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.
Files changed (636) hide show
  1. synkit/CRN/Benchmark/__init__.py +53 -0
  2. synkit/CRN/Benchmark/crosschecks.py +13 -0
  3. synkit/CRN/Benchmark/kegg.py +12 -0
  4. synkit/CRN/Benchmark/networks.py +13 -0
  5. synkit/CRN/Benchmark/scaling.py +13 -0
  6. synkit/CRN/Benchmark/validate.py +13 -0
  7. synkit/CRN/Construct/__init__.py +16 -0
  8. synkit/CRN/Construct/abstract.py +668 -0
  9. synkit/CRN/Construct/arity.py +36 -0
  10. synkit/CRN/Construct/builder.py +619 -0
  11. synkit/CRN/Construct/derivation.py +63 -0
  12. synkit/CRN/Construct/flattener.py +100 -0
  13. synkit/CRN/Construct/keys.py +14 -0
  14. synkit/CRN/Construct/mixtures.py +117 -0
  15. synkit/CRN/Construct/rdkit_worker.py +69 -0
  16. synkit/CRN/Construct/smiles.py +99 -0
  17. synkit/CRN/Construct/state.py +31 -0
  18. synkit/CRN/Construct/strategy.py +75 -0
  19. synkit/CRN/Construct/worker.py +42 -0
  20. synkit/CRN/IO/__init__.py +36 -0
  21. synkit/CRN/IO/sbml.py +925 -0
  22. synkit/CRN/Pathway/__init__.py +72 -0
  23. synkit/CRN/Pathway/_adapter.py +333 -0
  24. synkit/CRN/Pathway/pathfinder.py +500 -0
  25. synkit/CRN/Pathway/reachability.py +796 -0
  26. synkit/CRN/Pathway/realizability.py +1322 -0
  27. synkit/CRN/Petrinet/__init__.py +93 -0
  28. synkit/CRN/Petrinet/analyzer.py +486 -0
  29. synkit/CRN/Petrinet/minimal_semiflows.py +436 -0
  30. synkit/CRN/Petrinet/net.py +1041 -0
  31. synkit/CRN/Petrinet/persistence.py +97 -0
  32. synkit/CRN/Petrinet/semiflows.py +483 -0
  33. synkit/CRN/Petrinet/siphon_search.py +402 -0
  34. synkit/CRN/Petrinet/structure.py +286 -0
  35. synkit/CRN/Props/__init__.py +130 -0
  36. synkit/CRN/Props/_rank.py +29 -0
  37. synkit/CRN/Props/deficiency.py +953 -0
  38. synkit/CRN/Props/dynamics.py +832 -0
  39. synkit/CRN/Props/helper.py +151 -0
  40. synkit/CRN/Props/stoich.py +751 -0
  41. synkit/CRN/Props/thermo.py +584 -0
  42. synkit/CRN/Query/__init__.py +66 -0
  43. synkit/CRN/Query/cache.py +41 -0
  44. synkit/CRN/Query/kegg_api.py +99 -0
  45. synkit/CRN/Query/kegg_extract.py +714 -0
  46. synkit/CRN/Query/kegg_impute.py +707 -0
  47. synkit/CRN/Query/kegg_parse.py +480 -0
  48. synkit/CRN/Query/to_syncrn.py +290 -0
  49. synkit/CRN/README.md +234 -0
  50. synkit/CRN/Structure/__init__.py +12 -0
  51. synkit/CRN/Structure/_graph_io.py +713 -0
  52. synkit/CRN/Structure/_matrices.py +88 -0
  53. synkit/CRN/Structure/_parse.py +544 -0
  54. synkit/CRN/Structure/reaction.py +237 -0
  55. synkit/CRN/Structure/rule.py +55 -0
  56. synkit/CRN/Structure/species.py +46 -0
  57. synkit/CRN/Structure/syncrn.py +929 -0
  58. synkit/CRN/Symmetry/__init__.py +20 -0
  59. synkit/CRN/Symmetry/_common.py +1059 -0
  60. synkit/CRN/Symmetry/_ir.py +940 -0
  61. synkit/CRN/Symmetry/automorphism.py +472 -0
  62. synkit/CRN/Symmetry/canon.py +441 -0
  63. synkit/CRN/Symmetry/isomorphism.py +412 -0
  64. synkit/CRN/Symmetry/symmetry.py +61 -0
  65. synkit/CRN/Symmetry/wl_canon.py +967 -0
  66. synkit/CRN/Visualize/__init__.py +11 -0
  67. synkit/CRN/Visualize/labels.py +113 -0
  68. synkit/CRN/Visualize/layout.py +708 -0
  69. synkit/CRN/Visualize/palette.py +292 -0
  70. synkit/CRN/Visualize/validation.py +122 -0
  71. synkit/CRN/Visualize/vis.py +1152 -0
  72. synkit/CRN/__init__.py +233 -0
  73. synkit/CRN/_build.py +50 -0
  74. synkit/CRN/_native_build.py +175 -0
  75. synkit/CRN/analysis.py +629 -0
  76. synkit/CRN/backend.py +74 -0
  77. synkit/CRN/cpp/CMakeLists.txt +58 -0
  78. synkit/CRN/cpp/algebra.cpp +46 -0
  79. synkit/CRN/cpp/closure.cpp +29 -0
  80. synkit/CRN/cpp/exact.h +55 -0
  81. synkit/CRN/cpp/pathway.cpp +46 -0
  82. synkit/CRN/cpp/semiflows.cpp +209 -0
  83. synkit/CRN/cpp/structural.cpp +240 -0
  84. synkit/CRN/cpp/symmetry.cpp +45 -0
  85. synkit/CRN/cpp/write_manifest.cmake +28 -0
  86. synkit/CRN/kinds.py +137 -0
  87. synkit/CRN/lib/synkit_crn.dll +0 -0
  88. synkit/CRN/lib/synkit_crn.json +33 -0
  89. synkit/CRN/native.py +388 -0
  90. synkit/CRN/native_analysis.py +459 -0
  91. synkit/Chem/Cluster/__init__.py +0 -0
  92. synkit/Chem/Cluster/butina.py +140 -0
  93. synkit/Chem/Fingerprint/__init__.py +0 -0
  94. synkit/Chem/Fingerprint/fp_calculator.py +155 -0
  95. synkit/Chem/Fingerprint/smiles_featurizer.py +258 -0
  96. synkit/Chem/Fingerprint/transformation_fp.py +139 -0
  97. synkit/Chem/Mapper/README.rst +43 -0
  98. synkit/Chem/Mapper/__init__.py +255 -0
  99. synkit/Chem/Mapper/_compat.py +130 -0
  100. synkit/Chem/Mapper/adapters/__init__.py +1 -0
  101. synkit/Chem/Mapper/adapters/prediction.py +126 -0
  102. synkit/Chem/Mapper/adapters/template.py +412 -0
  103. synkit/Chem/Mapper/chem/__init__.py +52 -0
  104. synkit/Chem/Mapper/chem/aam.py +673 -0
  105. synkit/Chem/Mapper/chem/blind.py +160 -0
  106. synkit/Chem/Mapper/chem/its.py +309 -0
  107. synkit/Chem/Mapper/chem/smiles.py +564 -0
  108. synkit/Chem/Mapper/graph/__init__.py +66 -0
  109. synkit/Chem/Mapper/graph/automorphism.py +395 -0
  110. synkit/Chem/Mapper/graph/blockcut.py +98 -0
  111. synkit/Chem/Mapper/graph/labeled_graph.py +104 -0
  112. synkit/Chem/Mapper/graph/refine.py +176 -0
  113. synkit/Chem/Mapper/graph/synkit_adapter.py +110 -0
  114. synkit/Chem/Mapper/io/__init__.py +13 -0
  115. synkit/Chem/Mapper/io/idxmapstr.py +82 -0
  116. synkit/Chem/Mapper/mapper.py +685 -0
  117. synkit/Chem/Mapper/reaction_search.py +554 -0
  118. synkit/Chem/Mapper/reporting/__init__.py +1 -0
  119. synkit/Chem/Mapper/reporting/alternatives.py +451 -0
  120. synkit/Chem/Mapper/reporting/analysis.py +681 -0
  121. synkit/Chem/Mapper/reporting/native_analysis.py +485 -0
  122. synkit/Chem/Mapper/reporting/spectrum.py +642 -0
  123. synkit/Chem/Mapper/solvers/__init__.py +1 -0
  124. synkit/Chem/Mapper/solvers/exact/__init__.py +141 -0
  125. synkit/Chem/Mapper/solvers/exact/assignment/__init__.py +1 -0
  126. synkit/Chem/Mapper/solvers/exact/assignment/assignment_certificate.py +113 -0
  127. synkit/Chem/Mapper/solvers/exact/assignment/assignment_domains.py +162 -0
  128. synkit/Chem/Mapper/solvers/exact/assignment/assignment_verification.py +58 -0
  129. synkit/Chem/Mapper/solvers/exact/assignment/incremental_assignment.py +247 -0
  130. synkit/Chem/Mapper/solvers/exact/certificate.py +128 -0
  131. synkit/Chem/Mapper/solvers/exact/core.py +183 -0
  132. synkit/Chem/Mapper/solvers/exact/distance_search/__init__.py +1 -0
  133. synkit/Chem/Mapper/solvers/exact/distance_search/bounds.py +319 -0
  134. synkit/Chem/Mapper/solvers/exact/distance_search/exhaustive.py +179 -0
  135. synkit/Chem/Mapper/solvers/exact/distance_search/inputs.py +283 -0
  136. synkit/Chem/Mapper/solvers/exact/distance_search/records.py +242 -0
  137. synkit/Chem/Mapper/solvers/exact/distance_search/search.py +1025 -0
  138. synkit/Chem/Mapper/solvers/exact/distance_search/verify.py +378 -0
  139. synkit/Chem/Mapper/solvers/exact/edit_support.py +375 -0
  140. synkit/Chem/Mapper/solvers/exact/hybrid.py +224 -0
  141. synkit/Chem/Mapper/solvers/exact/hydrogen.py +264 -0
  142. synkit/Chem/Mapper/solvers/exact/kernel_solvers/__init__.py +1 -0
  143. synkit/Chem/Mapper/solvers/exact/kernel_solvers/branching.py +499 -0
  144. synkit/Chem/Mapper/solvers/exact/kernel_solvers/enumerate.py +1050 -0
  145. synkit/Chem/Mapper/solvers/exact/kernel_solvers/enumeration_result.py +30 -0
  146. synkit/Chem/Mapper/solvers/exact/kernel_solvers/kernel.py +256 -0
  147. synkit/Chem/Mapper/solvers/exact/kernel_solvers/milp.py +194 -0
  148. synkit/Chem/Mapper/solvers/exact/native/__init__.py +1 -0
  149. synkit/Chem/Mapper/solvers/exact/native/build.py +154 -0
