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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  544. synkit/Synthesis/MSR/__init__.py +0 -0
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  550. synkit/Synthesis/RBL/__init__.py +80 -0
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  560. synkit/Synthesis/Reactor/__init__.py +60 -0
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  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
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  575. synkit/Synthesis/Reactor/stereo/__init__.py +1 -0
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  578. synkit/Synthesis/Reactor/variants/__init__.py +1 -0
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  588. synkit/Utils/__init__.py +0 -0
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  599. synkit/Vis/epd/render.py +543 -0
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  608. synkit/Vis/molecule/reaction.py +285 -0
  609. synkit/Vis/molecule_drawer.py +33 -0
  610. synkit/Vis/mtg/__init__.py +17 -0
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  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 +1,877 @@
1
+ """Non-mutating pushout-style construction with explicit provenance."""
2
+
3
+ from __future__ import annotations
4
+
5
+ import copy
6
+ from dataclasses import dataclass, field
7
+ from enum import Enum
8
+ from typing import Any, Hashable, Mapping, Sequence
9
+
10
+ import networkx as nx
11
+
12
+ from synkit.Graph.Stereo import (
13
+ PermutationWitness,
14
+ StereoConfiguration,
15
+ StereoRelation,
16
+ descriptor_id,
17
+ parse_virtual_reference,
18
+ stereo_registry_layers,
19
+ virtual_reference,
20
+ )
21
+ from synkit.Graph.Stereo.legacy import (
22
+ StereoSemanticComparison,
23
+ StereoSemanticsMode,
24
+ legacy_canonical_form,
25
+ legacy_classify_stereo_change,
26
+ )
27
+ from synkit.Graph.Morphism import (
28
+ StereoEffect,
29
+ StereoReferenceDelta,
30
+ StereoTransportError,
31
+ transport_stereo_descriptor,
32
+ transport_stereo_registry,
33
+ )
34
+
35
+ from .identity import stable_value
36
+ from .interface import (
37
+ DEFAULT_INTERFACE_EDGE_KEYS,
38
+ DEFAULT_INTERFACE_NODE_KEYS,
39
+ FusionInterface,
40
+ )
41
+
42
+
43
+ class FusionConstructionIssueCode(str, Enum):
44
+ """Stable construction and audit failures."""
45
+
46
+ UNSUPPORTED_GRAPH = "FUSION_CONSTRUCTION_UNSUPPORTED_GRAPH"
47
+ TARGET_MISMATCH = "FUSION_CONSTRUCTION_TARGET_MISMATCH"
48
+ NODE_CONFLICT = "FUSION_CONSTRUCTION_NODE_CONFLICT"
49
+ EDGE_CONFLICT = "FUSION_CONSTRUCTION_EDGE_CONFLICT"
50
+ STEREO_CONFLICT = "FUSION_CONSTRUCTION_STEREO_CONFLICT"
51
+ SOURCE_MUTATED = "FUSION_CONSTRUCTION_SOURCE_MUTATED"
52
+ ENDPOINT_NONCOMMUTATIVE = "FUSION_ENDPOINT_NONCOMMUTATIVE"
53
+
54
+
55
+ @dataclass(frozen=True)
56
+ class FusionConstructionIssue:
57
+ code: FusionConstructionIssueCode
58
+ message: str
59
+ context: Mapping[str, Any] = field(default_factory=dict)
60
+
61
+ def to_dict(self) -> dict[str, Any]:
62
+ return {
63
+ "code": self.code.value,
64
+ "message": self.message,
65
+ "context": dict(self.context),
66
+ }
67
+
68
+
69
+ class FusionConstructionError(ValueError):
70
+ """Raised when a quotient cannot be constructed without a conflict."""
71
+
72
+ def __init__(self, *issues: FusionConstructionIssue):
73
+ self.issues = tuple(issues)
74
+ super().__init__("; ".join(issue.message for issue in self.issues))
75
+
76
+
77
+ @dataclass(frozen=True)
78
+ class FusionStereoReplay:
79
+ """Result of replaying one local proof-v2 stereo transport."""
