;
|
|
313
|
+
c1 = c2;
|
|
314
|
+
}
|
|
315
|
+
for (i = cell1; i <= cell2; ++i)
|
|
316
|
+
workperm[bucket[count[i]]++] = lab[i];
|
|
317
|
+
for (i = cell1; i <= cell2; ++i) lab[i] = workperm[i];
|
|
318
|
+
if (!ISELEMENT(active,cell1))
|
|
319
|
+
{
|
|
320
|
+
ADDELEMENT(active,cell1);
|
|
321
|
+
DELELEMENT(active,maxpos);
|
|
322
|
+
}
|
|
323
|
+
}
|
|
324
|
+
}
|
|
325
|
+
}
|
|
326
|
+
|
|
327
|
+
longcode = MASH(longcode,*numcells);
|
|
328
|
+
*code = CLEANUP(longcode);
|
|
329
|
+
}
|
|
330
|
+
#endif /* else case of MAXM==1 */
|
|
331
|
+
|
|
332
|
+
/*****************************************************************************
|
|
333
|
+
* *
|
|
334
|
+
* refine1(g,lab,ptn,level,numcells,count,active,code,m,n) is the same as *
|
|
335
|
+
* refine(g,lab,ptn,level,numcells,count,active,code,m,n), except that *
|
|
336
|
+
* m==1 is assumed for greater efficiency. The results are identical in all *
|
|
337
|
+
* respects. See refine (above) for the specs. *
|
|
338
|
+
* *
|
|
339
|
+
*****************************************************************************/
|
|
340
|
+
|
|
341
|
+
void
|
|
342
|
+
refine1(graph *g, int *lab, int *ptn, int level, int *numcells,
|
|
343
|
+
int *count, set *active, int *code, int m, int n)
|
|
344
|
+
{
|
|
345
|
+
int i,c1,c2,labc1;
|
|
346
|
+
setword x;
|
|
347
|
+
int split1,split2,cell1,cell2;
|
|
348
|
+
int cnt,bmin,bmax;
|
|
349
|
+
long longcode;
|
|
350
|
+
set *gptr,workset0;
|
|
351
|
+
int maxcell,maxpos,hint;
|
|
352
|
+
|
|
353
|
+
#if !MAXN
|
|
354
|
+
DYNALLOC1(int,workperm,workperm_sz,n,"refine1");
|
|
355
|
+
DYNALLOC1(int,bucket,bucket_sz,n+2,"refine1");
|
|
356
|
+
#endif
|
|
357
|
+
|
|
358
|
+
longcode = *numcells;
|
|
359
|
+
split1 = -1;
|
|
360
|
+
maxpos = 0;
|
|
361
|
+
|
|
362
|
+
hint = 0;
|
|
363
|
+
while (*numcells < n && ((split1 = hint, ISELEMENT1(active,split1))
|
|
364
|
+
|| (split1 = nextelement(active,1,split1)) >= 0
|
|
365
|
+
|| (split1 = nextelement(active,1,-1)) >= 0))
|
|
366
|
+
{
|
|
367
|
+
DELELEMENT1(active,split1);
|
|
368
|
+
for (split2 = split1; ptn[split2] > level; ++split2) {}
|
|
369
|
+
longcode = MASH(longcode,split1+split2);
|
|
370
|
+
if (split1 == split2) /* trivial splitting cell */
|
|
371
|
+
{
|
|
372
|
+
gptr = GRAPHROW(g,lab[split1],1);
|
|
373
|
+
for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
|
|
374
|
+
{
|
|
375
|
+
for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
|
|
376
|
+
if (cell1 == cell2) continue;
|
|
377
|
+
c1 = cell1;
|
|
378
|
+
c2 = cell2;
|
|
379
|
+
while (c1 <= c2)
|
|
380
|
+
{
|
|
381
|
+
labc1 = lab[c1];
|
|
382
|
+
if (ISELEMENT1(gptr,labc1))
|
|
383
|
+
++c1;
|
|
384
|
+
else
|
|
385
|
+
{
|
|
386
|
+
lab[c1] = lab[c2];
|
|
387
|
+
lab[c2] = labc1;
|
|
388
|
+
--c2;
|
|
389
|
+
}
|
|
390
|
+
}
|
|
391
|
+
if (c2 >= cell1 && c1 <= cell2)
|
|