  150. synkit/Chem/Mapper/solvers/exact/native/candidates.py +593 -0
  151. synkit/Chem/Mapper/solvers/exact/native/canonical.py +396 -0
  152. synkit/Chem/Mapper/solvers/exact/native/disk_frontier.py +415 -0
  153. synkit/Chem/Mapper/solvers/exact/native/frontier.py +390 -0
  154. synkit/Chem/Mapper/solvers/exact/native/hydrogen_quotient.py +213 -0
  155. synkit/Chem/Mapper/solvers/exact/native/its.py +528 -0
  156. synkit/Chem/Mapper/solvers/exact/native/native_distance.cpp +2803 -0
  157. synkit/Chem/Mapper/solvers/exact/native/orbit_aggregation.py +328 -0
  158. synkit/Chem/Mapper/solvers/exact/native/parallel.py +205 -0
  159. synkit/Chem/Mapper/solvers/exact/native/pmcd.py +203 -0
  160. synkit/Chem/Mapper/solvers/exact/native/runtime.py +40 -0
  161. synkit/Chem/Mapper/solvers/exact/native/search.py +294 -0
  162. synkit/Chem/Mapper/solvers/exact/native/separator.py +224 -0
  163. synkit/Chem/Mapper/solvers/exact/native_build.py +12 -0
  164. synkit/Chem/Mapper/solvers/exact/pabs/__init__.py +1 -0
  165. synkit/Chem/Mapper/solvers/exact/pabs/cost_lattice.py +43 -0
  166. synkit/Chem/Mapper/solvers/exact/pabs/factor_spectrum.py +110 -0
  167. synkit/Chem/Mapper/solvers/exact/pabs/multi_shell.py +368 -0
  168. synkit/Chem/Mapper/solvers/exact/pabs/propagation.py +679 -0
  169. synkit/Chem/Mapper/solvers/exact/pabs/propagation_bounds.py +436 -0
  170. synkit/Chem/Mapper/solvers/exact/pabs/propagation_limits.py +13 -0
  171. synkit/Chem/Mapper/solvers/exact/pabs/propagation_search.py +856 -0
  172. synkit/Chem/Mapper/solvers/exact/pabs/propagation_symmetry.py +66 -0
  173. synkit/Chem/Mapper/solvers/exact/pabs/residual_typed_bonds.py +136 -0
  174. synkit/Chem/Mapper/solvers/exact/pabs/reward_frontier.py +201 -0
  175. synkit/Chem/Mapper/solvers/exact/pabs/separator_bound.py +258 -0
  176. synkit/Chem/Mapper/solvers/exact/pabs/separator_spectrum.py +308 -0
  177. synkit/Chem/Mapper/solvers/exact/pabs/sparse_reward_bound.py +207 -0
  178. synkit/Chem/Mapper/solvers/exact/pabs/suffix_spectrum.py +299 -0
  179. synkit/Chem/Mapper/solvers/exact/search.py +55 -0
  180. synkit/Chem/Mapper/solvers/exact/seeds/__init__.py +1 -0
  181. synkit/Chem/Mapper/solvers/exact/seeds/seed.py +104 -0
  182. synkit/Chem/Mapper/solvers/exact/seeds/seed_fragments.py +148 -0
  183. synkit/Chem/Mapper/solvers/exact/seeds/seed_relaxation.py +181 -0
  184. synkit/Chem/Mapper/solvers/exact/symmetry.py +223 -0
  185. synkit/Chem/Mapper/solvers/native/__init__.py +4 -0
  186. synkit/Chem/Mapper/solvers/native/assignment.py +99 -0
  187. synkit/Chem/Mapper/solvers/native/astar.py +22 -0
  188. synkit/Chem/Mapper/solvers/native/build.py +385 -0
  189. synkit/Chem/Mapper/solvers/native/classification.py +641 -0
  190. synkit/Chem/Mapper/solvers/native/core.py +378 -0
  191. synkit/Chem/Mapper/solvers/native/cpp/CMakeLists.txt +120 -0
  192. synkit/Chem/Mapper/solvers/native/cpp/examples/map_reaction.cpp +29 -0
  193. synkit/Chem/Mapper/solvers/native/cpp/examples/slap_graph.cpp +63 -0
  194. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/assignment/assignment.h +18 -0
  195. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/astar/astar.h +18 -0
  196. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/astar/bound.h +33 -0
  197. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/core/pmcd_witness.h +16 -0
  198. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/core/runtime.h +130 -0
  199. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/hydrogen/hydrogen.h +73 -0
  200. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/mapper.h +175 -0
  201. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/mces/mces.h +9 -0
  202. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/pabs/seed.h +34 -0
  203. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/reaction/reaction.h +30 -0
  204. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/sepdp/sepdp.h +21 -0
  205. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/slap.h +72 -0
  206. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/solvers/solvers.h +16 -0
  207. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/symmetry/classification.h +140 -0
  208. synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/symmetry/cpabs.h +33 -0
  209. synkit/Chem/Mapper/solvers/native/cpp/src/assignment/abb.cpp +302 -0
  210. synkit/Chem/Mapper/solvers/native/cpp/src/astar/CMakeLists.txt +12 -0
  211. synkit/Chem/Mapper/solvers/native/cpp/src/astar/README.md +47 -0
  212. synkit/Chem/Mapper/solvers/native/cpp/src/astar/astar.cpp +228 -0
  213. synkit/Chem/Mapper/solvers/native/cpp/src/astar/astar_graph.cpp +37 -0
  214. synkit/Chem/Mapper/solvers/native/cpp/src/astar/bound.cpp +212 -0
  215. synkit/Chem/Mapper/solvers/native/cpp/src/core/dispatch.cpp +272 -0
  216. synkit/Chem/Mapper/solvers/native/cpp/src/core/pmcd_witness.cpp +36 -0
  217. synkit/Chem/Mapper/solvers/native/cpp/src/hydrogen/hydrogen.cpp +380 -0
  218. synkit/Chem/Mapper/solvers/native/cpp/src/mces/README.md +57 -0
  219. synkit/Chem/Mapper/solvers/native/cpp/src/mces/mces.cpp +287 -0
  220. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/bridge.cpp +334 -0
  221. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/chemical_floor.inc +181 -0
  222. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/endpoint_symmetry.inc +104 -0
  223. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/exact_helpers.h +20 -0
  224. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_assignment_certificate.h +165 -0
  225. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_certificate.h +125 -0
  226. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_model.h +365 -0
  227. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_provider.inc +319 -0
  228. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_rounding.inc +170 -0
  229. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_test_hooks.h +342 -0
  230. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/objective_reduction.inc +137 -0
  231. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/overlap_dual.inc +351 -0
  232. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/profile_seed.inc +214 -0
  233. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/seed_heuristics.inc +640 -0
  234. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/sparse_embedding.cpp +430 -0
  235. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/sparse_root_lp.h +176 -0
  236. synkit/Chem/Mapper/solvers/native/cpp/src/pabs/test_hooks.inc +262 -0
  237. synkit/Chem/Mapper/solvers/native/cpp/src/reaction/reaction.cpp +611 -0
  238. synkit/Chem/Mapper/solvers/native/cpp/src/sepdp/README.md +61 -0
  239. synkit/Chem/Mapper/solvers/native/cpp/src/sepdp/sepdp.cpp +253 -0
  240. synkit/Chem/Mapper/solvers/native/cpp/src/slap.cpp +810 -0
  241. synkit/Chem/Mapper/solvers/native/cpp/src/solvers/formulation.h +138 -0
  242. synkit/Chem/Mapper/solvers/native/cpp/src/solvers/maxsat.cpp +526 -0
  243. synkit/Chem/Mapper/solvers/native/cpp/src/solvers/ortools.cpp +475 -0
  244. synkit/Chem/Mapper/solvers/native/cpp/src/solvers/seed.h +80 -0
  245. synkit/Chem/Mapper/solvers/native/cpp/src/solvers/weighted_cnf.h +256 -0
  246. synkit/Chem/Mapper/solvers/native/cpp/src/supporting/README.md +43 -0
  247. synkit/Chem/Mapper/solvers/native/cpp/src/supporting/dfs.cpp +123 -0
  248. synkit/Chem/Mapper/solvers/native/cpp/src/supporting/edit_support.cpp +224 -0
  249. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/classification.cpp +553 -0
  250. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/classification_pipeline.cpp +124 -0
