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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@@ -0,0 +1,138 @@
1
+ #pragma once
2
+
3
+ // Shared unrestricted assignment model for the optional OR-Tools engines.
4
+ // A2/B2 and costs are doubled chemical distance. If y = x_ij AND x_kl,
5
+ // D2 = sum(A2) + sum(B2) - 2 sum(min(A2_ik,B2_jl) y).
6
+ // All three AND inequalities are mandatory, including for numeric shells.
7
+ #include <algorithm>
8
+ #include <cstdint>
9
+ #include <functional>
10
+ #include <limits>
11
+ #include <map>
12
+ #include <stdexcept>
13
+ #include <utility>
14
+ #include <vector>
15
+
16
+ namespace synkit_mapper::solvers::detail {
17
+ constexpr int64_t kInfinity = std::numeric_limits<int64_t>::max() / 4;
18
+ using Terms = std::vector<std::pair<int, int64_t>>;
19
+ struct Row {
20
+ Terms terms;
21
+ int64_t lower, upper;
22
+ };
23
+ struct Product {
24
+ int variable, left, right;
25
+ int64_t benefit;
26
+ };
27
+ struct Formulation {
28
+ int n = 0, cost = -1, variables = 0;
29
+ int64_t maximum = 0;
30
+ std::vector<int> x;
31
+ std::vector<Row> rows;
32
+ std::vector<Product> products;
33
+ int64_t aggregate_constraints = 0;
34
+ int64_t accounted_bytes() const {
35
+ int64_t size = sizeof(*this) + x.capacity() * sizeof(int) +
36
+ rows.capacity() * sizeof(Row) +
37
+ products.capacity() * sizeof(Product);
38
+ for (const auto &row : rows)
39
+ size += row.terms.capacity() * sizeof(Terms::value_type);
40
+ return size;
41
+ }
42
+ int variable() {
43
+ if (variables == std::numeric_limits<int>::max())
44
+ throw std::overflow_error(
45
+ "Assignment model exceeds int variable indices");
46
+ return variables++;
47
+ }
48
+ void add(Terms terms, int64_t lower, int64_t upper) {
49
+ rows.push_back({std::move(terms), lower, upper});
50
+ }
51
+ };
52
+
53
+ inline Formulation formulate(int n, const int64_t *a, const int64_t *b,
54
+ const int32_t *left, const int32_t *right,
55
+ const std::function<void()> &check,
56
+ const uint8_t *allowed = nullptr) {
57
+ Formulation f;
58
+ f.n = n;
59
+ f.x.resize(static_cast<size_t>(n) * n, -1);
60
+ for (int i = 0; i < n; ++i) {
61
+ check();
62
+ Terms row;
63
+ for (int j = 0; j < n; ++j)
64
+ if (left[i] == right[j] && (!allowed || allowed[i * n + j])) {
65
+ int x = f.variable();
66
+ f.x[i * n + j] = x;
67
+ row.emplace_back(x, 1);
68
+ }
69
+ f.add(std::move(row), 1, 1);
70
+ }
71
+ for (int j = 0; j < n; ++j) {
72
+ check();
73
+ Terms column;
74
+ for (int i = 0; i < n; ++i)
75
+ if (f.x[i * n + j] >= 0)
76
+ column.emplace_back(f.x[i * n + j], 1);
77
+ f.add(std::move(column), 1, 1);
78
+ }
79
+ struct Edge {
80
+ int i, k;
81
+ int64_t weight;
82
+ };
83
+ std::vector<Edge> left_edges, right_edges;
84
+ for (int i = 0; i < n; ++i) {
85
+ check();
86
+ for (int k = i + 1; k < n; ++k) {
87
+ if (a[i * n + k])
88
+ left_edges.push_back({i, k, a[i * n + k]});
89
+ if (b[i * n + k])
90
+ right_edges.push_back({i, k, b[i * n + k]});