80
+
81
+ valid: bool
82
+ issues: tuple[str, ...] = ()
83
+
84
+
85
+ def _configuration_mapping(
86
+ configuration: StereoConfiguration,
87
+ reference_mapping: Mapping[int, int],
88
+ ) -> dict[Any, Any]:
89
+ mapping: dict[Any, Any] = dict(reference_mapping)
90
+ for reference in configuration.frame:
91
+ virtual = parse_virtual_reference(reference)
92
+ if virtual is not None and virtual.center in reference_mapping:
93
+ mapping[reference] = virtual_reference(
94
+ virtual.kind,
95
+ reference_mapping[virtual.center],
96
+ )
97
+ return mapping
98
+
99
+
100
+ def _configuration_payload(configuration: StereoConfiguration) -> dict[str, Any]:
101
+ return {
102
+ "shape": configuration.shape,
103
+ "frame": stable_value(configuration.frame),
104
+ "specification": configuration.specification.value,
105
+ "canonical_frame": stable_value(configuration.canonical_frame),
106
+ }
107
+
108
+
109
+ def _relation_payload(relation: StereoRelation) -> dict[str, Any]:
110
+ return {
111
+ "kind": relation.kind.value,
112
+ "shape": relation.shape,
113
+ "class_id": (
114
+ list(relation.class_id) if relation.class_id is not None else None
115
+ ),
116
+ "witness": (
117
+ list(relation.witness.permutation.image)
118
+ if relation.witness is not None
119
+ else None
120
+ ),
121
+ "source_canonical": stable_value(relation.source_canonical),
122
+ "target_canonical": stable_value(relation.target_canonical),
123
+ }
124
+
125
+
126
+ @dataclass(frozen=True)
127
+ class FusionStereoEvidence:
128
+ """Replayable local orbit evidence for one transported descriptor."""
129
+
130
+ side: str
131
+ layer: str
132
+ source_descriptor_id: str
133
+ target_descriptor_id: str
134
+ effect: StereoEffect
135
+ source_configuration: StereoConfiguration
136
+ interface_configuration: StereoConfiguration
137
+ target_configuration: StereoConfiguration
138
+ reference_mapping: tuple[tuple[int, int], ...]
139
+ source_to_interface: StereoRelation
140
+ interface_to_candidate: StereoRelation
141
+ direct_relation: StereoRelation
142
+ composed_witness: PermutationWitness | None
143
+ endpoint_orbit: tuple[Any, ...]
144
+
145
+ @classmethod
146
+ def create(
147
+ cls,
148
+ *,
149
+ side: str,
150
+ layer: str,
151
+ source_descriptor_id: str,
152
+ target_descriptor_id: str,
153
+ effect: StereoEffect,
154
+ source_configuration: StereoConfiguration,
155
+ interface_configuration: StereoConfiguration,
156
+ target_configuration: StereoConfiguration,
157
+ reference_mapping: Mapping[int, int],
158
+ ) -> "FusionStereoEvidence":
159
+ rebased = source_configuration.relabel(
160
+ _configuration_mapping(source_configuration, reference_mapping)
161
+ )
162
+ source_relation = rebased.relation_to(interface_configuration)
163
+ target_relation = interface_configuration.relation_to(target_configuration)
164
+ direct_relation = rebased.relation_to(target_configuration)
165
+ composed = (
166
+ source_relation.witness.then(target_relation.witness)
167
+ if source_relation.witness is not None
168
+ and target_relation.witness is not None
169
+ else None
170
+ )
171
+ evidence = cls(
172
+ side,
173
+ layer,
174
+ source_descriptor_id,
175
+ target_descriptor_id,
176
+ StereoEffect(effect),
177
+ source_configuration,
178
+ interface_configuration,
179
+ target_configuration,
180
+ tuple(sorted(reference_mapping.items())),
181
+ source_relation,
182
+ target_relation,
183
+ direct_relation,
184
+ composed,
185
+ target_configuration.canonical_frame,
186
+ )
187
+ replay = evidence.replay()
188
+ if not replay.valid:
189
+ raise FusionConstructionError(
190
+ FusionConstructionIssue(
191
+ FusionConstructionIssueCode.STEREO_CONFLICT,
192
+ "Fusion stereo evidence is not replayable.",
193
+ {
194
+ "side": side,
195
+ "layer": layer,
196
+ "descriptor_id": source_descriptor_id,
197
+ "issues": replay.issues,
198
+ },
199
+ )
200
+ )
201
+ return evidence
202
+
203
+ def replay(self) -> FusionStereoReplay:
204
+ issues: list[str] = []
205
+ relations = (
206
+ ("source_to_interface", self.source_to_interface),
207
+ ("interface_to_candidate", self.interface_to_candidate),
208
+ ("direct_relation", self.direct_relation),
209
+ )
210
+ for name, relation in relations:
211
+ if relation.witness is None:
212
+ issues.append(f"{name}:missing_witness")
213
+ rebased = self.source_configuration.relabel(
214
+ _configuration_mapping(
215
+ self.source_configuration,
216
+ dict(self.reference_mapping),
217
+ )
218
+ )
219
+ if self.source_to_interface.witness is not None and (
220
+ self.source_to_interface.witness.apply(rebased.frame)
221
+ != self.interface_configuration.frame
222
+ ):
223
+ issues.append("source_to_interface:witness_replay")
224
+ if self.interface_to_candidate.witness is not None and (
225
+ self.interface_to_candidate.witness.apply(
226
+ self.interface_configuration.frame
227
+ )
228
+ != self.target_configuration.frame
229
+ ):
230
+ issues.append("interface_to_candidate:witness_replay")
231
+ if self.composed_witness is None:
232
+ issues.append("composition:missing_witness")
233
+ elif self.composed_witness.apply(rebased.frame) != (
234
+ self.target_configuration.frame
235
+ ):
236
+ issues.append("composition:witness_replay")
237
+ classified = rebased.relation_to(self.target_configuration)
238
+ if (
239
+ classified.kind is not self.direct_relation.kind
240
+ or classified.class_id != self.direct_relation.class_id
241
+ ):
242
+ issues.append("direct_relation:classification")
243
+ if self.endpoint_orbit != self.target_configuration.canonical_frame:
244
+ issues.append("endpoint:orbit")
245
+ return FusionStereoReplay(not issues, tuple(issues))
246
+
247
+ def canonical_signature(self) -> tuple[Any, ...]:
248
+ """Return numbering- and operand-independent local proof identity."""
