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
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  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 +1,640 @@
1
+ // Private to bridge.cpp; not a standalone translation unit.
2
+ // Only neighbors of the two source or target vertices can contribute to a
3
+ // two-swap delta. All four weights vanish outside this union. The inverse
4
+ // permutation is maintained on acceptance; no feasible mapping is restricted.
5
+ class SparseSeedSwap {
6
+ const Problem &p;
7
+ std::vector<Perm> left, right;
8
+ std::vector<uint32_t> marked;
9
+ uint32_t epoch = 0;
10
+ bool ready = false;
11
+ void prepare() {
12
+ if (ready)
13
+ return;
14
+ left.resize(p.n);
15
+ right.resize(p.n);
16
+ marked.assign(p.n, 0);
17
+ for (int i = 0; i < p.n; ++i)
18
+ for (int j = 0; j < p.n; ++j)
19
+ if (i != j) {
20
+ if (p.a2[i * p.n + j])
21
+ left[i].push_back(j);
22
+ if (p.b2[i * p.n + j])
23
+ right[i].push_back(j);
24
+ }
25
+ ready = true;
26
+ }
27
+
28
+ public:
29
+ explicit SparseSeedSwap(const Problem &problem) : p(problem) {}
30
+ int64_t delta(const Perm &mapping, const Perm &inverse, int i, int j) {
31
+ prepare();
32
+ if (++epoch == 0) {
33
+ std::fill(marked.begin(), marked.end(), 0);
34
+ epoch = 1;
35
+ }
36
+ const int a = mapping[i], b = mapping[j];
37
+ int64_t change = 0;
38
+ auto visit = [&](int k) {
39
+ if (k == i || k == j || marked[k] == epoch)
40
+ return;
41
+ marked[k] = epoch;
42
+ const int c = mapping[k];
43
+ change += std::abs(p.a2[i * p.n + k] - p.b2[b * p.n + c]) +
44
+ std::abs(p.a2[j * p.n + k] - p.b2[a * p.n + c]) -
45
+ std::abs(p.a2[i * p.n + k] - p.b2[a * p.n + c]) -
46
+ std::abs(p.a2[j * p.n + k] - p.b2[b * p.n + c]);
47
+ };
48
+ for (int k : left[i])
49
+ visit(k);
50
+ for (int k : left[j])
51
+ visit(k);
52
+ for (int k : right[a])
53
+ visit(inverse[k]);
54
+ for (int k : right[b])
55
+ visit(inverse[k]);
56
+ return change;
57
+ }
58
+ int64_t overlap(const Perm &mapping, int i, int j) {
59
+ prepare();
60
+ int64_t reward = 0;
61
+ for (int k : left[i])
62
+ reward += std::min(p.a2[i * p.n + k], p.b2[j * p.n + mapping[k]]);
63
+ return reward;
64
+ }
65
+ static void accept(Perm &mapping, Perm &inverse, int i, int j) {
66
+ std::swap(mapping[i], mapping[j]);
67
+ inverse[mapping[i]] = i;
68
+ inverse[mapping[j]] = j;
69
+ }
70
+ };
71
+
72
+ // Soft structural context only proposes a full typed permutation. In
73
+ // particular equal WL colors never remove a domain value or certify symmetry.
74
+ // Unique-type vertices retain fixed colors so score-anchor degree changes do
75
+ // not contaminate every heavy-atom color in subsequent refinement rounds.