392
|
+
{
|
|
393
|
+
ptn[c2] = level;
|
|
394
|
+
longcode = MASH(longcode,c2);
|
|
395
|
+
++*numcells;
|
|
396
|
+
if (ISELEMENT1(active,cell1) || c2-cell1 >= cell2-c1)
|
|
397
|
+
{
|
|
398
|
+
ADDELEMENT1(active,c1);
|
|
399
|
+
if (c1 == cell2) hint = c1;
|
|
400
|
+
}
|
|
401
|
+
else
|
|
402
|
+
{
|
|
403
|
+
ADDELEMENT1(active,cell1);
|
|
404
|
+
if (c2 == cell1) hint = cell1;
|
|
405
|
+
}
|
|
406
|
+
}
|
|
407
|
+
}
|
|
408
|
+
}
|
|
409
|
+
|
|
410
|
+
else /* nontrivial splitting cell */
|
|
411
|
+
{
|
|
412
|
+
workset0 = 0;
|
|
413
|
+
for (i = split1; i <= split2; ++i)
|
|
414
|
+
ADDELEMENT1(&workset0,lab[i]);
|
|
415
|
+
longcode = MASH(longcode,split2-split1+1);
|
|
416
|
+
|
|
417
|
+
for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
|
|
418
|
+
{
|
|
419
|
+
for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
|
|
420
|
+
if (cell1 == cell2) continue;
|
|
421
|
+
i = cell1;
|
|
422
|
+
if ((x = workset0 & g[lab[i]]) != 0)
|
|
423
|
+
cnt = POPCOUNT(x);
|
|
424
|
+
else
|
|
425
|
+
cnt = 0;
|
|
426
|
+
count[i] = bmin = bmax = cnt;
|
|
427
|
+
bucket[cnt] = 1;
|
|
428
|
+
while (++i <= cell2)
|
|
429
|
+
{
|
|
430
|
+
if ((x = workset0 & g[lab[i]]) != 0)
|
|
431
|
+
cnt = POPCOUNT(x);
|
|
432
|
+
else
|
|
433
|
+
cnt = 0;
|
|
434
|
+
while (bmin > cnt) bucket[--bmin] = 0;
|
|
435
|
+
while (bmax < cnt) bucket[++bmax] = 0;
|
|
436
|
+
++bucket[cnt];
|
|
437
|
+
count[i] = cnt;
|
|
438
|
+
}
|
|
439
|
+
if (bmin == bmax)
|
|
440
|
+
{
|
|
441
|
+
longcode = MASH(longcode,bmin+cell1);
|
|
442
|
+
continue;
|
|
443
|
+
}
|
|
444
|
+
c1 = cell1;
|
|
445
|
+
maxcell = -1;
|
|
446
|
+
for (i = bmin; i <= bmax; ++i)
|
|
447
|
+
if (bucket[i])
|
|
448
|
+
{
|
|
449
|
+
c2 = c1 + bucket[i];
|
|
450
|
+
bucket[i] = c1;
|
|
451
|
+
longcode = MASH(longcode,i+c1);
|
|
452
|
+
if (c2-c1 > maxcell)
|
|
453
|
+
{
|
|
454
|
+
maxcell = c2-c1;
|
|
455
|
+
maxpos = c1;
|
|
456
|
+
}
|
|
457
|
+
if (c1 != cell1)
|
|
458
|
+
{
|
|
459
|
+
ADDELEMENT1(active,c1);
|
|
460
|
+
if (c2-c1 == 1) hint = c1;
|
|
461
|
+
++*numcells;
|
|
462
|
+
}
|
|
463
|
+
if (c2 <= cell2) ptn[c2-1] = level;
|
|
464
|
+
c1 = c2;
|
|
465
|
+
}
|
|
466
|
+
for (i = cell1; i <= cell2; ++i)
|
|
467
|
+
workperm[bucket[count[i]]++] = lab[i];
|
|
468
|
+
for (i = cell1; i <= cell2; ++i) lab[i] = workperm[i];
|
|
469
|
+
if (!ISELEMENT1(active,cell1))
|
|
470
|
+
{
|
|
471
|
+
ADDELEMENT1(active,cell1);
|
|
472
|
+
DELELEMENT1(active,maxpos);
|
|
473
|
+
}
|
|
474
|
+
}
|
|
475
|
+
}
|
|
476
|
+
}
|
|
477
|
+
|
|
478
|
+
longcode = MASH(longcode,*numcells);
|
|
479
|
+
*code = CLEANUP(longcode);
|
|
480
|
+
}
|
|
481
|
+
|
|
482
|
+
/*****************************************************************************
|
|
483
|
+
* *
|
|
484
|
+
* cheapautom(ptn,level,digraph,n) returns TRUE if the partition at the *
|
|
485
|
+