91
+ int64_t increment = a[i * n + k] + b[i * n + k];
92
+ if (increment > kInfinity - f.maximum)
93
+ throw std::overflow_error(
94
+ "Assignment cost exceeds supported integer range");
95
+ f.maximum += increment;
96
+ }
97
+ }
98
+ Terms cost;
99
+ size_t checks = 0;
100
+ for (const auto &e : left_edges) {
101
+ check();
102
+ std::map<int, Terms> aggregate;
103
+ for (const auto &g : right_edges)
104
+ for (int direction = 0; direction != 2; ++direction) {
105
+ if (!(++checks % 1024))
106
+ check();
107
+ int j = direction ? g.k : g.i, l = direction ? g.i : g.k;
108
+ int u = f.x[e.i * n + j], v = f.x[e.k * n + l];
109
+ if (u < 0 || v < 0)
110
+ continue;
111
+ int y = f.variable();
112
+ f.add({{y, 1}, {u, -1}}, -kInfinity, 0);
113
+ f.add({{y, 1}, {v, -1}}, -kInfinity, 0);
114
+ f.add({{y, 1}, {u, -1}, {v, -1}}, -1, kInfinity);
115
+ int64_t benefit = 2 * std::min(e.weight, g.weight);
116
+ cost.emplace_back(y, benefit);
117
+ f.products.push_back({y, u, v, benefit});
118
+ aggregate[u].emplace_back(y, 1);
119
+ aggregate[v].emplace_back(y, 1);
120
+ }
121
+ // RLT strengthening: for a fixed source edge and one endpoint image,
122
+ // at most one product can be selected. In integral models this follows
123
+ // from bijectivity; the aggregate inequality strengthens the MILP LP.
124
+ for (auto &[assignment, terms] : aggregate) {
125
+ check();
126
+ if (terms.size() < 2)
127
+ continue;
128
+ terms.emplace_back(assignment, -1);
129
+ f.add(std::move(terms), -kInfinity, 0);
130
+ ++f.aggregate_constraints;
131
+ }
132
+ }
133
+ f.cost = f.variable();
134
+ cost.emplace_back(f.cost, 1);
135
+ f.add(std::move(cost), f.maximum, f.maximum);
136
+ return f;
137
+ }
138
+ } // namespace synkit_mapper::solvers::detail
@@ -0,0 +1,526 @@
1
+ #include "formulation.h"
2
+ #include "seed.h"
3
+ #include "synkit_mapper/core/runtime.h"
4
+ #include "synkit_mapper/solvers/solvers.h"
5
+ #include "weighted_cnf.h"
6
+
7
+ #include <cerrno>
8
+ #include <cstdio>
9
+ #include <cstdlib>
10
+ #include <cstring>
11
+ #include <filesystem>
12
+ #include <fstream>
13
+ #include <memory>
14
+ #include <sstream>
15
+ #include <stdexcept>
16
+ #include <string>
17
+ #include <vector>
18
+
19
+ #if defined(__unix__) || defined(__APPLE__)
20
+ #include <fcntl.h>
21
+ #include <poll.h>
22
+ #include <signal.h>
23
+ #include <sys/resource.h>
24
+ #include <sys/types.h>
25
+ #include <sys/wait.h>
26
+ #include <unistd.h>
27
+ #endif
28
+
29
+ #ifndef SYNKIT_MAPPER_OPENWBO_EXECUTABLE
30
+ #define SYNKIT_MAPPER_OPENWBO_EXECUTABLE ""
31
+ #endif
32
+
33
+ #ifndef SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE
34
+ #define SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE ""
35
+ #endif
36
+
37
+ namespace synkit_mapper {
38
+ namespace {
39
+ struct RunMetadata {
40
+ int64_t products = 0, constraints = 0, formulation_bytes = 0, cnf_bytes = 0,
41
+ cnf_variables = 0, cnf_clauses = 0, seed_cost = -1,