249
+ relation_signature = lambda relation: ( # noqa: E731
250
+ relation.kind.value,
251
+ relation.shape,
252
+ relation.class_id,
253
+ (
254
+ relation.witness.permutation.image
255
+ if relation.witness is not None
256
+ else None
257
+ ),
258
+ )
259
+ return (
260
+ self.layer,
261
+ self.effect.value,
262
+ self.source_configuration.shape,
263
+ self.source_configuration.specification.value,
264
+ self.interface_configuration.specification.value,
265
+ self.target_configuration.specification.value,
266
+ len(self.reference_mapping),
267
+ relation_signature(self.source_to_interface),
268
+ relation_signature(self.interface_to_candidate),
269
+ relation_signature(self.direct_relation),
270
+ (
271
+ self.composed_witness.permutation.image
272
+ if self.composed_witness is not None
273
+ else None
274
+ ),
275
+ )
276
+
277
+ def to_dict(self) -> dict[str, Any]:
278
+ return {
279
+ "side": self.side,
280
+ "layer": self.layer,
281
+ "source_descriptor_id": self.source_descriptor_id,
282
+ "target_descriptor_id": self.target_descriptor_id,
283
+ "effect": self.effect.value,
284
+ "source_configuration": _configuration_payload(self.source_configuration),
285
+ "reference_mapping": [list(pair) for pair in self.reference_mapping],
286
+ "interface_configuration": _configuration_payload(
287
+ self.interface_configuration
288
+ ),
289
+ "source_to_interface": _relation_payload(self.source_to_interface),
290
+ "interface_to_candidate": _relation_payload(self.interface_to_candidate),
291
+ "target_configuration": _configuration_payload(self.target_configuration),
292
+ "direct_relation": _relation_payload(self.direct_relation),
293
+ "composed_witness": (
294
+ list(self.composed_witness.permutation.image)
295
+ if self.composed_witness is not None
296
+ else None
297
+ ),
298
+ "endpoint_orbit": stable_value(self.endpoint_orbit),
299
+ }
300
+
301
+
302
+ @dataclass(frozen=True)
303
+ class FusionProvenance:
304
+ """Origin records for every node, edge, and wildcard substitution."""
305
+
306
+ node_sources: tuple[tuple[int, tuple[tuple[str, Hashable], ...]], ...]
307
+ edge_sources: tuple[
308
+ tuple[tuple[int, int], tuple[tuple[str, Hashable, Hashable], ...]], ...
309
+ ]
310
+ wildcard_substitutions: tuple[tuple[Hashable, tuple[Any, ...]], ...] = ()
311
+ stereo_evidence: tuple[FusionStereoEvidence, ...] = ()
312
+ stereo_comparisons: tuple[StereoSemanticComparison, ...] = ()
313
+
314
+ def to_dict(self) -> dict[str, Any]:
315
+ return {
316
+ "node_sources": [
317
+ {
318
+ "fused_node": fused,
319
+ "sources": [
320
+ {"side": side, "node": repr(node)} for side, node in sources
321
+ ],
322
+ }
323
+ for fused, sources in self.node_sources
324
+ ],
325
+ "edge_sources": [
326
+ {
327
+ "fused_edge": edge,
328
+ "sources": [
329
+ {"side": side, "edge": (repr(left), repr(right))}
330
+ for side, left, right in sources
331
+ ],
332
+ }
333
+ for edge, sources in self.edge_sources
334
+ ],
335
+ "wildcard_substitutions": [
336
+ {"interface_node": repr(node), "constraint": stable_value(value)}
337
+ for node, value in self.wildcard_substitutions
338
+ ],
339
+ "stereo_evidence": [
340
+ evidence.to_dict() for evidence in self.stereo_evidence
341
+ ],
342
+ "stereo_comparisons": [
343
+ comparison.to_dict() for comparison in self.stereo_comparisons
344
+ ],
345
+ }
346
+
347
+
348
+ @dataclass(frozen=True)
349
+ class EndpointCertificate:
350
+ """Commuting inclusion evidence for both source graphs."""