* specified level in the partition nest (lab,ptn) {lab is not needed here} *
|
|
486
|
+
* satisfies a simple sufficient condition for its cells to be the orbits of *
|
|
487
|
+
* some subgroup of the automorphism group. Otherwise it returns FALSE. *
|
|
488
|
+
* It always returns FALSE if digraph!=FALSE. *
|
|
489
|
+
* *
|
|
490
|
+
* nauty assumes that this function will always return TRUE for any *
|
|
491
|
+
* partition finer than one for which it returns TRUE. *
|
|
492
|
+
* *
|
|
493
|
+
*****************************************************************************/
|
|
494
|
+
|
|
495
|
+
boolean
|
|
496
|
+
cheapautom(int *ptn, int level, boolean digraph, int n)
|
|
497
|
+
{
|
|
498
|
+
int i,k,nnt;
|
|
499
|
+
|
|
500
|
+
if (digraph) return FALSE;
|
|
501
|
+
|
|
502
|
+
k = n;
|
|
503
|
+
nnt = 0;
|
|
504
|
+
for (i = 0; i < n; ++i)
|
|
505
|
+
{
|
|
506
|
+
--k;
|
|
507
|
+
if (ptn[i] > level)
|
|
508
|
+
{
|
|
509
|
+
++nnt;
|
|
510
|
+
while (ptn[++i] > level) {}
|
|
511
|
+
}
|
|
512
|
+
}
|
|
513
|
+
|
|
514
|
+
return (k <= nnt + 1 || k <= 4);
|
|
515
|
+
}
|
|
516
|
+
|
|
517
|
+
/*****************************************************************************
|
|
518
|
+
* *
|
|
519
|
+
* bestcell(g,lab,ptn,level,tc_level,m,n) returns the index in lab of the *
|
|
520
|
+
* start of the "best non-singleton cell" for fixing. If there is no *
|
|
521
|
+
* non-singleton cell it returns n. *
|
|
522
|
+
* This implementation finds the first cell which is non-trivially joined *
|
|
523
|
+
* to the greatest number of other cells. *
|
|
524
|
+
* *
|
|
525
|
+
* GLOBALS ACCESSED: bit<r>,workperm<rw>,workset<rw>,bucket<rw> *
|
|
526
|
+
* *
|
|
527
|
+
*****************************************************************************/
|
|
528
|
+
|
|
529
|
+
static int
|
|
530
|
+
bestcell(const graph *g, const int *lab, const int *ptn, int level,
|
|
531
|
+
int tc_level, int m, int n)
|
|
532
|
+
{
|
|
533
|
+
int i;
|
|
534
|
+
set *gp;
|
|
535
|
+
setword setword1,setword2;
|
|
536
|
+
int v1,v2,nnt;
|
|
537
|
+
|
|
538
|
+
#if !MAXN
|
|
539
|
+
DYNALLOC1(int,workperm,workperm_sz,n,"bestcell");
|
|
540
|
+
DYNALLOC1(set,workset,workset_sz,m,"bestcell");
|
|
541
|
+
DYNALLOC1(int,bucket,bucket_sz,n+2,"bestcell");
|
|
542
|
+
#endif
|
|
543
|
+
|
|
544
|
+
/* find non-singleton cells: put starts in workperm[0..nnt-1] */
|
|
545
|
+
|
|
546
|
+
i = nnt = 0;
|
|
547
|
+
|
|
548
|
+
while (i < n)
|
|
549
|
+
{
|
|
550
|
+
if (ptn[i] > level)
|
|
551
|
+
{
|
|
552
|
+
workperm[nnt++] = i;
|
|
553
|
+
while (ptn[i] > level) ++i;
|
|
554
|
+
}
|
|
555
|
+
++i;
|
|
556
|
+
}
|
|
557
|
+
|
|
558
|
+
if (nnt == 0) return n;
|
|
559
|
+
|
|
560
|
+
/* set bucket[i] to # non-trivial neighbours of n.s. cell i */
|
|
561
|
+
|
|
562
|
+
for (i = nnt; --i >= 0;) bucket[i] = 0;
|
|
563
|
+
|
|
564
|
+