42
+ engine_peak_rss = -1;
43
+ double seed_seconds = 0;
44
+ };
45
+ thread_local RunMetadata metadata;
46
+ bool modern_engine() {
47
+ return std::strlen(SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE) != 0;
48
+ }
49
+ const char *engine_path() {
50
+ return modern_engine() ? SYNKIT_MAPPER_EVALMAXSAT_EXECUTABLE
51
+ : SYNKIT_MAPPER_OPENWBO_EXECUTABLE;
52
+ }
53
+ using solvers::detail::Formulation;
54
+ using solvers::detail::kInfinity;
55
+ using solvers::detail::Terms;
56
+ struct PhaseTimer {
57
+ double &total;
58
+ Clock::time_point start = Clock::now();
59
+ ~PhaseTimer() { total += elapsed(start); }
60
+ };
61
+ #if defined(__unix__) || defined(__APPLE__)
62
+ struct TemporaryFiles {
63
+ std::string directory, input, output;
64
+ TemporaryFiles() {
65
+ auto pattern =
66
+ (std::filesystem::temp_directory_path() / "synkit-maxsat-XXXXXX")
67
+ .string();
68
+ std::vector<char> name(pattern.begin(), pattern.end());
69
+ name.push_back('\0');
70
+ char *created = ::mkdtemp(name.data());
71
+ if (!created)
72
+ throw std::runtime_error("Cannot create MaxSAT temporary directory");
73
+ directory = created;
74
+ input = directory + (modern_engine() ? "/mapping.wcnf" : "/mapping.opb");
75
+ output = directory + "/solver.log";
76
+ }
77
+ ~TemporaryFiles() {
78
+ ::unlink(input.c_str());
79
+ ::unlink(output.c_str());
80
+ ::rmdir(directory.c_str());
81
+ }
82
+ };
83
+ pid_t wait_child(pid_t pid, int *status, int options) {
84
+ #if defined(__linux__) || defined(__APPLE__)
85
+ struct rusage usage{};
86
+ pid_t observed = ::wait4(pid, status, options, &usage);
87
+ if (observed == pid) {
88
+ #if defined(__APPLE__)
89
+ int64_t bytes = usage.ru_maxrss;
90
+ #else
91
+ int64_t bytes = static_cast<int64_t>(usage.ru_maxrss) * 1024;
92
+ #endif
93
+ metadata.engine_peak_rss = std::max(metadata.engine_peak_rss, bytes);
94
+ }
95
+ return observed;
96
+ #else
97
+ return ::waitpid(pid, status, options);
98
+ #endif
99
+ }
100
+ struct Child {
101
+ pid_t pid = -1;
102
+ ~Child() {
103
+ if (pid > 0) {
104
+ ::kill(pid, SIGKILL);
105
+ int status;
106
+ while (wait_child(pid, &status, 0) < 0 && errno == EINTR) {
107
+ }
108
+ }
109
+ }
110
+ };
111
+ struct Response {
112
+ enum State { Unknown, Feasible, Optimum, Infeasible } state = Unknown;
113
+ std::vector<int8_t> values;
114
+ };
115
+
116
+ Response run_openwbo(const TemporaryFiles &files, int variables,
117
+ Budget &budget) {
118
+ budget.check();
119
+ int output = ::open(files.output.c_str(), O_WRONLY | O_CREAT | O_TRUNC, 0600);
120
+ if (output < 0)
121
+ throw std::runtime_error("Cannot open MaxSAT output file");
122
+ const char *executable = engine_path();
123
+ const bool modern = modern_engine();
124
+ Child child;
125
+ child.pid = ::fork();
126
+ if (child.pid == 0) {
127
+ // Only async-signal-safe calls between fork and exec (Python may have
128
+ // other threads). No shell, interpolation, or inherited solver state.