76
+ void propose_context_seed(const Problem &p, const Perm &profile,
77
+ const std::vector<int> &tr,
78
+ const std::vector<int> &tp, Perm &best,
79
+ int64_t &best2, int64_t lower2, Budget &budget) {
80
+ const int n = p.n;
81
+ if (n > 512 || budget.remaining() < 0.15)
82
+ return;
83
+ const auto begun = Clock::now();
84
+ const double allowance = std::min(0.02, budget.remaining() * 0.05);
85
+ auto expired = [&]() {
86
+ budget.check();
87
+ return elapsed(begun) >= allowance;
88
+ };
89
+ std::map<int, int> counts;
90
+ for (int t : tr)
91
+ ++counts[t];
92
+ std::vector<Perm> ar(n), ap(n);
93
+ for (int i = 0; i < n; ++i) {
94
+ if (expired())
95
+ return;
96
+ for (int j = 0; j < n; ++j) {
97
+ if (p.a2[i * n + j])
98
+ ar[i].push_back(j);
99
+ if (p.b2[i * n + j])
100
+ ap[i].push_back(j);
101
+ }
102
+ }
103
+ Perm cr = tr, cp = tp, penalty(n * n, 0);
104
+ for (int round = 0; round < 3; ++round) {
105
+ std::map<std::vector<int64_t>, int> intern;
106
+ auto refine = [&](const Perm &colors, const Perm &types,
107
+ const std::vector<Perm> &adj, const int64_t *matrix,
108
+ Perm &next) {
109
+ next.resize(n);
110
+ for (int i = 0; i < n; ++i) {
111
+ if (expired())
112
+ return false;
113
+ std::vector<int64_t> key;
114
+ if (counts.at(types[i]) == 1)
115
+ key = {-1, types[i]};
116
+ else {
117
+ std::vector<std::pair<int, int64_t>> incident;
118
+ for (int j : adj[i])
119
+ incident.emplace_back(colors[j], matrix[i * n + j]);
120
+ std::sort(incident.begin(), incident.end());
121
+ key = {0, colors[i], static_cast<int64_t>(incident.size())};
122
+ for (auto entry : incident) {
123
+ key.push_back(entry.first);
124
+ key.push_back(entry.second);
125
+ }
126
+ }
127
+ next[i] = intern.emplace(std::move(key), intern.size()).first->second;
128
+ }
129
+ return true;
130
+ };
131
+ Perm nr, np;
132
+ if (!refine(cr, tr, ar, p.a2, nr) || !refine(cp, tp, ap, p.b2, np))
133
+ return;
134
+ cr = std::move(nr);
135
+ cp = std::move(np);
136
+ for (int i = 0; i < n; ++i) {
137
+ if (expired())
138
+ return;
139
+ for (int j = 0; j < n; ++j)
140
+ if (tr[i] == tp[j] && cr[i] != cp[j])
141
+ penalty[i * n + j] += round + 1;
142
+ }
143
+ }
144
+ Perm costs(n * n, INF), candidate, u, v;
145
+ for (int i = 0; i < n; ++i) {
146
+ if (expired())
147
+ return;
148
+ for (int j = 0; j < n; ++j)
149
+ if (tr[i] == tp[j]) {
150
+ // Keep all arithmetic strictly within the existing LAP integer range.
151
+ if (profile[i * n + j] > (INF - 7) / 8)
152
+ return;
153
+ costs[i * n + j] = profile[i * n + j] * 8 + penalty[i * n + j];
154
+ }
155
+ }
156
+ if (Solver::assignment(costs, n, candidate, u, v) >= INF / 2)
157
+ return;
158
+ budget.check();
159
+ std::vector<bool> seen(n, false);
160
+ for (int i = 0; i < n; ++i) {
161
+ const int j = candidate[i];
162
+ if (j < 0 || j >= n || seen[j] || tr[i] != tp[j])
163
+ throw std::runtime_error("Invalid context-LAP seed");
164
+ seen[j] = true;
165
+ }
166
+ int64_t score = mapping_cost2(
167
+ p, std::vector<int32_t>(candidate.begin(), candidate.end()));
168
+ budget.check();
169
+
170
+ // Polish this alternative without discarding the already polished profile
171
+ // incumbent. Every swap is a full typed permutation; its exact sparse delta
172
+ // is independently checked again with the whole score before acceptance.