  251. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/classification_stream.h +13 -0
  252. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/cpabs.cpp +455 -0
  253. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/edge_deck.cpp +743 -0
  254. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/COPYRIGHT +44 -0
  255. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt +202 -0
  256. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naugraph.c +732 -0
  257. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naurng.c +94 -0
  258. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naurng.h +49 -0
  259. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nausparse.c +1771 -0
  260. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nausparse.h +133 -0
  261. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nautil.c +750 -0
  262. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/naututil.h +355 -0
  263. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nauty.c +1256 -0
  264. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/nauty.h +1544 -0
  265. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/schreier.c +1131 -0
  266. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/schreier.h +70 -0
  267. synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/sorttemplates.c +580 -0
  268. synkit/Chem/Mapper/solvers/native/hydrogen.py +711 -0
  269. synkit/Chem/Mapper/solvers/native/implicit.py +506 -0
  270. synkit/Chem/Mapper/solvers/native/implicit_certificate.py +187 -0
  271. synkit/Chem/Mapper/solvers/native/implicit_preparation.py +309 -0
  272. synkit/Chem/Mapper/solvers/native/lib/synkit_mapper.dll +0 -0
  273. synkit/Chem/Mapper/solvers/native/mces.py +16 -0
  274. synkit/Chem/Mapper/solvers/native/reaction.py +179 -0
  275. synkit/Chem/Mapper/solvers/native/reaction_build.py +277 -0
  276. synkit/Chem/Mapper/solvers/native/reaction_text.py +26 -0
  277. synkit/Chem/Mapper/solvers/native/runtime.py +242 -0
  278. synkit/Chem/Mapper/solvers/native/sepdp.py +47 -0
  279. synkit/Chem/Mapper/solvers/native/slap.py +266 -0
  280. synkit/Chem/Mapper/solvers/native/solvers.py +67 -0
  281. synkit/Chem/Mapper/solvers/native/stereo.py +86 -0
  282. synkit/Chem/Mapper/solvers/native/supporting.py +34 -0
  283. synkit/Chem/Mapper/solvers/native/symmetry.py +91 -0
  284. synkit/Chem/Mapper/solvers/slap/__init__.py +29 -0
  285. synkit/Chem/Mapper/solvers/slap/lap.py +174 -0
  286. synkit/Chem/Mapper/solvers/slap/sequential.py +696 -0
  287. synkit/Chem/Mapper/validation/__init__.py +1 -0
  288. synkit/Chem/Mapper/validation/aam_validator.py +442 -0
  289. synkit/Chem/Mapper/validation/annotations.py +274 -0
  290. synkit/Chem/Mapper/validation/bonds.py +124 -0
  291. synkit/Chem/Mapper/validation/cohorts.py +72 -0
  292. synkit/Chem/Mapper/validation/identifiability.py +150 -0
  293. synkit/Chem/Mapper/validation/numerical_scope.py +36 -0
  294. synkit/Chem/Mapper/validation/orbits.py +137 -0
  295. synkit/Chem/Molecule/__init__.py +0 -0
  296. synkit/Chem/Molecule/_chirality_loci.py +165 -0
  297. synkit/Chem/Molecule/_chirality_types.py +231 -0
  298. synkit/Chem/Molecule/_helical_loci.py +167 -0
  299. synkit/Chem/Molecule/_stereo_axis_evidence.py +202 -0
  300. synkit/Chem/Molecule/_stereo_element_detection.py +193 -0
  301. synkit/Chem/Molecule/_stereo_orientation_constraints.py +511 -0
  302. synkit/Chem/Molecule/_tetrahedral_carriers.py +63 -0
  303. synkit/Chem/Molecule/atom_features.py +379 -0
  304. synkit/Chem/Molecule/chirality.py +1041 -0
  305. synkit/Chem/Molecule/cip_assignment.py +569 -0
  306. synkit/Chem/Molecule/cip_ranking.py +843 -0
  307. synkit/Chem/Molecule/coordinate_stereo.py +503 -0
  308. synkit/Chem/Molecule/derived_stereo_naming.py +165 -0
  309. synkit/Chem/Molecule/descriptors.py +452 -0
  310. synkit/Chem/Molecule/formula.py +249 -0
  311. synkit/Chem/Molecule/global_stereo.py +175 -0
  312. synkit/Chem/Molecule/graph_annotator.py +300 -0
  313. synkit/Chem/Molecule/standardize.py +817 -0
  314. synkit/Chem/Molecule/stereo_evidence.py +179 -0
  315. synkit/Chem/Molecule/stereo_perception.py +1032 -0
  316. synkit/Chem/Molecule/valence.py +123 -0
  317. synkit/Chem/Reaction/Mapper/__init__.py +44 -0
  318. synkit/Chem/Reaction/__init__.py +20 -0
  319. synkit/Chem/Reaction/aam_validator.py +5 -0
  320. synkit/Chem/Reaction/balance_check.py +138 -0
  321. synkit/Chem/Reaction/canon_rsmi.py +249 -0
  322. synkit/Chem/Reaction/cleaning.py +58 -0
  323. synkit/Chem/Reaction/deionize.py +199 -0
  324. synkit/Chem/Reaction/explicit_h_audit.py +232 -0
  325. synkit/Chem/Reaction/fix_aam.py +64 -0
  326. synkit/Chem/Reaction/neutralize.py +207 -0
  327. synkit/Chem/Reaction/radical_wildcard.py +224 -0
  328. synkit/Chem/Reaction/standardize.py +203 -0
  329. synkit/Chem/Reaction/tautomerize.py +205 -0
  330. synkit/Chem/__init__.py +1 -0
  331. synkit/Chem/utils.py +315 -0
  332. synkit/Data/__init__.py +0 -0
  333. synkit/Data/aldol.json.gz +1 -0
  334. synkit/Data/gen_partial_aam.py +147 -0
  335. synkit/Data/paracetamol.json.gz +1 -0
  336. synkit/Graph/Canon/__init__.py +16 -0
  337. synkit/Graph/Canon/_native/__init__.py +13 -0
  338. synkit/Graph/Canon/_native/build.py +93 -0
  339. synkit/Graph/Canon/_native/lib/synkit_canon.dll +0 -0
  340. synkit/Graph/Canon/_native/prepare.py +49 -0
  341. synkit/Graph/Canon/_native/runtime.py +140 -0
  342. synkit/Graph/Canon/_native/search.py +137 -0
  343. synkit/Graph/Canon/canon_algs.py +228 -0
  344. synkit/Graph/Canon/canon_graph.py +531 -0
  345. synkit/Graph/Canon/cpp/CMakeLists.txt +42 -0
  346. synkit/Graph/Canon/cpp/README.md +123 -0
  347. synkit/Graph/Canon/cpp/examples/canonical_graph.cpp +16 -0
  348. synkit/Graph/Canon/cpp/include/synkit_canon/canon.h +85 -0
  349. synkit/Graph/Canon/cpp/src/canonical.cpp +391 -0
  350. synkit/Graph/Canon/cpp/src/symmetry.h +83 -0
  351. synkit/Graph/Canon/cpp/tests/symmetry.cpp +93 -0
  352. synkit/Graph/Canon/exact.py +1020 -0
  353. synkit/Graph/Canon/exact_refinement.py +368 -0
  354. synkit/Graph/Canon/nauty.py +143 -0
  355. synkit/Graph/Context/__init__.py +0 -0
  356. synkit/Graph/Context/hier_context.py +244 -0
  357. synkit/Graph/Context/radius_expand.py +252 -0
  358. synkit/Graph/FG/__init__.py +19 -0
  359. synkit/Graph/FG/api.py +39 -0
  360. synkit/Graph/FG/audit.py +155 -0
  361. synkit/Graph/FG/catalog.py +919 -0
  362. synkit/Graph/FG/detector.py +288 -0
  363. synkit/Graph/FG/model.py +97 -0
  364. synkit/Graph/FG/recognizers.py +274 -0
  365. synkit/Graph/FG/ring_system.py +154 -0
  366. synkit/Graph/Feature/Descriptors/topology.py +857 -0
  367. synkit/Graph/Feature/Fingerprint/__init__.py +0 -0
  368. synkit/Graph/Feature/Fingerprint/wl_rxn_fps.py +222 -0
  369. synkit/Graph/Feature/__init__.py +5 -0
  370. synkit/Graph/Feature/graph_descriptors.py +323 -0
  371. synkit/Graph/Feature/graph_fps.py +96 -0
  372. synkit/Graph/Feature/graph_signature.py +239 -0
  373. synkit/Graph/Feature/hash_fps.py +133 -0
  374. synkit/Graph/Feature/morgan_fps.py +88 -0
  375. synkit/Graph/Feature/path_fps.py +81 -0
  376. synkit/Graph/Feature/wl_hash.py +134 -0
  377. synkit/Graph/Fusion/__init__.py +85 -0
  378. synkit/Graph/Fusion/candidate.py +559 -0
  379. synkit/Graph/Fusion/constructor.py +877 -0
  380. synkit/Graph/Fusion/identity.py +184 -0
  381. synkit/Graph/Fusion/interface.py +700 -0
  382. synkit/Graph/Fusion/search.py +241 -0
  383. synkit/Graph/Hyrogen/__init__.py +6 -0
  384. synkit/Graph/Hyrogen/_misc.py +591 -0
  385. synkit/Graph/Hyrogen/hcomplete.py +995 -0