129
+ if (::dup2(output, STDOUT_FILENO) < 0 || ::dup2(output, STDERR_FILENO) < 0)
130
+ ::_exit(126);
131
+ ::close(output);
132
+ if (modern)
133
+ ::execl(executable, executable, "--old", files.input.c_str(),
134
+ static_cast<char *>(nullptr));
135
+ else
136
+ ::execl(executable, executable, "-formula=1", "-algorithm=4",
137
+ "-verbosity=0", "-print-model", files.input.c_str(),
138
+ static_cast<char *>(nullptr));
139
+ ::_exit(127);
140
+ }
141
+ ::close(output);
142
+ if (child.pid < 0)
143
+ throw std::runtime_error("Cannot start native Open-WBO engine");
144
+ int status = 0;
145
+ while (true) {
146
+ budget.check();
147
+ pid_t observed = wait_child(child.pid, &status, WNOHANG);
148
+ if (observed == child.pid) {
149
+ child.pid = -1;
150
+ break;
151
+ }
152
+ if (observed < 0 && errno != EINTR)
153
+ throw std::runtime_error("Cannot wait for native Open-WBO engine");
154
+ ::poll(nullptr, 0,
155
+ 5); // Cancellation/deadline polling; not a solver worker.
156
+ }
157
+ if (!WIFEXITED(status) ||
158
+ (WEXITSTATUS(status) != 0 && WEXITSTATUS(status) != 10 &&
159
+ WEXITSTATUS(status) != 20 && WEXITSTATUS(status) != 30)) {
160
+ std::ifstream failed(files.output);
161
+ std::string diagnostic((std::istreambuf_iterator<char>(failed)), {});
162
+ if (diagnostic.size() > 2000)
163
+ diagnostic = diagnostic.substr(diagnostic.size() - 2000);
164
+ throw std::runtime_error("Native Open-WBO failed (wait status " +
165
+ std::to_string(status) + "): " + diagnostic);
166
+ }
167
+ Response response;
168
+ response.values.resize(variables, -1);
169
+ std::ifstream stream(files.output);
170
+ std::string line;
171
+ while (std::getline(stream, line)) {
172
+ if (line == "s OPTIMUM FOUND")
173
+ response.state = Response::Optimum;
174
+ else if (line == "s UNSATISFIABLE")
175
+ response.state = Response::Infeasible;
176
+ else if (line == "s SATISFIABLE")
177
+ response.state = Response::Feasible;
178
+ else if (line.rfind("v ", 0) == 0) {
179
+ std::istringstream literals(line.substr(2));
180
+ std::string literal;
181
+ size_t parsed = 0;
182
+ while (literals >> literal) {
183
+ if (!(++parsed % 1024))
184
+ budget.check();
185
+ bool positive = literal[0] != '-';
186
+ size_t offset = positive ? 0 : 1;
187
+ if (offset >= literal.size() || (!modern && literal[offset] != 'x'))
188
+ throw std::runtime_error("Unexpected Open-WBO PB model literal");
189
+ size_t prefix = offset + (modern ? 0 : 1), used = 0;
190
+ long long variable = std::stoll(literal.substr(prefix), &used);
191
+ if (used != literal.size() - prefix || variable < 1 ||
192
+ variable > variables)
193
+ throw std::runtime_error("Invalid Open-WBO PB variable identifier");
194
+ response.values[variable - 1] = positive;
195
+ }
196
+ }
197
+ }
198
+ if (!stream.eof())
199
+ throw std::runtime_error("Cannot read Open-WBO output");
200
+ if (response.state == Response::Unknown)
201
+ throw std::runtime_error(
202
+ "Open-WBO terminated without a certified solver status");
203
+ budget.check();
204
+ return response;
205
+ }
206
+
207
+ void expression(std::ostream &out, const Terms &terms, Budget &budget) {
208
+ size_t written = 0;
209
+ for (auto [variable, coefficient] : terms) {
210
+ if (!(++written % 1024))
211
+ budget.check();
212
+ out << (coefficient >= 0 ? " +" : " ") << coefficient << " x"
213
+ << variable + 1;
214
+ }
215
+ }
216
+ void row(std::ostream &out, const Terms &terms, int64_t lower, int64_t upper,
217
+ Budget &budget) {
218
+ if (lower == upper) {
219
+ expression(out, terms, budget);
220
+ out << " = " << lower << " ;\n";
221
+ } else {
222
+ if (lower > -kInfinity) {
223
+ expression(out, terms, budget);
224
+ out << " >= " << lower << " ;\n";
225
+ }
226
+ if (upper < kInfinity) {
227
+ expression(out, terms, budget);
228
+ out << " <= " << upper << " ;\n";
229
+ }
230
+ }
231
+ }
232
+
233
+ // The shared sparse product model is reused, except the integer cost variable
234
+ // becomes one forced Boolean z. The chemical objective is C*z - sum(w*y)
235
+ // with z=1. In the satisfaction phase z=0 and actual cost is constrained by
236
+ // sum(w*y)+z == C-target (or >= for a ball). Each y is an exact conjunction.