173
+ Perm inverse(n), marked(n, -1);
174
+ for (int i = 0; i < n; ++i)
175
+ inverse[candidate[i]] = i;
176
+ int epoch = 0;
177
+ for (int pass = 0; pass < 8 && score > lower2 && !expired(); ++pass) {
178
+ bool improved = false;
179
+ for (int i = 0; i < n && score > lower2 && !expired(); ++i)
180
+ for (int j = i + 1; j < n && score > lower2; ++j) {
181
+ if (tr[i] != tr[j])
182
+ continue;
183
+ ++epoch;
184
+ const int a = candidate[i], b = candidate[j];
185
+ int64_t delta = 0;
186
+ auto visit = [&](int k) {
187
+ if (k == i || k == j || marked[k] == epoch)
188
+ return;
189
+ marked[k] = epoch;
190
+ const int c = candidate[k];
191
+ delta += std::abs(p.a2[i * n + k] - p.b2[b * n + c]) +
192
+ std::abs(p.a2[j * n + k] - p.b2[a * n + c]) -
193
+ std::abs(p.a2[i * n + k] - p.b2[a * n + c]) -
194
+ std::abs(p.a2[j * n + k] - p.b2[b * n + c]);
195
+ };
196
+ for (int k : ar[i])
197
+ visit(k);
198
+ for (int k : ar[j])
199
+ visit(k);
200
+ for (int k : ap[a])
201
+ visit(inverse[k]);
202
+ for (int k : ap[b])
203
+ visit(inverse[k]);
204
+ if (delta < 0) {
205
+ std::swap(candidate[i], candidate[j]);
206
+ inverse[candidate[i]] = i;
207
+ inverse[candidate[j]] = j;
208
+ score += delta;
209
+ improved = true;
210
+ }
211
+ }
212
+ if (!improved)
213
+ break;
214
+ }
215
+ if (score != mapping_cost2(
216
+ p, std::vector<int32_t>(candidate.begin(), candidate.end())))
217
+ throw std::runtime_error("Context seed polish disagrees with full score");
218
+ budget.check();
219
+ if (score < best2) {
220
+ best = std::move(candidate);
221
+ best2 = score;
222
+ }
223
+ }
224
+ // This entire routine supplies upper candidates only. Balanced WL cells are
225
+ // temporary labels for one restricted SLAP proposal; they never enter exact
226
+ // domains, lower bounds, endpoint groups, or enumeration/classification.
227
+ static thread_local int64_t coherent_seed_statistics[20] = {};
228
+ static thread_local Perm coherent_seed_mapping;
229
+
230
+ double propose_coherent_seed(const Problem &p, const Perm &profile,
231
+ const Perm &tr, const Perm &tp, Perm &best,
232
+ int64_t &best2, int64_t lower2, Budget &budget) {
233
+ const int n = p.n;
234
+ const double remaining = budget.remaining();
235
+ if (n < 256 || n > 512 || best2 - lower2 < 24 ||
236
+ (remaining >= 0 && remaining < 0.25))
237
+ return 0;
238
+ const auto begun = Clock::now();
239
+ // Borrow from, rather than supplement, the existing large-problem SLAP
240
+ // allowance. Its later unrestricted call is debited by all elapsed work.
241
+ const double nominal = remaining < 0 ? 1.0 : std::min(1.0, remaining * 0.20);
242
+ const double allowance = std::min(0.15, nominal * 0.90);
243
+ coherent_seed_statistics[0] = 1;
244
+ coherent_seed_statistics[2] = best2;
245
+ coherent_seed_statistics[15] = static_cast<int64_t>(allowance * 1e9);
246
+ auto expired = [&]() {
247
+ budget.check();
248
+ return elapsed(begun) >= allowance;
249
+ };
250
+ auto finish = [&]() {
251
+ const double seconds = elapsed(begun);
252
+ coherent_seed_statistics[11] = best2;
253
+ coherent_seed_statistics[14] = static_cast<int64_t>(seconds * 1e9);
254
+ coherent_seed_statistics[16] = coherent_seed_statistics[14];
255
+ return seconds;
256
+ };
257
+ std::map<int, int> counts;
258
+ for (int t : tr)
259
+ ++counts[t];