  386. synkit/Graph/Hyrogen/hcomplete_legacy.py +368 -0
  387. synkit/Graph/Hyrogen/hcompletion_algorithms.py +713 -0
  388. synkit/Graph/Hyrogen/hextend.py +570 -0
  389. synkit/Graph/Hyrogen/hextend_legacy.py +215 -0
  390. synkit/Graph/ITS/__init__.py +4 -0
  391. synkit/Graph/ITS/its_builder.py +120 -0
  392. synkit/Graph/ITS/its_construction.py +719 -0
  393. synkit/Graph/ITS/its_decompose.py +572 -0
  394. synkit/Graph/ITS/its_destruction.py +331 -0
  395. synkit/Graph/ITS/its_expand.py +1251 -0
  396. synkit/Graph/ITS/its_relabel.py +187 -0
  397. synkit/Graph/ITS/its_reverter.py +356 -0
  398. synkit/Graph/ITS/normalize_aam.py +145 -0
  399. synkit/Graph/ITS/partial_its.py +238 -0
  400. synkit/Graph/ITS/rc_extractor.py +656 -0
  401. synkit/Graph/ITS/stereo.py +74 -0
  402. synkit/Graph/MTG/__init__.py +107 -0
  403. synkit/Graph/MTG/gluing.py +451 -0
  404. synkit/Graph/MTG/history.py +928 -0
  405. synkit/Graph/MTG/inventory.py +118 -0
  406. synkit/Graph/MTG/local.py +447 -0
  407. synkit/Graph/MTG/mcs_matcher.py +246 -0
  408. synkit/Graph/MTG/mtg.py +611 -0
  409. synkit/Graph/MTG/mtg_explore.py +74 -0
  410. synkit/Graph/MTG/observation.py +209 -0
  411. synkit/Graph/MTG/process.py +577 -0
  412. synkit/Graph/MTG/queries.py +66 -0
  413. synkit/Graph/MTG/realization.py +95 -0
  414. synkit/Graph/MTG/series_parallel.py +107 -0
  415. synkit/Graph/MTG/utils.py +424 -0
  416. synkit/Graph/Matcher/__init__.py +10 -0
  417. synkit/Graph/Matcher/approx_mcs.py +1264 -0
  418. synkit/Graph/Matcher/auto_est.py +736 -0
  419. synkit/Graph/Matcher/automorphism.py +314 -0
  420. synkit/Graph/Matcher/batch_cluster.py +224 -0
  421. synkit/Graph/Matcher/dedup_matches.py +247 -0
  422. synkit/Graph/Matcher/graph_cluster.py +191 -0
  423. synkit/Graph/Matcher/graph_matcher.py +312 -0
  424. synkit/Graph/Matcher/graph_morphism.py +421 -0
  425. synkit/Graph/Matcher/mcs_matcher.py +804 -0
  426. synkit/Graph/Matcher/multi_turbo_iso.py +186 -0
  427. synkit/Graph/Matcher/orbit.py +284 -0
  428. synkit/Graph/Matcher/partial_matcher.py +694 -0
  429. synkit/Graph/Matcher/sing.py +544 -0
  430. synkit/Graph/Matcher/subgraph_matcher.py +812 -0
  431. synkit/Graph/Matcher/turbo_iso.py +272 -0
  432. synkit/Graph/Matcher/wl_sel.py +537 -0
  433. synkit/Graph/Mech/__init__.py +26 -0
  434. synkit/Graph/Mech/conversion.py +1466 -0
  435. synkit/Graph/Mech/conversion_debug.py +237 -0
  436. synkit/Graph/Mech/electron_accounting.py +200 -0
  437. synkit/Graph/Mech/lwg_editor.py +406 -0
  438. synkit/Graph/Mech/lwg_ops.py +313 -0
  439. synkit/Graph/Morphism/__init__.py +99 -0
  440. synkit/Graph/Morphism/constraints.py +460 -0
  441. synkit/Graph/Morphism/llg.py +999 -0
  442. synkit/Graph/Morphism/morphism.py +349 -0
  443. synkit/Graph/Morphism/stereo.py +258 -0
  444. synkit/Graph/Morphism/stereo_morphism.py +383 -0
  445. synkit/Graph/Morphism/stereo_morphism_helpers.py +957 -0
  446. synkit/Graph/Morphism/stereo_morphism_types.py +117 -0
  447. synkit/Graph/Stereo/__init__.py +376 -0
  448. synkit/Graph/Stereo/_descriptor_core.py +207 -0
  449. synkit/Graph/Stereo/_descriptor_serialization.py +138 -0
  450. synkit/Graph/Stereo/canonical.py +648 -0
  451. synkit/Graph/Stereo/changes.py +964 -0
  452. synkit/Graph/Stereo/composition.py +391 -0
  453. synkit/Graph/Stereo/configured.py +946 -0
  454. synkit/Graph/Stereo/couplings.py +245 -0
  455. synkit/Graph/Stereo/descriptors.py +1030 -0
  456. synkit/Graph/Stereo/enumeration.py +597 -0
  457. synkit/Graph/Stereo/extended_descriptors.py +406 -0
  458. synkit/Graph/Stereo/global_configured.py +152 -0
  459. synkit/Graph/Stereo/global_stereo.py +304 -0
  460. synkit/Graph/Stereo/identity.py +648 -0
  461. synkit/Graph/Stereo/interchange.py +496 -0
  462. synkit/Graph/Stereo/legacy.py +460 -0
  463. synkit/Graph/Stereo/matching.py +899 -0
  464. synkit/Graph/Stereo/native.py +154 -0
  465. synkit/Graph/Stereo/orbits.py +668 -0
  466. synkit/Graph/Stereo/outcomes.py +99 -0
  467. synkit/Graph/Stereo/pairwise.py +350 -0
  468. synkit/Graph/Stereo/rdkit_adapter.py +662 -0
  469. synkit/Graph/Stereo/rdkit_identity.py +118 -0
  470. synkit/Graph/Stereo/rdkit_resonance.py +140 -0
  471. synkit/Graph/Stereo/reaction_interchange.py +266 -0
  472. synkit/Graph/Stereo/semantics.py +296 -0
  473. synkit/Graph/Stereo/supports.py +257 -0
  474. synkit/Graph/Stereo/wire.py +339 -0
  475. synkit/Graph/Wildcard/__init__.py +0 -0
  476. synkit/Graph/Wildcard/fuse_graph.py +156 -0
  477. synkit/Graph/Wildcard/graph_wc.py +303 -0
  478. synkit/Graph/Wildcard/its_merge.py +857 -0
  479. synkit/Graph/Wildcard/radwc.py +114 -0
  480. synkit/Graph/Wildcard/wc_matcher.py +576 -0
  481. synkit/Graph/Wildcard/wildcard.py +225 -0
  482. synkit/Graph/__init__.py +17 -0
  483. synkit/Graph/canon_graph.py +14 -0
  484. synkit/Graph/syn_graph.py +199 -0
  485. synkit/Graph/utils.py +324 -0
  486. synkit/IO/__init__.py +4 -0
  487. synkit/IO/chem_converter.py +1059 -0
  488. synkit/IO/combinatorial/__init__.py +8 -0
  489. synkit/IO/combinatorial/gml_to_graph.py +223 -0
  490. synkit/IO/combinatorial/graph_to_gml.py +280 -0
  491. synkit/IO/combinatorial/graph_to_smarts.py +186 -0
  492. synkit/IO/combinatorial/smarts_expander.py +147 -0
  493. synkit/IO/combinatorial/smarts_generalizer.py +133 -0
  494. synkit/IO/combinatorial/smarts_to_graph.py +179 -0
  495. synkit/IO/conversion.py +42 -0
  496. synkit/IO/data_io.py +269 -0
  497. synkit/IO/data_process.py +143 -0
  498. synkit/IO/debug.py +73 -0
  499. synkit/IO/gml_to_nx.py +150 -0
  500. synkit/IO/graph_to_mol.py +199 -0
  501. synkit/IO/mol_to_graph.py +1105 -0
  502. synkit/IO/mol_to_graph_chemistry.py +545 -0
  503. synkit/IO/nx_to_gml.py +209 -0
  504. synkit/IO/smiles_to_id.py +123 -0
  505. synkit/Mechanism/__init__.py +151 -0
  506. synkit/Mechanism/adapters.py +136 -0
  507. synkit/Mechanism/audit.py +323 -0
  508. synkit/Mechanism/benchmark.py +638 -0
  509. synkit/Mechanism/compatibility.py +13 -0
  510. synkit/Mechanism/drawing.py +85 -0
  511. synkit/Mechanism/electron_models.py +725 -0
  512. synkit/Mechanism/equivalence.py +521 -0
  513. synkit/Mechanism/evidence.py +262 -0
  514. synkit/Mechanism/interchange.py +141 -0
  515. synkit/Mechanism/model.py +918 -0
  516. synkit/Mechanism/neighbor_stereo.py +312 -0
  517. synkit/Mechanism/radical_data.py +740 -0
  518. synkit/Mechanism/replay.py +986 -0
  519. synkit/Mechanism/schema.py +264 -0
  520. synkit/Mechanism/stereo_state.py +416 -0
  521. synkit/Mechanism/symbols.py +91 -0
  522. synkit/Rule/Apply/__init__.py +35 -0
  523. synkit/Rule/Apply/conditions.py +45 -0
  524. synkit/Rule/Apply/dpo.py +998 -0
  525. synkit/Rule/Apply/rule_matcher.py +218 -0
  526. synkit/Rule/Apply/validation.py +354 -0
  527. synkit/Rule/Compose/__init__.py +106 -0
  528. synkit/Rule/Compose/_identity.py +43 -0
  529. synkit/Rule/Compose/composition.py +976 -0
  530. synkit/Rule/Compose/laws.py +439 -0
  531. synkit/Rule/Compose/search.py +771 -0
  532. synkit/Rule/Compose/synrule.py +170 -0
  533. synkit/Rule/Modify/__init__.py +0 -0
  534. synkit/Rule/Modify/implict_rule.py +56 -0
  535. synkit/Rule/Modify/longest_path.py +92 -0
  536. synkit/Rule/Modify/molecule_rule.py +115 -0
  537. synkit/Rule/Modify/prune_templates.py +78 -0
  538. synkit/Rule/Modify/rule_utils.py +194 -0
  539. synkit/Rule/Modify/strip_rule.py +97 -0
  540. synkit/Rule/__init__.py +28 -0
  541. synkit/Rule/generic_stereo.py +884 -0
  542. synkit/Rule/stereo_identity.py +271 -0
  543. synkit/Rule/syn_rule.py +1090 -0
  544. synkit/Synthesis/MSR/__init__.py +0 -0