237
+ void write_problem(const TemporaryFiles &files, const Formulation &f,
238
+ bool optimize, int query, int64_t target,
239
+ const std::vector<std::vector<int32_t>> &blocked,
240
+ int64_t seed_cost, Budget &budget) {
241
+ std::ofstream stream(files.input, std::ios::binary | std::ios::trunc);
242
+ if (!stream)
243
+ throw std::runtime_error("Cannot write native MaxSAT input");
244
+ stream << "* Native sparse full-space atom assignment, doubled CD\nmin:";
245
+ const auto &cost_terms = f.rows.back().terms;
246
+ if (optimize && f.maximum) {
247
+ stream << " +" << f.maximum << " x" << f.cost + 1;
248
+ size_t written = 0;
249
+ for (auto [variable, coefficient] : cost_terms) {
250
+ if (!(++written % 1024))
251
+ budget.check();
252
+ if (variable != f.cost)
253
+ stream << " -" << coefficient << " x" << variable + 1;
254
+ }
255
+ } else
256
+ stream << " +1 x" << f.cost + 1;
257
+ stream << " ;\n";
258
+ row(stream, {{f.cost, 1}}, optimize && f.maximum ? 1 : 0,
259
+ optimize && f.maximum ? 1 : 0, budget);
260
+ for (size_t i = 0; i + 1 < f.rows.size(); ++i) {
261
+ if (!(i % 1024))
262
+ budget.check();
263
+ row(stream, f.rows[i].terms, f.rows[i].lower, f.rows[i].upper, budget);
264
+ }
265
+ if (optimize && seed_cost >= 0 && f.maximum > seed_cost) {
266
+ Terms overlap;
267
+ for (auto term : cost_terms)
268
+ if (term.first != f.cost)
269
+ overlap.push_back(term);
270
+ row(stream, overlap, f.maximum - seed_cost, kInfinity, budget);
271
+ }
272
+ if (!optimize) {
273
+ int64_t bound = f.maximum - std::min(target, f.maximum);
274
+ row(stream, cost_terms, bound,
275
+ query == SYNKIT_AT_MOST_DISTANCE ? kInfinity : bound, budget);
276
+ }
277
+ for (size_t b = 0; b < blocked.size(); ++b) {
278
+ if (!(b % 256))
279
+ budget.check();
280
+ Terms nogood;
281
+ for (int i = 0; i < f.n; ++i)
282
+ nogood.emplace_back(f.x[i * f.n + blocked[b][i]], 1);
283
+ row(stream, nogood, -kInfinity, f.n - 1, budget);
284
+ }
285
+ // Upstream maps the file read-only, uses strlen(), and incorrectly attempts
286
+ // to write if its length differs from st_size. Keep no interior NUL and
287
+ // ensure kernel zero-padding exists in the final mmap page.
