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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"""Proof-bearing identity, reversal, and parallel-independence laws."""
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EnvironmentToken,
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"""Stable failed premises for concurrency and algebraic laws."""
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code: LawIssueCode
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+
first_then_second: tuple[DPOApplication, DPOApplication]
|
|
91
|
+
second_then_first: tuple[DPOApplication, DPOApplication]
|
|
92
|
+
result_isomorphism: LLGMorphism
|
|
93
|
+
independence: ParallelIndependenceCertificate
|
|
94
|
+
|
|
95
|
+
def replay(self) -> bool:
|
|
96
|
+
if len(self.first_then_second) != 2 or len(self.second_then_first) != 2:
|
|
97
|
+
return False
|
|
98
|
+
applications = self.first_then_second + self.second_then_first
|
|
99
|
+
return (
|
|
100
|
+
self.independence.independent
|
|
101
|
+
and all(
|
|
102
|
+
item.result == item.certificate.result
|
|
103
|
+
and item.certificate.replay().valid
|
|
104
|
+
for item in applications
|
|
105
|
+
)
|
|
106
|
+
and self._application_links_valid()
|
|
107
|
+
and self.result_isomorphism.is_isomorphism
|
|
108
|
+
and self.result_isomorphism.source == self.first_then_second[1].result
|
|
109
|
+
and self.result_isomorphism.target == self.second_then_first[1].result
|
|
110
|
+
)
|
|
111
|
+
|
|
112
|
+
def _application_links_valid(self) -> bool:
|
|
113
|
+
first, after_first = self.first_then_second
|
|
114
|
+
second, after_second = self.second_then_first
|
|
115
|
+
left, right = first.certificate, second.certificate
|
|
116
|
+
first_access = _rule_access(left.rule, dict(left.match))
|
|
117
|
+
second_access = _rule_access(right.rule, dict(right.match))
|
|
118
|
+
checks = (
|
|
119
|
+
left.host == right.host,
|
|
120
|
+
after_first.certificate.host == first.result,
|
|
121
|
+
after_second.certificate.host == second.result,
|
|
122
|
+
after_first.certificate.rule == right.rule,
|
|
123
|
+
after_second.certificate.rule == left.rule,
|
|
124
|
+
dict(after_first.certificate.match) == dict(right.match),
|
|
125
|
+
dict(after_second.certificate.match) == dict(left.match),
|
|
126
|
+
self.independence.first_application == first,
|
|
127
|
+
self.independence.second_application == second,
|
|
128
|
+
self.independence.first_access == first_access,
|
|
129
|
+
self.independence.second_access == second_access,
|
|
130
|
+
not _access_issues(first_access, second_access),
|
|
131
|
+
)
|
|
132
|
+
return all(checks)
|
|
133
|
+
|
|
134
|
+
|
|
135
|
+
def identity_rule(
|
|
136
|
+
graph: LewisLabelledGraph,
|
|
137
|
+
*,
|
|
138
|
+
boundary: SystemBoundary | str = SystemBoundary.ABSTRACT,
|
|
139
|
+
name: str = "identity",
|
|
140
|
+
) -> RuleSpan:
|
|
141
|
+
"""Return the identity span on one LLG object."""
|
|
142
|
+
return RuleSpan.from_mapping(
|
|
143
|
+
graph,
|
|
144
|
+
graph,
|
|
145
|
+
{node: node for node in graph.node_ids},
|
|
146
|
+
boundary=boundary,
|
|
147
|
+
name=name,
|
|
148
|
+
)
|
|
149
|
+
|
|
150
|
+
|
|
151
|
+
def reverse_rule(rule: RuleSpan, *, span_only: bool = False) -> RuleSpan:
|
|
152
|
+
"""Reverse an unguarded rule, or explicitly project a reversed bare span.
|
|
153
|
+
|
|
154
|
+
Execution conditions require their own inverse construction. They must
|
|
155
|
+
never be silently discarded when reversing a guarded rule.