  545. synkit/Synthesis/MSR/path_finder.py +239 -0
  546. synkit/Synthesis/Metrics/__init__.py +0 -0
  547. synkit/Synthesis/Metrics/_base.py +52 -0
  548. synkit/Synthesis/Metrics/_plot.py +129 -0
  549. synkit/Synthesis/Metrics/_ranking.py +179 -0
  550. synkit/Synthesis/RBL/__init__.py +80 -0
  551. synkit/Synthesis/RBL/engine.py +1249 -0
  552. synkit/Synthesis/RBL/matching.py +652 -0
  553. synkit/Synthesis/RBL/overlap.py +336 -0
  554. synkit/Synthesis/RBL/pipeline.py +376 -0
  555. synkit/Synthesis/RBL/policy.py +139 -0
  556. synkit/Synthesis/RBL/proof.py +370 -0
  557. synkit/Synthesis/RBL/reaction.py +506 -0
  558. synkit/Synthesis/RBL/state.py +169 -0
  559. synkit/Synthesis/RBL/validation.py +1060 -0
  560. synkit/Synthesis/Reactor/__init__.py +60 -0
  561. synkit/Synthesis/Reactor/core/__init__.py +1 -0
  562. synkit/Synthesis/Reactor/core/engine.py +967 -0
  563. synkit/Synthesis/Reactor/core/product.py +621 -0
  564. synkit/Synthesis/Reactor/core/rewrite.py +561 -0
  565. synkit/Synthesis/Reactor/core/strategy.py +44 -0
  566. synkit/Synthesis/Reactor/matching/__init__.py +1 -0
  567. synkit/Synthesis/Reactor/matching/mixin.py +920 -0
  568. synkit/Synthesis/Reactor/matching/policy.py +345 -0
  569. synkit/Synthesis/Reactor/matching/symmetry.py +309 -0
  570. synkit/Synthesis/Reactor/output/__init__.py +1 -0
  571. synkit/Synthesis/Reactor/output/deduplication.py +703 -0
  572. synkit/Synthesis/Reactor/output/policy.py +16 -0
  573. synkit/Synthesis/Reactor/output/serialization.py +485 -0
  574. synkit/Synthesis/Reactor/output/structural.py +893 -0
  575. synkit/Synthesis/Reactor/stereo/__init__.py +1 -0
  576. synkit/Synthesis/Reactor/stereo/assignment.py +35 -0
  577. synkit/Synthesis/Reactor/stereo/mixin.py +780 -0
  578. synkit/Synthesis/Reactor/variants/__init__.py +1 -0
  579. synkit/Synthesis/Reactor/variants/imbalanced.py +180 -0
  580. synkit/Synthesis/Reactor/variants/partial.py +84 -0
  581. synkit/Synthesis/Reactor/workflow/__init__.py +1 -0
  582. synkit/Synthesis/Reactor/workflow/batch.py +550 -0
  583. synkit/Synthesis/Reactor/workflow/benchmark.py +143 -0
  584. synkit/Synthesis/Reactor/workflow/postprocess.py +267 -0
  585. synkit/Synthesis/Reactor/workflow/rule_filter.py +210 -0
  586. synkit/Synthesis/__init__.py +0 -0
  587. synkit/Synthesis/reactor_utils.py +316 -0
  588. synkit/Utils/__init__.py +0 -0
  589. synkit/Utils/utils.py +172 -0
  590. synkit/Vis/__init__.py +91 -0
  591. synkit/Vis/crn/__init__.py +40 -0
  592. synkit/Vis/epd/__init__.py +20 -0
  593. synkit/Vis/epd/arrows.py +425 -0
  594. synkit/Vis/epd/chem.py +197 -0
  595. synkit/Vis/epd/constants.py +83 -0
  596. synkit/Vis/epd/layout.py +283 -0
  597. synkit/Vis/epd/mapping.py +51 -0
  598. synkit/Vis/epd/models.py +136 -0
  599. synkit/Vis/epd/render.py +543 -0
  600. synkit/Vis/epd/utils.py +108 -0
  601. synkit/Vis/epd/visualizer.py +811 -0
  602. synkit/Vis/graph_visualizer.py +375 -0
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  607. synkit/Vis/molecule/drawer.py +563 -0
  608. synkit/Vis/molecule/reaction.py +285 -0
  609. synkit/Vis/molecule_drawer.py +33 -0
  610. synkit/Vis/mtg/__init__.py +17 -0
  611. synkit/Vis/mtg/drawer.py +769 -0
  612. synkit/Vis/mtg_drawer.py +34 -0
  613. synkit/Vis/pdf_writer.py +146 -0
  614. synkit/Vis/reaction/__init__.py +19 -0
  615. synkit/Vis/reaction/rule.py +141 -0
  616. synkit/Vis/reaction/rxn.py +532 -0
  617. synkit/Vis/reaction_drawer.py +41 -0
  618. synkit/Vis/space/__init__.py +17 -0
  619. synkit/Vis/space/chemical.py +80 -0
  620. synkit/Vis/space/embedding.py +87 -0
  621. synkit/Vis/vis_synedu/Vis/__init__.py +7 -0
  622. synkit/Vis/vis_synedu/Vis/dpo.py +862 -0
  623. synkit/Vis/vis_synedu/rxn_vis.py +377 -0
  624. synkit/Vis/vis_synedu/vis.py +501 -0
  625. synkit/Vis/visual_drawer.py +215 -0
  626. synkit/Vis/visual_model.py +520 -0
  627. synkit/__init__.py +3 -0
  628. synkit/_native.py +91 -0
  629. synkit/examples.py +50 -0
  630. synkit/version.py +23 -0
  631. synkit-1.6.5.dist-info/METADATA +156 -0
  632. synkit-1.6.5.dist-info/RECORD +636 -0
  633. synkit-1.6.5.dist-info/WHEEL +4 -0
  634. synkit-1.6.5.dist-info/licenses/LICENSE +21 -0
  635. synkit-1.6.5.dist-info/licenses/synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/COPYRIGHT +44 -0
  636. synkit-1.6.5.dist-info/licenses/synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt +202 -0
@@ -0,0 +1,287 @@
1
+ #include "synkit_mapper/mces/mces.h"
2
+ #include "../solvers/seed.h"
3
+ #include "synkit_mapper/core/runtime.h"
4
+ #include <limits>
5
+ #include <numeric>
6
+ #include <sstream>
7
+ #include <string>
8
+
9
+ namespace synkit_mapper {
10
+ namespace {
11
+ struct Vertex {
12
+ int32_t source, target;
13
+ };
14
+ struct Metadata {
15
+ int64_t vertices = 0, edges = 0, graph_bytes = 0;
16
+ };
17
+ thread_local Metadata metadata;
18
+ struct PhaseTimer {
19
+ double &total;
20
+ Clock::time_point start = Clock::now();
21
+ ~PhaseTimer() { total += elapsed(start); }
22
+ };
23
+ class CliqueSearch {
24
+ const Problem &p;
25
+ const Request &r;
26
+ Callback callback;
27
+ void *userdata;
28
+ Statistics &s;
29
+ Budget budget;
30
+ std::vector<Vertex> vertices;
31
+ std::vector<std::vector<uint64_t>> adjacency;
32
+ std::vector<int64_t> pair_upper;
33
+ std::vector<int> clique;
34
+ int64_t constant = 0, best_overlap = -1, target_overlap = 0, base_bytes = 0,
35
+ live_bytes = 0;
36
+ bool optimize = false, at_most = false;
37
+ bool adjacent(int a, int b) const {
38
+ return (adjacency[a][b / 64] >> (b % 64)) & 1ULL;
39
+ }
40
+ int64_t weight(int a, int b) const {
41
+ const auto &u = vertices[a], &v = vertices[b];
42
+ return std::min(p.a2[u.source * p.n + v.source],
43
+ p.b2[u.target * p.n + v.target]);
44
+ }
45
+ void memory(int64_t extra) {
46
+ int64_t proposed = live_bytes + extra;
47
+ if (r.memory_limit_bytes >= 0 &&
48
+ base_bytes + proposed > r.memory_limit_bytes)
49
+ throw Stop{SYNKIT_STOP_MEMORY};
50
+ live_bytes = proposed;
51
+ s.peak_memory_bytes =
52
+ std::max(s.peak_memory_bytes, base_bytes + live_bytes);
53
+ }
54
+ void visit(const std::vector<int> &candidates, int64_t overlap) {
55
+ budget.check();
56
+ if (r.max_states >= 0 && s.nodes >= r.max_states)
57
+ throw Stop{SYNKIT_STOP_STATES};
58
+ ++s.nodes;
59
+ if (static_cast<int>(clique.size()) == p.n) {
60
+ ++s.leaves;
61
+ std::vector<int32_t> mapping(p.n, -1);
62
+ for (int v : clique)
63
+ mapping[vertices[v].source] = vertices[v].target;
64
+ int64_t cost = mapping_cost2(p, mapping);
65
+ if (cost != constant - 2 * overlap)
66
+ throw std::runtime_error(
67
+ "Weighted MCES overlap disagrees with chemical rescoring");
68
+ if (s.incumbent2 < 0 || cost < s.incumbent2)
69
+ s.incumbent2 = cost;
70
+ if (optimize) {
71
+ best_overlap = std::max(best_overlap, overlap);
72
+ return;
73
+ }
74
+ if ((at_most && overlap < target_overlap) ||
75
+ (!at_most && overlap != target_overlap))
76
+ return;
77
+ ++s.candidate_count;
78
+ s.labeled_count = s.candidate_count;
79
+ int stop = 0;
80
+ {
81
+ PhaseTimer timer{s.callback_seconds};
82
+ if (callback)
83
+ stop = callback(mapping.data(), cost, userdata);
84
+ }
85
+ if (stop)
86
+ throw Stop{SYNKIT_STOP_CALLBACK};
87
+ budget.check();
88
+ if (r.max_candidates >= 0 && s.candidate_count >= r.max_candidates)
89
+ throw Stop{SYNKIT_STOP_CANDIDATES};
90
+ return;
91
+ }
92
+ // Source rows form a proper coloring of the association graph: no clique
93
+ // contains two vertices with the same source. A full clique needs every
94
+ // remaining color, giving both a size bound and safe weighted bounds.