288
+ const auto page_size = ::sysconf(_SC_PAGESIZE);
289
+ if (page_size > 0 && static_cast<int64_t>(stream.tellp()) % page_size == 0)
290
+ stream.put('\n');
291
+ stream.close();
292
+ if (!stream)
293
+ throw std::runtime_error("Failed to complete MaxSAT input file");
294
+ }
295
+
296
+ std::pair<std::vector<int32_t>, int64_t> project(const Problem &problem,
297
+ const Formulation &f,
298
+ const Response &response,
299
+ Budget &budget) {
300
+ std::vector<int32_t> mapping(problem.n, -1);
301
+ for (int i = 0; i < problem.n; ++i)
302
+ for (int j = 0; j < problem.n; ++j) {
303
+ int x = f.x[i * problem.n + j];
304
+ if (x >= 0) {
305
+ if (response.values[x] < 0)
306
+ throw std::runtime_error("Open-WBO omitted an atom variable");
307
+ if (response.values[x])
308
+ mapping[i] = j;
309
+ }
310
+ }
311
+ int64_t cost = mapping_cost2(problem, mapping);
312
+ int64_t actual = f.maximum;
313
+ size_t checked = 0;
314
+ for (auto [variable, coefficient] : f.rows.back().terms)
315
+ if (variable != f.cost) {
316
+ if (!(++checked % 1024))
317
+ budget.check();
318
+ if (response.values[variable] < 0)
319
+ throw std::runtime_error("Open-WBO omitted a product variable");
320
+ actual -= coefficient * response.values[variable];
321
+ }
322
+ if (cost != actual)
323
+ throw std::runtime_error(
324
+ "Open-WBO cost disagrees with independent rescoring");
325
+ return {std::move(mapping), cost};
326
+ }
327
+ #endif
328
+ } // namespace
329
+
330
+ const char *maxsat_solver_version() {
331
+ return modern_engine()
332
+ ? "EvalMaxSAT CLI, OLL/CaDiCaL, external native process"
333
+ : "Open-WBO 2.1, OLL/Glucose4.1, external native process";
334
+ }
335
+ const char *maxsat_run_metadata() {
336
+ static thread_local std::string value;
337
+ std::ostringstream out;
338
+ out << "{\"formulation\":\""
339
+ << (modern_engine() ? "exact_weighted_cnf_seed_v2"
340
+ : "sparse_pb_rlt_seed_v2")
341
+ << "\",\"engine\":\"" << (modern_engine() ? "EvalMaxSAT" : "Open-WBO")
342
+ << "\",\"product_variables\":" << metadata.products
343
+ << ",\"model_constraints\":" << metadata.constraints
344
+ << ",\"accounted_formulation_bytes\":" << metadata.formulation_bytes
345
+ << ",\"accounted_cnf_bytes\":" << metadata.cnf_bytes
346
+ << ",\"cnf_variables\":" << metadata.cnf_variables
347
+ << ",\"cnf_clauses\":" << metadata.cnf_clauses
348
+ << ",\"seed_cost2\":" << metadata.seed_cost
349
+ << ",\"seed_seconds\":" << metadata.seed_seconds
350
+ << ",\"engine_peak_rss_bytes\":" << metadata.engine_peak_rss
351
+ << ",\"engine_peak_rss_scope\":\"child_process_lifetime_including_fork_"
352
+ "exec\""
353
+ << ",\"cnf_reused_for_enumeration\":"
354
+ << (modern_engine() ? "true" : "false")
355
+ << ",\"seed_scope\":\"input_only_feasible_incumbent_bound\"}";
356
+ value = out.str();
357
+ return value.c_str();
358
+ }
359
+
360
+ int solve_maxsat(const Problem &problem, const Request &request,
361
+ Callback callback, void *userdata, Statistics &stats) {
362