|
|
156
|
+
"""
|
|
157
|
+
if rule.condition is not None and not span_only:
|
|
158
|
+
raise LawError(
|
|
159
|
+
LawIssue(
|
|
160
|
+
LawIssueCode.CONDITION_REVERSAL,
|
|
161
|
+
"Reversal of a guarded rule needs a transported inverse condition.",
|
|
162
|
+
)
|
|
163
|
+
)
|
|
164
|
+
environment = rule.environment
|
|
165
|
+
if environment is not None:
|
|
166
|
+
environment = EnvironmentToken(
|
|
167
|
+
environment.name,
|
|
168
|
+
tuple((element, -count) for element, count in environment.element_delta),
|
|
169
|
+
-environment.electron_delta,
|
|
170
|
+
tuple((isotope, -count) for isotope, count in environment.isotope_delta),
|
|
171
|
+
)
|
|
172
|
+
return RuleSpan(
|
|
173
|
+
rule.right,
|
|
174
|
+
rule.interface,
|
|
175
|
+
rule.left,
|
|
176
|
+
rule.right_arm,
|
|
177
|
+
rule.left_arm,
|
|
178
|
+
boundary=rule.boundary,
|
|
179
|
+
environment=environment,
|
|
180
|
+
name=f"reverse({rule.name})",
|
|
181
|
+
)
|
|
182
|
+
|
|
183
|
+
|
|
184
|
+
def _map_edge(
|
|
185
|
+
mapping: Mapping[Hashable, Hashable], edge: frozenset[Hashable]
|
|
186
|
+
) -> frozenset[Hashable]:
|
|
187
|
+
return frozenset(mapping[node] for node in edge)
|
|
188
|
+
|
|
189
|
+
|
|
190
|
+
def _rule_access(rule: RuleSpan, match: Mapping[Hashable, Hashable]) -> RuleAccess:
|
|
191
|
+
left_preserved_nodes = set(rule.left_arm.mapping.values())
|
|
192
|
+
right_to_interface = {
|
|
193
|
+
node: interface for interface, node in rule.right_arm.mapping.items()
|
|
194
|
+
}
|
|
195
|
+
left_edges = set(rule.left.edge_keys)
|
|
196
|
+
preserved_left_edges = set(rule.left_arm.edge_mapping.values())
|
|
197
|
+
preserved_right_edges = set(rule.right_arm.edge_mapping.values())
|
|
198
|
+
write_nodes = set()
|
|
199
|
+
for interface in rule.interface.node_ids:
|
|
200
|
+
left_node = rule.left_arm.mapping[interface]
|
|
201
|
+
right_node = rule.right_arm.mapping[interface]
|
|
202
|
+
if rule.left.node_labels(left_node, semantic=True) != rule.right.node_labels(
|
|
203
|
+
right_node, semantic=True
|
|
204
|
+
):
|
|
205
|
+
write_nodes.add(match[left_node])
|
|
206
|
+
write_edges = set()
|
|
207
|
+
for interface_edge in rule.interface.edge_keys:
|
|
208
|
+
left_edge = rule.left_arm.edge_mapping[interface_edge]
|
|
209
|
+
right_edge = rule.right_arm.edge_mapping[interface_edge]
|
|
210
|
+
if rule.left.edge_labels(left_edge, semantic=True) != rule.right.edge_labels(
|
|
211
|
+
right_edge, semantic=True
|
|
212
|
+
):
|
|
213
|
+
write_edges.add(_map_edge(match, left_edge))
|
|
214
|
+
added_host_edges = set()
|
|
215
|
+
for right_edge in set(rule.right.edge_keys) - preserved_right_edges:
|
|
216
|
+
if not right_edge <= set(right_to_interface):
|
|
217
|
+
continue
|
|
218
|
+
left_endpoints = frozenset(
|
|
219
|
+
rule.left_arm.mapping[right_to_interface[node]] for node in right_edge
|
|
220
|
+
)
|
|
221
|
+
added_host_edges.add(_map_edge(match, left_endpoints))
|
|
222
|
+
return RuleAccess(
|
|
223
|
+
frozenset(match.values()),
|
|
224
|
+
frozenset(_map_edge(match, edge) for edge in left_edges),
|
|
225
|
+
frozenset(
|
|
226
|
+
match[node] for node in set(rule.left.node_ids) - left_preserved_nodes
|
|
227
|
+
),
|
|
228
|
+
frozenset(_map_edge(match, edge) for edge in left_edges - preserved_left_edges),
|
|
229
|
+
frozenset(write_nodes),
|
|
230
|
+
frozenset(write_edges),
|
|
231
|
+
frozenset(added_host_edges),
|
|
232
|
+
)
|
|
233
|
+
|
|
234
|
+
|
|
235
|
+
def _intersection_issue(
|
|
236
|
+
code: LawIssueCode,
|
|
237
|
+
message: str,
|
|
238
|
+
first: frozenset[Any],
|
|
239
|
+
second: frozenset[Any],
|
|
240
|
+
) -> LawIssue | None:
|
|
241
|
+
conflict = first & second
|
|
242
|
+
if not conflict:
|
|
243
|
+
return None
|
|
244
|
+
return LawIssue(code, message, {"carriers": tuple(sorted(map(repr, conflict)))})
|
|
245
|
+
|
|
246
|
+
|
|
247
|
+
def _access_issues(first: RuleAccess, second: RuleAccess) -> tuple[LawIssue, ...]:
|
|
248
|
+
checks = (
|
|
249
|
+
(
|
|
250
|
+
LawIssueCode.DELETE_USE_NODE,
|
|
251
|
+
"The first event deletes a node used by the second.",
|
|
252
|
+
first.delete_nodes,
|
|
253
|
+
second.read_nodes,
|
|
254
|
+
),
|
|
255
|
+
(
|
|
256
|
+
LawIssueCode.DELETE_USE_NODE,
|
|
257
|
+
"The second event deletes a node used by the first.",
|
|
258
|
+
second.delete_nodes,
|
|
259
|
+
first.read_nodes,
|
|
260
|
+
),
|
|
261
|
+
(
|
|
262
|
+
LawIssueCode.DELETE_USE_EDGE,
|
|
263
|
+
"The first event deletes an edge used by the second.",
|
|
264
|
+
first.delete_edges,
|
|
265
|
+
second.read_edges,
|
|
266
|
+
),
|
|
267
|
+
(
|
|
268
|
+
LawIssueCode.DELETE_USE_EDGE,
|
|
269
|
+
"The second event deletes an edge used by the first.",
|
|
270
|
+
second.delete_edges,
|
|
271
|
+
first.read_edges,
|
|
272
|
+
),
|
|
273
|
+
(
|
|
274
|
+
LawIssueCode.LABEL_WRITE_NODE,
|
|
275
|
+
"The first event changes a node label read by the second.",
|
|
276
|
+
first.write_nodes,
|
|
277
|
+
second.read_nodes,
|
|
278
|
+
),
|
|
279
|
+
(
|
|
280
|
+
LawIssueCode.LABEL_WRITE_NODE,
|
|
281
|
+
"The second event changes a node label read by the first.",
|
|
282
|
+
second.write_nodes,
|
|
283
|
+
first.read_nodes,
|
|
284
|
+
),
|
|
285
|
+
(
|
|
286
|
+
LawIssueCode.LABEL_WRITE_EDGE,
|
|
287
|
+