95
+ std::vector<uint8_t> selected(p.n, 0);
96
+ for (int v : clique)
97
+ selected[vertices[v].source] = 1;
98
+ std::vector<int64_t> maximum(p.n, -1),
99
+ minimum(p.n, std::numeric_limits<int64_t>::max());
100
+ size_t checked = 0;
101
+ for (int v : candidates) {
102
+ if (!(++checked % 1024))
103
+ budget.check();
104
+ int row = vertices[v].source;
105
+ int64_t increment = 0;
106
+ for (int q : clique)
107
+ increment += weight(v, q);
108
+ maximum[row] = std::max(maximum[row], increment);
109
+ minimum[row] = std::min(minimum[row], increment);
110
+ }
111
+ int64_t upper = overlap, lower = overlap;
112
+ for (int i = 0; i < p.n; ++i)
113
+ if (!selected[i]) {
114
+ if (maximum[i] < 0)
115
+ return;
116
+ upper += maximum[i];
117
+ lower += minimum[i];
118
+ for (int k = i + 1; k < p.n; ++k)
119
+ if (!selected[k])
120
+ upper += pair_upper[i * p.n + k];
121
+ }
122
+ if (optimize
123
+ ? upper <= best_overlap
124
+ : upper < target_overlap || (!at_most && lower > target_overlap))
125
+ return;
126
+ for (size_t i = 0; i < candidates.size(); ++i) {
127
+ budget.check();
128
+ int v = candidates[i];
129
+ std::vector<int> next;
130
+ next.reserve(candidates.size() - i - 1);
131
+ for (size_t j = i + 1; j < candidates.size(); ++j)
132
+ if (adjacent(v, candidates[j]))
133
+ next.push_back(candidates[j]);
134
+ if (next.size() + clique.size() + 1 < static_cast<size_t>(p.n))
135
+ continue;
136
+ int64_t increment = 0;
137
+ for (int q : clique)
138
+ increment += weight(v, q);
139
+ clique.push_back(v);
140
+ int64_t bytes = next.capacity() * sizeof(int);
141
+ memory(bytes);
142
+ try {
143
+ visit(next, overlap + increment);
144
+ } catch (...) {
145
+ live_bytes -= bytes;
146
+ clique.pop_back();
147
+ throw;
148
+ }
149
+ live_bytes -= bytes;
150
+ clique.pop_back();
151
+ }
152
+ }
153
+
154
+ public:
155
+ CliqueSearch(const Problem &problem, const Request &request, Callback cb,
156
+ void *data, Statistics &stats)
157
+ : p(problem), r(request), callback(cb), userdata(data), s(stats),
158
+ budget(request) {}
159
+ void solve() {
160
+ struct Finish {
161
+ Statistics &s;
162
+ Budget &b;
163
+ ~Finish() { s.elapsed_seconds = b.seconds(); }
164
+ } finish{s, budget};
165
+ try {
166
+ budget.check();
167
+ std::vector<int32_t> seed;
168
+ {
169
+ PhaseTimer timer{s.model_seconds};
170
+ for (int i = 0; i < p.n; ++i) {
171
+ budget.check();
172
+ for (int j = 0; j < p.n; ++j)
173
+ if (p.types_r[i] == p.types_p[j])
174
+ vertices.push_back({i, j});
175
+ for (int k = i + 1; k < p.n; ++k)
176
+ constant += p.a2[i * p.n + k] + p.b2[i * p.n + k];
177
+ }
178
+ if (vertices.size() > 8192) {
179
+ unsupported(s);
180
+ return;
181
+ }
182
+ metadata.vertices = vertices.size();
183
+ int64_t words = (vertices.size() + 63) / 64;
184
+ base_bytes = sizeof(*this) + vertices.capacity() * sizeof(Vertex) +
185
+ vertices.size() * (sizeof(std::vector<uint64_t>) +
186
+ words * sizeof(uint64_t)) +
187
+ static_cast<int64_t>(p.n) * p.n * sizeof(int64_t) +
188
+ p.n * sizeof(int);
189
+ metadata.graph_bytes = base_bytes;
190
+ memory(0);
191
+ adjacency.resize(vertices.size(), std::vector<uint64_t>(words, 0));
192
+ pair_upper.assign(p.n * p.n, 0);
193
+ size_t checks = 0;
194
+ for (size_t i = 0; i < vertices.size(); ++i) {
195
+ budget.check();
196
+ for (size_t j = i + 1; j < vertices.size(); ++j) {
197
+ if (!(++checks % 1024))
198
+ budget.check();
199
+ const auto &u = vertices[i], &v = vertices[j];
200
+ if (u.source == v.source || u.target == v.target)
201
+ continue;
202
+ adjacency[i][j / 64] |= uint64_t{1} << (j % 64);
203
+ adjacency[j][i / 64] |= uint64_t{1} << (i % 64);
204
+ ++metadata.edges;
205
+ int64_t w = weight(i, j);
206
+ auto &bound = pair_upper[u.source * p.n + v.source];
207
+ bound = std::max(bound, w);
208
+ pair_upper[v.source * p.n + u.source] = bound;
209
+ }
210
+ }
211
+ seed = solvers::detail::feasible_seed(p, budget);
212
+ if (!seed.empty())
213
+ s.incumbent2 = mapping_cost2(p, seed);
214
+ }
215
+ std::vector<int> root(vertices.size());
216
+ std::iota(root.begin(), root.end(), 0);
217
+ int64_t root_bytes = root.capacity() * sizeof(int);
218
+ memory(root_bytes);
219
+ if (r.query == SYNKIT_MINIMUM_CLASSES ||
220
+ r.query == SYNKIT_MINIMUM_PROOF) {
221
+ optimize = true;
222
+ if (s.incumbent2 >= 0)
223
+ best_overlap = (constant - s.incumbent2) / 2;
224
+ {
225
+ PhaseTimer timer{s.optimization_seconds};
226
+ visit(root, 0);
227
+ }
228
+ if (best_overlap < 0) {
229
+ s.search_complete = 1;
230
+ return;
231
+ }
232
+ s.minimum_proven = 1;
233
+ s.minimum2 = s.lower_bound2 = constant - 2 * best_overlap;
234
+ if (r.query == SYNKIT_MINIMUM_PROOF) {
235
+ s.search_complete = 1;
236
+ return;
237
+ }
238
+ target_overlap = best_overlap;
239
+ } else {
240
+ int64_t threshold = constant - r.target2;
241
+ if (r.query == SYNKIT_EXACT_DISTANCE &&
242
+ (threshold < 0 || threshold % 2)) {
243
+ s.search_complete = 1;
244
+ return;
245
+ }
246
+ at_most = r.query == SYNKIT_AT_MOST_DISTANCE;
247
+ target_overlap = threshold <= 0 ? 0 : (threshold + 1) / 2;
248
+ }
249
+ optimize = false;
250
+ {
251
+ PhaseTimer timer{s.enumeration_seconds};
252
+ visit(root, 0);
253
+ }
254
+ s.search_complete = 1;
255
+ } catch (const Stop &stop) {
256
+ stopped(s, stop.reason);
257
+ }
258
+ s.elapsed_seconds = budget.seconds();
259
+ }
260
+ };
261
+ } // namespace
262
+ const char *mces_run_metadata() {
263
+ static thread_local std::string value;
264
+ std::ostringstream out;
265
+ out << "{\"architecture\":\"weighted_association_graph_size_n_clique\","
266
+ "\"association_vertices\":"
267
+ << metadata.vertices << ",\"association_edges\":" << metadata.edges
268
+ << ",\"accounted_graph_bytes\":" << metadata.graph_bytes
269
+ << ",\"memory_scope\":\"accounted_native_graph_and_clique_candidates\","
270
+ "\"objective_equivalence\":\"D2=C-2*weighted_common_edge_overlap\"}";
271
+ value = out.str();
272
+ return value.c_str();
273
+ }
274
+ int solve_mces(const Problem &p, const Request &r, Callback callback,
275
+ void *userdata, Statistics &s) {
276
+ initialize(s, r);
277
+ metadata = {};
278
+ s.labeled_count = 0;
279
+ s.peak_frontier = s.peak_frontier_bytes = -1;
280
+ if (r.symmetry || r.classify || r.max_classes != -1 || r.max_frontier != -1 ||
281
+ p.n > 256)
282
+ return unsupported(s);
283
+ CliqueSearch search(p, r, callback, userdata, s);
284
+ search.solve();
285
+ return 0;
286
+ }
287
+ } // namespace synkit_mapper
@@ -0,0 +1,334 @@
1
+ // Compile the common exact kernel once, preserving its ABI3 exports.