for (v2 = 1; v2 < nnt; ++v2)
|
|
565
|
+
{
|
|
566
|
+
EMPTYSET(workset,m);
|
|
567
|
+
i = workperm[v2] - 1;
|
|
568
|
+
do
|
|
569
|
+
{
|
|
570
|
+
++i;
|
|
571
|
+
ADDELEMENT(workset,lab[i]);
|
|
572
|
+
}
|
|
573
|
+
while (ptn[i] > level);
|
|
574
|
+
for (v1 = 0; v1 < v2; ++v1)
|
|
575
|
+
{
|
|
576
|
+
gp = GRAPHROW(g,lab[workperm[v1]],m);
|
|
577
|
+
#if MAXM==1
|
|
578
|
+
setword1 = *workset & *gp;
|
|
579
|
+
setword2 = *workset & ~*gp;
|
|
580
|
+
#else
|
|
581
|
+
setword1 = setword2 = 0;
|
|
582
|
+
for (i = m; --i >= 0;)
|
|
583
|
+
{
|
|
584
|
+
setword1 |= workset[i] & gp[i];
|
|
585
|
+
setword2 |= workset[i] & ~gp[i];
|
|
586
|
+
}
|
|
587
|
+
#endif
|
|
588
|
+
if (setword1 != 0 && setword2 != 0)
|
|
589
|
+
{
|
|
590
|
+
++bucket[v1];
|
|
591
|
+
++bucket[v2];
|
|
592
|
+
}
|
|
593
|
+
}
|
|
594
|
+
}
|
|
595
|
+
|
|
596
|
+
/* find first greatest bucket value */
|
|
597
|
+
|
|
598
|
+
v1 = 0;
|
|
599
|
+
v2 = bucket[0];
|
|
600
|
+
for (i = 1; i < nnt; ++i)
|
|
601
|
+
if (bucket[i] > v2)
|
|
602
|
+
{
|
|
603
|
+
v1 = i;
|
|
604
|
+
v2 = bucket[i];
|
|
605
|
+
}
|
|
606
|
+
|
|
607
|
+
return (int)workperm[v1];
|
|
608
|
+
}
|
|
609
|
+
|
|
610
|
+
/*****************************************************************************
|
|
611
|
+
* *
|
|
612
|
+
* targetcell(g,lab,ptn,level,tc_level,digraph,hint,m,n) returns the index *
|
|
613
|
+
* in lab of the next cell to split. *
|
|
614
|
+
* hint is a suggestion for the answer, which is obeyed if it is valid. *
|
|
615
|
+
* Otherwise we use bestcell() up to tc_level and the first non-trivial *
|
|
616
|
+
* cell after that. *
|
|
617
|
+
* *
|
|
618
|
+
*****************************************************************************/
|
|
619
|
+
|
|
620
|
+
int
|
|
621
|
+
targetcell(graph *g, int *lab, int *ptn, int level,
|
|
622
|
+
int tc_level, boolean digraph, int hint, int m, int n)
|
|
623
|
+
{
|
|
624
|
+
int i;
|
|
625
|
+
|
|
626
|
+
if (hint >= 0 && ptn[hint] > level &&
|
|
627
|
+
(hint == 0 || ptn[hint-1] <= level))
|
|
628
|
+
return hint;
|
|
629
|
+
else if (level <= tc_level)
|
|
630
|
+
return bestcell(g,lab,ptn,level,tc_level,m,n);
|
|
631
|
+
else
|
|
632
|
+
{
|
|
633
|
+
for (i = 0; i < n && ptn[i] <= level; ++i) {}
|
|
634
|
+
return (i == n ? 0 : i);
|
|
635
|
+
}
|
|
636
|
+
}
|
|
637
|
+
|
|
638
|
+
/*****************************************************************************
|
|
639
|
+
* *
|
|
640
|
+
* densenauty(g,lab,ptn,orbits,&options,&stats,m,n,h) *
|
|
641
|
+
* is a slightly simplified interface to nauty(). It allocates enough *
|
|
642
|
+
* workspace for 500 automorphisms and checks that the densegraph dispatch *
|
|
643
|
+
* vector is in use. *
|
|
644
|
+
* *
|
|
645
|
+
*****************************************************************************/
|
|
646
|
+
|
|
647
|
+
void
|
|
648
|
+