260
+ std::vector<Perm> ar(n), ap(n);
261
+ for (int i = 0; i < n; ++i) {
262
+ if (expired())
263
+ return finish();
264
+ for (int j = 0; j < n; ++j) {
265
+ if (p.a2[i * n + j])
266
+ ar[i].push_back(j);
267
+ if (p.b2[i * n + j])
268
+ ap[i].push_back(j);
269
+ }
270
+ }
271
+ Perm cr = tr, cp = tp, penalty(n * n, 0), chosen_r, chosen_p;
272
+ int smallest_maximum = n + 1, selected_depth = 0;
273
+ double smallest_ambiguity = std::numeric_limits<double>::infinity();
274
+ std::vector<double> log_factorial(n + 1, 0.0);
275
+ for (int i = 2; i <= n; ++i)
276
+ log_factorial[i] = log_factorial[i - 1] + std::log(static_cast<double>(i));
277
+ for (int round = 0; round < 32; ++round) {
278
+ std::map<std::vector<int64_t>, int> intern;
279
+ auto refine = [&](const Perm &colors, const Perm &types,
280
+ const std::vector<Perm> &adj, const int64_t *matrix,
281
+ Perm &next) {
282
+ next.resize(n);
283
+ for (int i = 0; i < n; ++i) {
284
+ if (expired())
285
+ return false;
286
+ std::vector<int64_t> key;
287
+ if (counts.at(types[i]) == 1)
288
+ key = {-1, types[i]};
289
+ else {
290
+ std::vector<std::pair<int, int64_t>> incident;
291
+ for (int j : adj[i])
292
+ incident.emplace_back(colors[j], matrix[i * n + j]);
293
+ std::sort(incident.begin(), incident.end());
294
+ key = {0, colors[i], static_cast<int64_t>(incident.size())};
295
+ for (auto edge : incident) {
296
+ key.push_back(edge.first);
297
+ key.push_back(edge.second);
298
+ }
299
+ }
300
+ next[i] = intern.emplace(std::move(key), intern.size()).first->second;
301
+ }
302
+ return true;
303
+ };
304
+ Perm nr, np;
305
+ if (!refine(cr, tr, ar, p.a2, nr) || !refine(cp, tp, ap, p.b2, np))
306
+ return finish();
307
+ cr = std::move(nr);
308
+ cp = std::move(np);
309
+ for (int i = 0; i < n; ++i) {
310
+ if (expired())
311
+ return finish();
312
+ for (int j = 0; j < n; ++j)
313
+ if (tr[i] == tp[j] && cr[i] != cp[j])
314
+ penalty[i * n + j] += round + 1;
315
+ }
316
+ const int depth = round + 1;
317
+ if (depth != 8 && depth != 16 && depth != 32)
318
+ continue;
319
+ std::map<int, int> nr_counts, np_counts;
320
+ for (int c : cr)
321
+ ++nr_counts[c];
322
+ for (int c : cp)
323
+ ++np_counts[c];
324
+ std::map<std::pair<int, int>, int> registry;
325
+ Perm lr(n), lp(n);
326
+ for (int i = 0; i < n; ++i) {
327
+ const int rc = nr_counts[cr[i]] == np_counts[cr[i]] ? cr[i] : -1;
328
+ const int pc = nr_counts[cp[i]] == np_counts[cp[i]] ? cp[i] : -1;
329
+ lr[i] = registry.emplace(std::make_pair(tr[i], rc), registry.size())
330
+ .first->second;
331
+ lp[i] = registry.emplace(std::make_pair(tp[i], pc), registry.size())
332
+ .first->second;
333
+ }
334
+ Perm balance(registry.size(), 0), sizes(registry.size(), 0);
335
+ for (int c : lr) {
336
+ ++balance[c];
337
+ ++sizes[c];
338
+ }
339
+ for (int c : lp)
340
+ --balance[c];
341
+ if (std::any_of(balance.begin(), balance.end(),
342
+ [](int value) { return value != 0; }))
343
+ throw std::runtime_error("Unbalanced coherent heuristic labels");
344
+ const int maximum = *std::max_element(sizes.begin(), sizes.end());
345
+ // Estimate actual SLAP neighborhood-class work. A large fallback cell
346
+ // can already split almost completely against its fixed neighbor labels.
347
+ // These exact signatures only rank candidate starts; they prove nothing.