"The first event changes an edge label read by the second.",
|
|
288
|
+
first.write_edges,
|
|
289
|
+
second.read_edges,
|
|
290
|
+
),
|
|
291
|
+
(
|
|
292
|
+
LawIssueCode.LABEL_WRITE_EDGE,
|
|
293
|
+
"The second event changes an edge label read by the first.",
|
|
294
|
+
second.write_edges,
|
|
295
|
+
first.read_edges,
|
|
296
|
+
),
|
|
297
|
+
(
|
|
298
|
+
LawIssueCode.ADD_ADD_EDGE,
|
|
299
|
+
"Both events add the same simple host edge.",
|
|
300
|
+
first.add_edges,
|
|
301
|
+
second.add_edges,
|
|
302
|
+
),
|
|
303
|
+
)
|
|
304
|
+
return tuple(
|
|
305
|
+
issue
|
|
306
|
+
for code, message, left, right in checks
|
|
307
|
+
if (issue := _intersection_issue(code, message, left, right)) is not None
|
|
308
|
+
)
|
|
309
|
+
|
|
310
|
+
|
|
311
|
+
def check_parallel_independence(
|
|
312
|
+
first: RuleSpan,
|
|
313
|
+
first_match: Mapping[Hashable, Hashable],
|
|
314
|
+
second: RuleSpan,
|
|
315
|
+
second_match: Mapping[Hashable, Hashable],
|
|
316
|
+
host: LewisLabelledGraph,
|
|
317
|
+
) -> ParallelIndependenceCertificate:
|
|
318
|
+
"""Decide the sufficient DPO carrier conditions for two host events."""
|
|
319
|
+
applications: list[DPOApplication | None] = []
|
|
320
|
+
issues: list[LawIssue] = []
|
|
321
|
+
for position, (rule, match) in enumerate(
|
|
322
|
+
((first, first_match), (second, second_match)), start=1
|
|
323
|
+
):
|
|
324
|
+
try:
|
|
325
|
+
applications.append(apply_dpo(rule, host, match))
|
|
326
|
+
except DPOError as error:
|
|
327
|
+
applications.append(None)
|
|
328
|
+
issues.append(
|
|
329
|
+
LawIssue(
|
|
330
|
+
LawIssueCode.COMPONENT_APPLICATION,
|
|
331
|
+
"A component event is not applicable to the common host.",
|
|
332
|
+
{
|
|
333
|
+
"position": position,
|
|
334
|
+
"issues": tuple(issue.to_dict() for issue in error.issues),
|
|
335
|
+
},
|
|
336
|
+
)
|
|
337
|
+
)
|
|
338
|
+
if issues:
|
|
339
|
+
return ParallelIndependenceCertificate(
|
|
340
|
+
None, None, applications[0], applications[1], tuple(issues)
|
|
341
|
+
)
|
|
342
|
+
first_access = _rule_access(first, first_match)
|
|
343
|
+
second_access = _rule_access(second, second_match)
|
|
344
|
+
return ParallelIndependenceCertificate(
|
|
345
|
+
first_access,
|
|
346
|
+
second_access,
|
|
347
|
+
applications[0],
|
|
348
|
+
applications[1],
|
|
349
|
+
_access_issues(first_access, second_access),
|
|
350
|
+
)
|
|
351
|
+
|
|
352
|
+
|
|
353
|
+
def find_llg_isomorphism(
|
|
354
|
+
source: LewisLabelledGraph, target: LewisLabelledGraph
|
|
355
|
+
) -> LLGMorphism | None:
|
|
356
|
+
"""Return a strict LLG isomorphism witness, or ``None``."""