densenauty(graph *g, int *lab, int *ptn, int *orbits,
|
|
649
|
+
optionblk *options, statsblk *stats, int m, int n, graph *h)
|
|
650
|
+
{
|
|
651
|
+
int i;
|
|
652
|
+
boolean digraph;
|
|
653
|
+
graph *gi;
|
|
654
|
+
|
|
655
|
+
if (options->dispatch != &dispatch_graph)
|
|
656
|
+
{
|
|
657
|
+
fprintf(ERRFILE,"Error: densenauty() needs standard options block\n");
|
|
658
|
+
exit(1);
|
|
659
|
+
}
|
|
660
|
+
|
|
661
|
+
digraph = options->digraph;
|
|
662
|
+
if (!digraph)
|
|
663
|
+
{
|
|
664
|
+
for (i = 0, gi = g; i < n; ++i, gi += m)
|
|
665
|
+
if (ISELEMENT(gi,i)) break;
|
|
666
|
+
|
|
667
|
+
if (i < n) options->digraph = TRUE;
|
|
668
|
+
}
|
|
669
|
+
|
|
670
|
+
#if !MAXN
|
|
671
|
+
/* Don't increase 2*500*m in the next line unless you also increase
|
|
672
|
+
the default declaration of dnwork[] earlier. */
|
|
673
|
+
DYNALLOC1(set,dnwork,dnwork_sz,2*500*m,"densenauty malloc");
|
|
674
|
+
#endif
|
|
675
|
+
|
|
676
|
+
nauty(g,lab,ptn,NULL,orbits,options,stats,dnwork,2*500*m,m,n,h);
|
|
677
|
+
options->digraph = digraph;
|
|
678
|
+
}
|
|
679
|
+
|
|
680
|
+
/*****************************************************************************
|
|
681
|
+
* *
|
|
682
|
+
* naugraph_check() checks that this file is compiled compatibly with the *
|
|
683
|
+
* given parameters. If not, call exit(1). *
|
|
684
|
+
* *
|
|
685
|
+
*****************************************************************************/
|
|
686
|
+
|
|
687
|
+
void
|
|
688
|
+
naugraph_check(int wordsize, int m, int n, int version)
|
|
689
|
+
{
|
|
690
|
+
if (wordsize != WORDSIZE)
|
|
691
|
+
{
|
|
692
|
+
fprintf(ERRFILE,"Error: WORDSIZE mismatch in naugraph.c\n");
|
|
693
|
+
exit(1);
|
|
694
|
+
}
|
|
695
|
+
|
|
696
|
+
#if MAXN
|
|
697
|
+
if (m > MAXM)
|
|
698
|
+
{
|
|
699
|
+
fprintf(ERRFILE,"Error: MAXM inadequate in naugraph.c\n");
|
|
700
|
+
exit(1);
|
|
701
|
+
}
|
|
702
|
+
|
|
703
|
+
if (n > MAXN)
|
|
704
|
+
{
|
|
705
|
+
fprintf(ERRFILE,"Error: MAXN inadequate in naugraph.c\n");
|
|
706
|
+
exit(1);
|
|
707
|
+
}
|
|
708
|
+
#endif
|
|
709
|
+
|
|
710
|
+
if (version < NAUTYREQUIRED)
|
|
711
|
+
{
|
|
712
|
+
fprintf(ERRFILE,"Error: naugraph.c version mismatch\n");
|
|
713
|
+
exit(1);
|
|
714
|
+
}
|
|
715
|
+
}
|
|
716
|
+
|
|
717
|
+
/*****************************************************************************
|
|
718
|
+
* *
|
|
719
|
+
* naugraph_freedyn() - free the dynamic memory in this module *
|
|
720
|
+
* *
|
|
721
|
+
*****************************************************************************/
|
|
722
|
+
|
|
723
|
+
void
|
|
724
|
+
naugraph_freedyn(void)
|
|
725
|
+
{
|
|
726
|
+
#if !MAXN
|
|
727
|
+
DYNFREE(workset,workset_sz);
|
|
728
|
+
DYNFREE(workperm,workperm_sz);
|
|
729
|
+
DYNFREE(bucket,bucket_sz);
|
|
730
|
+
DYNFREE(dnwork,dnwork_sz);
|
|
731
|
+
#endif
|
|
732
|
+
}
|