2
+ // The shared-core bridge owns preparation, optional bounds and phase
3
+ // accounting.
4
+ #include "../../../../exact/native/native_distance.cpp"
5
+ #include "exact_helpers.h"
6
+ #include "sparse_root_lp.h"
7
+ #include "synkit_mapper/core/pmcd_witness.h"
8
+ #include "synkit_mapper/core/runtime.h"
9
+ #include "synkit_mapper/pabs/seed.h"
10
+ #include "synkit_mapper/slap.h"
11
+ #include <set>
12
+ static thread_local int64_t bridge_embedding_statistics[14] = {};
13
+ static thread_local int64_t bridge_deck_statistics[14] = {};
14
+ #ifdef SYNKIT_MAPPER_TEST_HOOKS
15
+ static thread_local int64_t lp_assignment_statistics[6] = {};
16
+ #endif // SYNKIT_MAPPER_TEST_HOOKS
17
+
18
+ namespace synkit_mapper {
19
+ namespace {
20
+
21
+ #include "chemical_floor.inc"
22
+ #include "endpoint_symmetry.inc"
23
+ #include "seed_heuristics.inc"
24
+
25
+ struct Receiver {
26
+ const Problem &p;
27
+ const Request &r;
28
+ Callback callback;
29
+ void *userdata;
30
+ Statistics &s;
31
+ Budget &budget;
32
+ static int receive(const int *map, int cost4, void *pointer) {
33
+ auto &self = *static_cast<Receiver *>(pointer);
34
+ std::vector<int32_t> mapping(map, map + self.p.n);
35
+ int64_t cost = mapping_cost2(self.p, mapping);
36
+ if (cost4 != 2 * cost)
37
+ throw std::runtime_error(
38
+ "PABS quarter-CD witness does not match rescoring");
39
+ const auto start = Clock::now();
40
+ int stop =
41
+ self.callback ? self.callback(mapping.data(), cost, self.userdata) : 0;
42
+ self.s.callback_seconds += elapsed(start);
43
+ ++self.s.candidate_count;
44
+ if (stop) {
45
+ self.s.reason = SYNKIT_STOP_CALLBACK;
46
+ return 1;
47
+ }
48
+ if (self.budget.reason()) {
49
+ self.s.reason = self.budget.reason();
50
+ return 1;
51
+ }
52
+ return 0;
53
+ }
54
+ };
55
+ } // namespace
56
+
57
+ #include "overlap_dual.inc"
58
+
59
+ #include "profile_seed.inc"
60
+
61
+ int solve_pabs_original(const Problem &p, const Request &r, Callback callback,
62
+ void *userdata, Statistics &s) {
63
+ synkit_mapper_clear_pmcd_witness();
64
+ sparse_root_lp::clear();
65
+ std::fill(bridge_embedding_statistics, bridge_embedding_statistics + 14, 0);
66
+ std::fill(coherent_seed_statistics, coherent_seed_statistics + 20, 0);
67
+ coherent_seed_mapping.clear();
68
+ std::fill(conditioned_factor_cache_statistics,
69
+ conditioned_factor_cache_statistics + 8, 0);
70
+
71
+ std::fill(bridge_deck_statistics, bridge_deck_statistics + 14, 0);
72
+ bridge_deck_statistics[13] = -1;
73
+ Budget budget(r);
74
+ budget.check();
75
+ if (p.n > SYNKIT_PABS_MAX_VERTICES || r.classify || r.max_states != -1 ||
76
+ r.max_classes != -1 || r.max_frontier != -1 ||
77
+ r.memory_limit_bytes != -1 || r.cancel_token)
78
+ return unsupported(s);
79
+ const int n = p.n;
80
+ auto stage = Clock::now();
81
+ std::vector<int> a(n * n), b(n * n), cr(n), cp(n), order(n), pred(n * n, 0);
82
+ std::map<int32_t, int> types;
83
+ std::set<int> levels;
84
+ int64_t maximum2 = 0;
85
+ for (int i = 0; i < n; ++i) {
86
+ cr[i] = types.emplace(p.types_r[i], types.size()).first->second;
87
+ cp[i] = types.emplace(p.types_p[i], types.size()).first->second;
88
+ order[i] = i;
89
+ for (int j = 0; j < n; ++j) {
90
+ if (p.a2[i * n + j] > 1024 || p.b2[i * n + j] > 1024)
91
+ return unsupported(s);
92
+ a[i * n + j] = static_cast<int>(p.a2[i * n + j]);
93
+ b[i * n + j] = static_cast<int>(p.b2[i * n + j]);
94
+ levels.insert(a[i * n + j]);
95
+ levels.insert(b[i * n + j]);
96
+ if (j > i)
97
+ maximum2 += a[i * n + j] + b[i * n + j];
98
+ }
99
+ }
100
+ if (levels.size() > 16 || maximum2 > 500000)
101
+ return unsupported(s);
102
+ std::vector<int> rg, pg;
103
+ if (r.symmetry) {
104
+ rg = endpoint_generators(p, false, budget);
105
+ pg = endpoint_generators(p, true, budget);
106
+ }
107
+ std::stable_sort(order.begin(), order.end(), [&](int i, int j) {
108
+ int di = 0, dj = 0;
109
+ for (int k = 0; k < n; ++k) {
110
+ di += a[i * n + k] != 0;
111
+ dj += a[j * n + k] != 0;
112
+ }
113
+ return di > dj;
114
+ });
115
+ Perm seed;
116
+ RootDualBranchCertificate root_certificate;
117
+ sparse_root_lp::AssignmentCertificate assignment_certificate;
118
+ #ifdef SYNKIT_MAPPER_TEST_HOOKS
119
+ std::fill(lp_assignment_statistics, lp_assignment_statistics + 6, 0);
120
+ struct SaveAssignmentStatistics {
121
+ sparse_root_lp::AssignmentCertificate &certificate;
122
+ ~SaveAssignmentStatistics() {
123
+ lp_assignment_statistics[0] = certificate.ready;
124
+ lp_assignment_statistics[1] = certificate.m;
125
+ lp_assignment_statistics[2] = certificate.root_bound2;
126
+ lp_assignment_statistics[3] = certificate.calls;
127
+ lp_assignment_statistics[4] = certificate.prunes;
128
+ lp_assignment_statistics[5] = certificate.ready && certificate.m > 64;
129
+ }
130
+ } save_assignment_statistics{assignment_certificate};
131
+ #endif // SYNKIT_MAPPER_TEST_HOOKS
132
+
133
+ std::fill(conditioned_dual_statistics, conditioned_dual_statistics + 6, 0);
134
+ bool original_profile_zero = false;
135
+ try {
136
+ const bool polish =
137
+ r.query == SYNKIT_MINIMUM_CLASSES || r.query == SYNKIT_MINIMUM_PROOF;
138
+ if (!pabs::prepare_seed(p, budget, polish, seed, s.incumbent2,
139
+ s.lower_bound2, &original_profile_zero)) {
140
+ s.model_seconds += elapsed(stage);
141
+ return unsupported(s);
142
+ }
143
+
144
+ if (r.query == SYNKIT_MINIMUM_PROOF &&
145
+ (!original_profile_zero || s.incumbent2 > 8) &&
146
+ s.incumbent2 > s.lower_bound2 && budget.remaining() > 0.2) {
147
+ const int64_t dual = conditioned_overlap_dual_floor(
148
+ p, budget, std::min(0.03, budget.remaining() * 0.05),
149
+ root_certificate);
150
+ if (dual > s.incumbent2)
151
+ throw std::runtime_error("Invalid overlap dual bound");
152
+ s.lower_bound2 = std::max(s.lower_bound2, dual);
153
+ }
154
+ if (r.query == SYNKIT_MINIMUM_PROOF && n <= 256 &&
155
+ s.incumbent2 > s.lower_bound2 && budget.remaining() > 0.05) {
156
+ const int64_t lp_floor = sparse_root_lp::run(
157
+ p, budget, std::min(20.0, budget.remaining() * 0.7), s.incumbent2,
158
+ &seed, &s.incumbent2, &assignment_certificate);
159
+ budget.check();
160
+ if (lp_floor > s.incumbent2)
161
+ throw std::runtime_error("Invalid exact sparse LP bound");
162
+ s.lower_bound2 = std::max(s.lower_bound2, lp_floor);
163
+ }
164
+
165
+ if (r.query == SYNKIT_MINIMUM_PROOF && s.incumbent2 == s.lower_bound2) {
166
+ budget.check();
167
+ synkit_mapper_store_pmcd_witness(n, seed.data(), s.incumbent2, 1);
168
+ s.minimum_proven = 1;
169
+ s.minimum2 = s.incumbent2;
170
+ s.search_complete = 1;
171
+ s.model_seconds += elapsed(stage);
172
+ return 0;
173
+ }
174
+ } catch (...) {
175
+ s.model_seconds += elapsed(stage);
176
+ throw;
177
+ }
178
+ s.model_seconds += elapsed(stage);
179
+
180
+ // Eligibility uses the initial profile relaxation, before subsequent exact
181
+ // bounds strengthen it. This schedules an additional edge-deck proof only.