|
|
357
|
+
if source.schema != target.schema:
|
|
358
|
+
return None
|
|
359
|
+
node_keys = source.schema.semantic_node_keys
|
|
360
|
+
edge_keys = source.schema.semantic_edge_keys
|
|
361
|
+
matcher = nx.algorithms.isomorphism.GraphMatcher(
|
|
362
|
+
source.to_networkx(),
|
|
363
|
+
target.to_networkx(),
|
|
364
|
+
node_match=lambda left, right: all(
|
|
365
|
+
left[key] == right[key] for key in node_keys
|
|
366
|
+
),
|
|
367
|
+
edge_match=lambda left, right: all(
|
|
368
|
+
left[key] == right[key] for key in edge_keys
|
|
369
|
+
),
|
|
370
|
+
)
|
|
371
|
+
if not matcher.is_isomorphic():
|
|
372
|
+
return None
|
|
373
|
+
morphism = LLGMorphism(source, target, matcher.mapping)
|
|
374
|
+
return morphism if morphism.is_isomorphism else None
|
|
375
|
+
|
|
376
|
+
|
|
377
|
+
def commute_independent(
|
|
378
|
+
first: RuleSpan,
|
|
379
|
+
first_match: Mapping[Hashable, Hashable],
|
|
380
|
+
second: RuleSpan,
|
|
381
|
+
second_match: Mapping[Hashable, Hashable],
|
|
382
|
+
host: LewisLabelledGraph,
|
|
383
|
+
) -> CommutationCertificate:
|
|
384
|
+
"""Apply both independent linearizations and certify equal endpoints."""
|
|
385
|
+
independence = check_parallel_independence(
|
|
386
|
+
first, first_match, second, second_match, host
|
|
387
|
+
)
|
|
388
|
+
if not independence.independent:
|
|
389
|
+
raise LawError(*independence.issues)
|
|
390
|
+
try:
|
|
391
|
+
first_step = apply_dpo(first, host, first_match)
|
|
392
|
+
first_second = apply_dpo(second, first_step.result, second_match)
|
|
393
|
+
second_step = apply_dpo(second, host, second_match)
|
|
394
|
+
second_first = apply_dpo(first, second_step.result, first_match)
|
|
395
|
+
except DPOError as error:
|
|
396
|
+
raise LawError(
|
|
397
|
+
LawIssue(
|
|
398
|
+
LawIssueCode.SEQUENTIAL_APPLICATION,
|
|
399
|
+
"A claimed independent event failed after its peer.",
|
|
400
|
+
{"issues": tuple(issue.to_dict() for issue in error.issues)},
|
|
401
|
+
)
|
|
402
|
+
) from error
|
|
403
|
+
isomorphism = find_llg_isomorphism(first_second.result, second_first.result)
|
|
404
|
+
if isomorphism is None:
|
|
405
|
+
raise LawError(
|
|
406
|
+
LawIssue(
|
|
407
|
+
LawIssueCode.NONCOMMUTATIVE,
|
|
408
|
+
"The two independent linearizations have non-isomorphic endpoints.",
|
|
409
|
+
)
|
|
410
|
+
)
|
|
411
|
+
certificate = CommutationCertificate(
|
|
412
|
+
(first_step, first_second),
|
|
413
|
+
(second_step, second_first),
|
|
414
|
+
isomorphism,
|
|
415
|
+
independence,
|
|
416
|
+
)
|
|
417
|
+
if not certificate.replay():
|
|
418
|
+
raise LawError(
|
|
419
|
+
LawIssue(
|
|
420
|
+
LawIssueCode.NONCOMMUTATIVE,
|
|
421
|
+
"The commutation certificate does not replay.",
|
|
422
|
+
)
|
|
423
|
+
)
|
|
424
|
+
return certificate
|
|
425
|
+
|
|
426
|
+
|
|
427
|
+
__all__ = [
|
|
428
|
+
"CommutationCertificate",
|
|
429
|
+
"LawError",
|
|
430
|
+
"LawIssue",
|
|
431
|
+
"LawIssueCode",
|
|
432
|
+
"ParallelIndependenceCertificate",
|
|
433
|
+
"RuleAccess",
|
|
434
|
+
"check_parallel_independence",
|
|
435
|
+
"commute_independent",
|
|
436
|
+
"find_llg_isomorphism",
|
|
437
|
+
"identity_rule",
|
|
438
|
+
"reverse_rule",
|
|
439
|
+
]
|