+ initialize(stats, request);
363
+ metadata = {};
364
+ Budget budget(request);
365
+ struct Finish {
366
+ Statistics &s;
367
+ Budget &b;
368
+ ~Finish() { s.elapsed_seconds = b.seconds(); }
369
+ } finish{stats, budget};
370
+ if (request.max_states != -1 || request.max_classes != -1 ||
371
+ request.max_frontier != -1 || request.memory_limit_bytes != -1 ||
372
+ request.symmetry || request.classify)
373
+ return unsupported(stats);
374
+ #if defined(__unix__) || defined(__APPLE__)
375
+ if (!std::strlen(engine_path()))
376
+ return unsupported(stats);
377
+ if (::access(engine_path(), X_OK))
378
+ throw std::runtime_error("Configured Open-WBO executable is unavailable");
379
+ stats.labeled_count = 0;
380
+ stats.peak_frontier = stats.peak_frontier_bytes = -1;
381
+ try {
382
+ budget.check();
383
+ Formulation f;
384
+ {
385
+ PhaseTimer timer{stats.model_seconds};
386
+ f = solvers::detail::formulate(problem.n, problem.a2, problem.b2,
387
+ problem.types_r, problem.types_p,
388
+ [&] { budget.check(); });
389
+ }
390
+ if (request.query == SYNKIT_EXACT_DISTANCE && request.target2 > f.maximum) {
391
+ stats.search_complete = 1;
392
+ return 0;
393
+ }
394
+ metadata.products = f.products.size();
395
+ metadata.constraints = f.rows.size();
396
+ metadata.formulation_bytes = f.accounted_bytes();
397
+ {
398
+ PhaseTimer timer{stats.model_seconds};
399
+ PhaseTimer seed_timer{metadata.seed_seconds};
400
+ auto seed = solvers::detail::feasible_seed(problem, budget);
401
+ if (!seed.empty())
402
+ metadata.seed_cost = stats.incumbent2 = mapping_cost2(problem, seed);
403
+ }
404
+ TemporaryFiles files;
405
+ std::vector<std::vector<int32_t>> blocked;
406
+ std::unique_ptr<solvers::detail::WeightedCnf> satisfaction_cnf;
407
+ size_t encoded_blocks = 0;
408
+ auto run = [&](bool optimize, int64_t target) {
409
+ int variables = f.variables;
410
+ {
411
+ PhaseTimer timer{stats.model_seconds};
412
+ if (modern_engine()) {
413
+ std::unique_ptr<solvers::detail::WeightedCnf> optimization_cnf;
414
+ if (optimize)
415
+ optimization_cnf =
416
+ std::make_unique<solvers::detail::WeightedCnf>(f, budget);
417
+ bool fresh = !satisfaction_cnf;
418
+ if (!optimize && fresh)
419
+ satisfaction_cnf =
420
+ std::make_unique<solvers::detail::WeightedCnf>(f, budget);
421
+ auto &cnf = optimize ? *optimization_cnf : *satisfaction_cnf;
422
+ if (optimize) {
423
+ for (const auto &product : f.products)
424
+ cnf.soft.emplace_back(product.benefit, product.variable + 1);
425
+ if (metadata.seed_cost >= 0 && f.maximum > metadata.seed_cost) {
426
+ cnf.build_sum(f);
427
+ cnf.bound(f.maximum - metadata.seed_cost, true);
428
+ }
429
+ } else if (fresh) {
430
+ cnf.build_sum(f);
431
+ cnf.bound(f.maximum - std::min(target, f.maximum), true);
432
+ if (request.query != SYNKIT_AT_MOST_DISTANCE)
433
+ cnf.bound(f.maximum - target, false);
434
+ }
435
+ while (!optimize && encoded_blocks < blocked.size()) {
436
+ budget.check();
437
+ const auto &mapping = blocked[encoded_blocks++];