182
+ if ((r.query == SYNKIT_MINIMUM_CLASSES || r.query == SYNKIT_MINIMUM_PROOF) &&
183
+ original_profile_zero && s.incumbent2 > s.lower_bound2 && n <= 512) {
184
+ stage = Clock::now();
185
+ int64_t mass_a = 0, mass_b = 0, g = 0, edge_a = 0, edge_b = 0;
186
+ for (int i = 0; i < n; ++i)
187
+ for (int j = 0; j < i; ++j) {
188
+ mass_a += p.a2[i * n + j];
189
+ mass_b += p.b2[i * n + j];
190
+ g = std::gcd(g, p.a2[i * n + j]);
191
+ g = std::gcd(g, p.b2[i * n + j]);
192
+ edge_a += p.a2[i * n + j] > 0;
193
+ edge_b += p.b2[i * n + j] > 0;
194
+ }
195
+ const int units = g == 1 ? 3 : 2;
196
+ int64_t families[6] = {};
197
+ const bool small_families =
198
+ g > 0 && mass_a == mass_b &&
199
+ pabs::edge_deck_sizes(n, p.a2, p.b2, p.types_r, p.types_p, units,
200
+ families) == 0 &&
201
+ families[units - 1] <= 60000 && families[units + 2] <= 60000;
202
+ budget.check();
203
+ if (g > 0 && mass_a == mass_b && s.incumbent2 <= 16 * g &&
204
+ s.lower_bound2 < 2LL * (units + 1) * g && small_families) {
205
+ const double allowance = std::min(0.65, budget.remaining() * 0.70);
206
+ Perm candidate(n);
207
+ int64_t lower2 = 0, witness2 = -1;
208
+ const int result =
209
+ pabs::edge_deck(n, p.a2, p.b2, p.types_r, p.types_p, units, allowance,
210
+ 2000000, s.incumbent2, candidate.data(), &lower2,
211
+ &witness2, bridge_deck_statistics);
212
+ bridge_deck_statistics[12] = result;
213
+ budget.check();
214
+ if (result >= 0 && lower2 >= 0) {
215
+ if (lower2 > s.incumbent2)
216
+ throw std::runtime_error("Overlap bound exceeds feasible incumbent");
217
+ if (result == 1) {
218
+ const int64_t score = mapping_cost2(
219
+ p, std::vector<int32_t>(candidate.begin(), candidate.end()));
220
+ if (score != witness2 || score != lower2 || score < s.lower_bound2)
221
+ throw std::runtime_error("Invalid overlap minimum witness");
222
+ seed = std::move(candidate);
223
+ s.incumbent2 = score;
224
+ }
225
+ s.lower_bound2 = std::max(s.lower_bound2, lower2);
226
+ bridge_deck_statistics[13] = s.lower_bound2;
227
+ if (s.incumbent2 == s.lower_bound2) {
228
+ s.minimum_proven = 1;
229
+ s.minimum2 = s.incumbent2;
230
+ synkit_mapper_store_pmcd_witness(n, seed.data(), s.incumbent2, 1);
231
+ }
232
+ }
233
+ }
234
+ s.optimization_seconds += elapsed(stage);
235
+ }
236
+
237
+ int64_t raw[6] = {};
238
+ if (r.query == SYNKIT_MINIMUM_CLASSES || r.query == SYNKIT_MINIMUM_PROOF) {
239
+ if (!s.minimum_proven) {
240
+ int best4 = 0;
241
+ Perm best(n);
242
+ stage = Clock::now();
243
+ int status = native_minimum_impl(
244
+ n, types.size(), levels.size() - 1, budget.remaining(), a.data(),
245
+ b.data(), cr.data(), cp.data(), order.data(), pred.data(), pg.data(),
246
+ pg.size() / n, rg.data(), rg.size() / n, seed.data(), best.data(),
247
+ &best4, raw, 0, 0, false, static_cast<int>(2 * s.lower_bound2),
248
+ root_certificate.ready ? &root_certificate : nullptr,
249
+ conditioned_dual_statistics, nullptr,
250
+ assignment_certificate.ready
251
+ ? +[](const int *mapping, const int *used, [[maybe_unused]] int target, void *data) {
252
+ auto &certificate = *static_cast<
253
+ sparse_root_lp::AssignmentCertificate *>(data);
254
+ const int64_t bound = certificate.bound(mapping, used);
255
+ #ifdef SYNKIT_MAPPER_TEST_HOOKS
256
+ ++certificate.calls;
257
+ certificate.prunes += 2 * bound > target;
258
+ #endif // SYNKIT_MAPPER_TEST_HOOKS
259
+ return bound;
260
+ }
261
+ : nullptr,
262
+ &assignment_certificate);
263
+ s.optimization_seconds += elapsed(stage);
264
+ s.nodes += raw[0];
265
+ s.leaves += raw[1];
266
+ if (status < 0)
267
+ throw std::runtime_error("Legacy PABS minimum kernel error");
268
+ s.incumbent2 =
269
+ mapping_cost2(p, std::vector<int32_t>(best.begin(), best.end()));
270
+ if (best4 != 2 * s.incumbent2)
271
+ throw std::runtime_error("Invalid minimum witness units");
272
+ if (status) {
273
+ stopped(s, SYNKIT_STOP_TIME);
274
+ return 0;
275
+ }
276
+ synkit_mapper_store_pmcd_witness(n, best.data(), s.incumbent2, 1);
277
+ s.minimum_proven = 1;
278
+ s.minimum2 = s.incumbent2;
279
+ s.lower_bound2 = s.minimum2;
280
+ }
281
+ if (r.query == SYNKIT_MINIMUM_PROOF) {
282
+ s.search_complete = 1;
283
+ return 0;
284
+ }
285
+ }
286
+ budget.check();
287
+ int64_t target = (r.query == SYNKIT_MINIMUM_CLASSES ? s.minimum2 : r.target2);
288
+ if (r.query != SYNKIT_AT_MOST_DISTANCE && target > maximum2) {
289
+ s.search_complete = 1;
290
+ s.labeled_count = 0;
291
+ return 0;
292
+ }
293
+ target = std::min(target, maximum2);
294
+ Receiver receiver{p, r, callback, userdata, s, budget};
295
+ stage = Clock::now();
296
+ int status = synkit_distance_range(
297
+ n, types.size(), levels.size() - 1,
298
+ r.query == SYNKIT_AT_MOST_DISTANCE ? 0 : static_cast<int>(2 * target),
299
+ static_cast<int>(2 * target), budget.remaining(), r.max_candidates,
300
+ a.data(), b.data(), cr.data(), cp.data(), order.data(), pred.data(),
301
+ pg.data(), pg.size() / n, rg.data(), rg.size() / n, Receiver::receive,
302
+ &receiver, raw);
303
+ s.enumeration_seconds += elapsed(stage);
304
+ s.nodes += raw[0];
305
+ s.leaves += raw[1];
306
+ if (status < 0)
307
+ throw std::runtime_error("Legacy PABS range kernel error");
308
+ if (status) {
309
+ stopped(s, s.reason ? s.reason
310
+ : status == 2 ? SYNKIT_STOP_CANDIDATES
311
+ : status == 3 ? SYNKIT_STOP_CALLBACK
312
+ : SYNKIT_STOP_TIME);
313
+ } else
314
+ s.search_complete = 1;
315
+ s.labeled_count = rg.empty() && pg.empty() ? s.candidate_count : -1;
316
+ return 0;
317
+ }
318
+ } // namespace synkit_mapper
319
+
320
+ #include "objective_reduction.inc"
321
+
322
+ #ifdef SYNKIT_MAPPER_TEST_HOOKS
323
+ #include "test_hooks.inc"
324
+ #endif
325
+
326
+ #ifdef SYNKIT_MAPPER_TEST_HOOKS
327
+ extern "C" int synkit_private_lp_assignment_statistics(int64_t *out,
328
+ int capacity) {
329
+ if (!out || capacity < 6)
330
+ return -1;
331
+ std::copy(lp_assignment_statistics, lp_assignment_statistics + 6, out);
332
+ return 6;
333
+ }
334
+ #endif // SYNKIT_MAPPER_TEST_HOOKS