348
+ double ambiguity = 0;
349
+ int maximum_class = 0;
350
+ for (int side = 0; side < 2; ++side) {
351
+ const auto &labels = side ? lp : lr;
352
+ const auto &adj = side ? ap : ar;
353
+ const auto *matrix = side ? p.b2 : p.a2;
354
+ std::map<std::vector<int64_t>, int> classes;
355
+ for (int i = 0; i < n; ++i) {
356
+ if (expired())
357
+ return finish();
358
+ std::vector<std::pair<int, int64_t>> incident;
359
+ for (int j : adj[i])
360
+ incident.emplace_back(labels[j], matrix[i * n + j]);
361
+ std::sort(incident.begin(), incident.end());
362
+ std::vector<int64_t> key{labels[i],
363
+ static_cast<int64_t>(incident.size())};
364
+ for (auto edge : incident) {
365
+ key.push_back(edge.first);
366
+ key.push_back(edge.second);
367
+ }
368
+ ++classes[std::move(key)];
369
+ }
370
+ for (const auto &entry : classes) {
371
+ ambiguity += log_factorial[entry.second];
372
+ maximum_class = std::max(maximum_class, entry.second);
373
+ }
374
+ }
375
+ if (ambiguity < smallest_ambiguity ||
376
+ (ambiguity == smallest_ambiguity && maximum_class < smallest_maximum)) {
377
+ smallest_maximum = maximum_class;
378
+ smallest_ambiguity = ambiguity;
379
+ chosen_r = std::move(lr);
380
+ chosen_p = std::move(lp);
381
+ selected_depth = depth;
382
+ coherent_seed_statistics[6] = registry.size();
383
+ coherent_seed_statistics[5] = maximum;
384
+ coherent_seed_statistics[18] = maximum_class;
385
+ coherent_seed_statistics[19] = static_cast<int64_t>(ambiguity * 1e6);
386
+ }
387
+ }
388
+ coherent_seed_statistics[4] = selected_depth;
389
+
390
+ Perm candidate(n, -1), u, v;
391
+ for (const auto &entry : counts) {
392
+ if (expired())
393
+ return finish();
394
+ Perm rows, columns;
395
+ for (int i = 0; i < n; ++i)
396
+ if (tr[i] == entry.first)
397
+ rows.push_back(i);
398
+ for (int j = 0; j < n; ++j)
399
+ if (tp[j] == entry.first)
400
+ columns.push_back(j);
401
+ if (rows.size() != columns.size())
402
+ throw std::runtime_error("Coherent proposal hard-type inventory");
403
+ const int size = rows.size();
404
+ Perm costs(size * size), assigned;
405
+ for (int i = 0; i < size; ++i)
406
+ for (int j = 0; j < size; ++j) {
407
+ const int base = profile[rows[i] * n + columns[j]];
408
+ if (base > (INF - 529) / 1024)
409
+ return finish();
410
+ costs[i * size + j] = base * 1024 + penalty[rows[i] * n + columns[j]];
411
+ }
412
+ if (Solver::assignment(costs, size, assigned, u, v) >= INF / 2)
413
+ return finish();
414
+ for (int i = 0; i < size; ++i)
415
+ candidate[rows[i]] = columns[assigned[i]];
416
+ }
417
+ auto retain = [&](const int32_t *mapping, int64_t supplied) {
418
+ std::vector<int32_t> value(mapping, mapping + n);
419
+ std::vector<bool> seen(n, false);
420
+ for (int i = 0; i < n; ++i) {
421
+ const int j = value[i];
422
+ if (j < 0 || j >= n || seen[j] || p.types_r[i] != p.types_p[j])
423
+ throw std::runtime_error("Invalid coherent proposal typed bijection");
424
+ seen[j] = true;
425
+ }
426
+ const int64_t actual = mapping_cost2(p, value);
427
+ if (actual != supplied)
428
+ throw std::runtime_error("Coherent proposal full score mismatch");
429
+ if (actual < best2) {
430
+ best.assign(value.begin(), value.end());
431
+ best2 = actual;
432
+ coherent_seed_mapping = best;
433
+ coherent_seed_statistics[10] = 1;
434
+ }
435
+ };
436
+ const int64_t raw = mapping_cost2(
437
+ p, std::vector<int32_t>(candidate.begin(), candidate.end()));
438
+ retain(candidate.data(), raw);
439
+ coherent_seed_statistics[3] = raw;
440
+ coherent_seed_statistics[1] = 1;
441
+ coherent_seed_statistics[12] = static_cast<int64_t>(elapsed(begun) * 1e9);
442
+ if (!expired() && best2 > lower2) {
443
+ struct Receiver {
444
+ decltype(retain) &accept;
445
+ bool invalid = false;
446
+ static int receive(const int32_t *map, int64_t score, void *pointer) {
447
+ auto &self = *static_cast<Receiver *>(pointer);
448
+ try {
449
+ self.accept(map, score);
450
+ } catch (...) {
451
+ self.invalid = true;
452
+ }
453
+ return 1;
454
+ }
455
+ } receiver{retain};
456
+ Perm flags(n, 0);
457
+ SlapStatistics statistics{};
458
+ const auto slap_begun = Clock::now();
459
+ synkit_slap_solve(n, p.a2, p.b2, chosen_r.data(), chosen_p.data(),
460
+ flags.data(), 10000, allowance - elapsed(begun), -1, 1,
461
+ Receiver::receive, &receiver, &statistics);
462
+ coherent_seed_statistics[7] = statistics.candidates;
463
+ coherent_seed_statistics[8] = statistics.states;
464
+ coherent_seed_statistics[9] = statistics.reason;
465
+ coherent_seed_statistics[13] =
466
+ static_cast<int64_t>(elapsed(slap_begun) * 1e9);
467
+ if (receiver.invalid)
468
+ throw std::runtime_error("Invalid balanced coherent SLAP candidate");
469
+ budget.check();
470
+ }
471
+ return finish();
472
+ }
473
+
474
+ // This is an incumbent heuristic only: all candidates are full typed
475
+ // permutations, independently rescored before being retained. Neither the
476
+ // profile lower bound nor the exact PABS traversal depends on these starts.