438
+ std::vector<int> nogood;
439
+ for (int i = 0; i < f.n; ++i)
440
+ nogood.push_back(-f.x[i * f.n + mapping[i]] - 1);
441
+ cnf.add(std::move(nogood));
442
+ }
443
+ variables = cnf.variables;
444
+ metadata.cnf_variables = variables;
445
+ metadata.cnf_clauses = cnf.hard.size() + cnf.soft.size();
446
+ metadata.cnf_bytes =
447
+ std::max(metadata.cnf_bytes, cnf.accounted_bytes());
448
+ cnf.write(files.input);
449
+ } else
450
+ write_problem(files, f, optimize, request.query, target, blocked,
451
+ metadata.seed_cost, budget);
452
+ }
453
+ PhaseTimer timer{optimize ? stats.optimization_seconds
454
+ : stats.enumeration_seconds};
455
+ return run_openwbo(files, variables, budget);
456
+ };
457
+ int64_t target = request.target2;
458
+ if (request.query == SYNKIT_MINIMUM_CLASSES ||
459
+ request.query == SYNKIT_MINIMUM_PROOF) {
460
+ auto response = run(true, 0);
461
+ if (response.state == Response::Infeasible) {
462
+ stats.search_complete = 1;
463
+ return 0;
464
+ }
465
+ auto [mapping, cost] = project(problem, f, response, budget);
466
+ stats.incumbent2 = cost;
467
+ if (response.state != Response::Optimum) {
468
+ stopped(stats,
469
+ cancelled(request) ? SYNKIT_STOP_CANCELLED : SYNKIT_STOP_TIME);
470
+ return 0;
471
+ }
472
+ stats.minimum_proven = 1;
473
+ target = stats.minimum2 = stats.lower_bound2 = cost;
474
+ if (request.query == SYNKIT_MINIMUM_PROOF) {
475
+ stats.search_complete = 1;
476
+ return 0;
477
+ }
478
+ }
479
+ while (true) {
480
+ auto response = run(false, target);
481
+ if (response.state == Response::Infeasible) {
482
+ stats.search_complete = 1;
483
+ return 0;
484
+ }
485
+ auto [mapping, cost] = project(problem, f, response, budget);
486
+ if ((request.query == SYNKIT_AT_MOST_DISTANCE && cost > target) ||
487
+ (request.query != SYNKIT_AT_MOST_DISTANCE && cost != target))
488
+ throw std::runtime_error(
489
+ "Open-WBO emitted a mapping outside the requested shell");
490
+ budget.check();
491
+ ++stats.candidate_count;
492
+ if (stats.incumbent2 < 0 || cost < stats.incumbent2)
493
+ stats.incumbent2 = cost;
494
+ ++stats.leaves;
495
+ stats.labeled_count = stats.candidate_count;
496
+ int stop = 0;
497
+ {
498
+ PhaseTimer callback_timer{stats.callback_seconds};
499
+ PhaseTimer enumeration_timer{stats.enumeration_seconds};
500
+ if (callback)
501
+ stop = callback(mapping.data(), cost, userdata);
502
+ }
503
+ if (stop) {
504
+ stopped(stats, SYNKIT_STOP_CALLBACK);
505
+ return 0;
506
+ }
507
+ budget.check();
508
+ if (request.max_candidates >= 0 &&
509
+ stats.candidate_count >= request.max_candidates) {
510
+ stopped(stats, SYNKIT_STOP_CANDIDATES);
511
+ return 0;
512
+ }
513
+ blocked.push_back(std::move(mapping));
514
+ }
515
+ } catch (const Stop &stop) {
516
+ stopped(stats, stop.reason);
517
+ }
518
+ #else
519
+ (void)problem;
520
+ (void)callback;
521
+ (void)userdata;
522
+ return unsupported(stats);
523
+ #endif
524
+ return 0;
525
+ }
526
+ } // namespace synkit_mapper