477
+ void improve_incumbent(const Problem &p, const Perm &profile_costs,
478
+ const std::vector<int> &types_r,
479
+ const std::vector<int> &types_p, Perm &best,
480
+ int64_t lower2, Budget &budget, int64_t &best2,
481
+ double slap_debit = 0) {
482
+ const int n = p.n;
483
+ const double remaining = budget.remaining();
484
+ const double restart_cap =
485
+ remaining < 0 ? 0.25 : std::min(0.25, remaining * 0.03);
486
+ const double existing_slap_cap =
487
+ (n <= 512 && remaining >= 0)
488
+ ? std::max(0.0, (n <= 256 ? std::min(0.1, remaining * 0.12)
489
+ : std::min(1.0, remaining * 0.20)) -
490
+ slap_debit)
491
+ : 0.0;
492
+ // Same pre-SLAP clock and worst stage envelope; reuse time left by an
493
+ // early candidate instead of testing an already expired 3% timer.
494
+ const double seconds = std::max(restart_cap, existing_slap_cap);
495
+ if (seconds <= 0 || best2 <= lower2)
496
+ return;
497
+ const auto started = Clock::now();
498
+ auto expired = [&]() {
499
+ budget.check();
500
+ return elapsed(started) >= seconds;
501
+ };
502
+ if (n <= 512) {
503
+ struct SeedReceiver {
504
+ const Problem &problem;
505
+ Perm &best;
506
+ int64_t &best2;
507
+ bool invalid = false;
508
+ static int receive(const int32_t *mapping, int64_t cost2, void *pointer) {
509
+ auto &self = *static_cast<SeedReceiver *>(pointer);
510
+ std::vector<int32_t> candidate(mapping, mapping + self.problem.n);
511
+ std::vector<bool> seen(self.problem.n, false);
512
+ for (int i = 0; i < self.problem.n; ++i) {
513
+ const int j = candidate[i];
514
+ if (j < 0 || j >= self.problem.n || seen[j] ||
515
+ self.problem.types_r[i] != self.problem.types_p[j]) {
516
+ self.invalid = true;
517
+ return 1;
518
+ }
519
+ seen[j] = true;
520
+ }
521
+ const int64_t score = mapping_cost2(self.problem, candidate);
522
+ if (score != cost2) {
523
+ self.invalid = true;
524
+ return 1;
525
+ }
526
+ if (score < self.best2) {
527
+ self.best.assign(candidate.begin(), candidate.end());
528
+ self.best2 = score;
529
+ }
530
+ return 1;
531
+ }
532
+ } receiver{p, best, best2};
533
+ // Native SLAP supplies one heuristic candidate only. Its status, proxy
534
+ // costs and WL partitions never provide a bound or restrict PABS domains.
535
+ // Retain the existing small-problem allowance. Larger problems need more
536
+ // time to finish one SLAP candidate; an unfinished heuristic supplies no
537
+ // UB.
538
+ const double slap_seconds =
539
+ std::max(0.0, (n <= 256 ? std::min(0.1, remaining * 0.12)
540
+ : std::min(1.0, remaining * 0.20)) -
541
+ slap_debit);
542
+ coherent_seed_statistics[17] = static_cast<int64_t>(slap_seconds * 1e9);
543
+ std::vector<int32_t> flags(n, 0);
544
+ SlapStatistics statistics{};
545
+ if (slap_seconds > 0)
546
+ synkit_slap_solve(n, p.a2, p.b2, p.types_r, p.types_p, flags.data(),
547
+ 10000, slap_seconds, -1, 1, SeedReceiver::receive,
548
+ &receiver, &statistics);
549
+ if (receiver.invalid)
550
+ throw std::runtime_error("Invalid native SLAP incumbent candidate");
551
+ budget.check();
552
+ }
553
+ uint64_t random = 0x8cc8cebc9273a21bULL;
554
+ auto next = [&]() {
555
+ random ^= random << 13;
556
+ random ^= random >> 7;
557
+ random ^= random << 17;
558
+ return random;
559
+ };
560
+ auto score = [&](const Perm &mapping) {
561
+ return mapping_cost2(p,
562
+ std::vector<int32_t>(mapping.begin(), mapping.end()));
563
+ };
564
+ SparseSeedSwap swap_delta(p);
565
+ auto polish = [&](Perm &mapping) {
566
+ Perm inverse(n);
567
+ for (int k = 0; k < n; ++k)
568
+ inverse[mapping[k]] = k;
569
+ int64_t value = score(mapping);
570
+ for (int pass = 0; pass < 8 && value > lower2 && !expired(); ++pass) {
571
+ bool improved = false;
572
+ for (int i = 0; i < n && !expired(); ++i)
573
+ for (int j = i + 1; j < n; ++j) {
574
+ if (types_r[i] != types_r[j])
575
+ continue;
576
+ const int64_t delta = swap_delta.delta(mapping, inverse, i, j);
577
+ if (delta < 0) {
578
+ SparseSeedSwap::accept(mapping, inverse, i, j);
579
+ value += delta;
580
+ improved = true;
581
+ }
582
+ }
583
+ if (!improved)
584
+ break;
585
+ }
586
+ if (score(mapping) != value)
587
+ throw std::runtime_error("PABS restart seed does not match rescoring");
588
+ return value;
589
+ };
590
+ Perm costs(n * n), candidate, u, v;
591
+ for (int attempt = 0; attempt < 128 && best2 > lower2 && !expired();
592
+ ++attempt) {
593
+ candidate = best;
594
+ if (attempt % 4 == 3) {
595
+ // A deterministic perturbation can leave a two-swap local minimum.
596
+ for (int k = 0; k < 2 + attempt % 7; ++k) {
597
+ const int i = next() % n, j = next() % n;
598
+ if (types_r[i] == types_r[j])
599
+ std::swap(candidate[i], candidate[j]);
600
+ }
601
+ } else if (attempt % 4 == 0) {
602
+ // Perturb only seed costs. The unmodified profile-LAP bound is retained.
603
+ for (int i = 0; i < n; ++i)
604
+ for (int j = 0; j < n; ++j)
605
+ costs[i * n + j] = types_r[i] == types_p[j]
606
+ ? profile_costs[i * n + j] * 8 + next() % 8
607
+ : INF;
608
+ if (Solver::assignment(costs, n, candidate, u, v) >= INF / 2)
609
+ throw std::runtime_error("No compatible PABS restart assignment");
610
+ } else {
611
+ // Since |a-b| = a+b-2min(a,b), overlap-LAP is a useful local proxy.
612
+ // It is used solely to propose a feasible map, never as a lower bound.
613
+ Perm maximum(n, 0);
614
+ for (int i = 0; i < n; ++i) {
615
+ if (expired())
616
+ break;
617
+ for (int j = 0; j < n; ++j)
618
+ if (types_r[i] == types_p[j]) {
619
+ const int reward = swap_delta.overlap(candidate, i, j);
620
+ costs[i * n + j] = reward;
621
+ maximum[i] = std::max(maximum[i], reward);
622
+ }
623
+ }
624
+ if (expired())
625
+ break;
626
+ for (int i = 0; i < n; ++i)
627
+ for (int j = 0; j < n; ++j)
628
+ costs[i * n + j] = types_r[i] == types_p[j]
629
+ ? maximum[i] - costs[i * n + j] + next() % 4
630
+ : INF;
631
+ if (Solver::assignment(costs, n, candidate, u, v) >= INF / 2)
632
+ throw std::runtime_error("No compatible PABS overlap assignment");
633
+ }
634
+ const int64_t value = polish(candidate);
635
+ if (value < best2) {
636
+ best = std::move(candidate);
637
+ best2 = value;
638
+ }
639
+ }
640
+ }