351
+
352
+ forward_inclusion: tuple[tuple[Hashable, int], ...]
353
+ backward_inclusion: tuple[tuple[Hashable, int], ...]
354
+ forward_nodes_verified: int
355
+ backward_nodes_verified: int
356
+ forward_edges_verified: int
357
+ backward_edges_verified: int
358
+ replay_status: str = "not_requested"
359
+ replay_reason: str | None = None
360
+
361
+ def digest_payload(self) -> dict[str, Any]:
362
+ return {
363
+ "forward_nodes_verified": self.forward_nodes_verified,
364
+ "backward_nodes_verified": self.backward_nodes_verified,
365
+ "forward_edges_verified": self.forward_edges_verified,
366
+ "backward_edges_verified": self.backward_edges_verified,
367
+ "replay_status": self.replay_status,
368
+ "replay_reason": self.replay_reason,
369
+ }
370
+
371
+ def to_dict(self) -> dict[str, Any]:
372
+ return {
373
+ **self.digest_payload(),
374
+ "forward_inclusion": [
375
+ (repr(source), target) for source, target in self.forward_inclusion
376
+ ],
377
+ "backward_inclusion": [
378
+ (repr(source), target) for source, target in self.backward_inclusion
379
+ ],
380
+ }
381
+
382
+
383
+ @dataclass(frozen=True)
384
+ class FusionConstruction:
385
+ graph: nx.Graph = field(compare=False, repr=False)
386
+ interface: FusionInterface
387
+ provenance: FusionProvenance
388
+ endpoint_certificate: EndpointCertificate
389
+
390
+
391
+ def _legacy_transport_stereo_descriptor(
392
+ descriptor: Any,
393
+ mapping: Mapping[int, int],
394
+ effect: StereoEffect,
395
+ ) -> Any:
396
+ """Reproduce proof-v1 descriptor transport without orbit operations."""
397
+ aligned = transport_stereo_descriptor(
398
+ descriptor,
399
+ mapping,
400
+ StereoReferenceDelta(effect=StereoEffect.RETAIN),
401
+ )
402
+ if effect is StereoEffect.RETAIN:
403
+ return aligned
404
+ if effect is StereoEffect.UNSPECIFIED:
405
+ return type(aligned)(aligned.atoms, None, aligned.provenance)
406
+ if aligned.parity is None or aligned.descriptor_class == "square_planar":
407
+ return aligned
408
+ if aligned.descriptor_class == "planar_bond":
409
+ atoms = (aligned.atoms[1], aligned.atoms[0], *aligned.atoms[2:])
410
+ return type(aligned)(atoms, 0, aligned.provenance)
411
+ return type(aligned)(aligned.atoms, -aligned.parity, aligned.provenance)
412
+
413
+
414
+ def _attribute_signature(
415
+ attributes: Mapping[str, Any], keys: Sequence[str]
416
+ ) -> tuple[Any, ...]:
417
+ return tuple((key, stable_value(attributes.get(key))) for key in keys)
418
+
419
+
420
+ def _is_wildcard(
421
+ attributes: Mapping[str, Any], element_key: str, wildcard_element: Any
422
+ ) -> bool:
423
+ scalar = (
424
+ wildcard_element[0]
425
+ if isinstance(wildcard_element, (tuple, list))
426
+ else wildcard_element
427
+ )
428
+ return attributes.get(element_key) in (wildcard_element, scalar)
429
+
430
+
431
+ def _merge_node_attributes(
432
+ forward: Mapping[str, Any],
433
+ backward: Mapping[str, Any],
434
+ *,
435
+ node_keys: Sequence[str],
436
+ element_key: str,
437
+ wildcard_element: Any,
438
+ ) -> dict[str, Any]:
439
+ forward_wc = _is_wildcard(forward, element_key, wildcard_element)
440
+ backward_wc = _is_wildcard(backward, element_key, wildcard_element)
441
+ if not forward_wc and not backward_wc:
442
+ if _attribute_signature(forward, node_keys) != _attribute_signature(
443
+ backward, node_keys
444
+ ):
445
+ raise FusionConstructionError(
446
+ FusionConstructionIssue(
447
+ FusionConstructionIssueCode.NODE_CONFLICT,
448
+ "Concrete quotient nodes have incompatible attributes.",
449
+ )
450
+ )
451
+ preferred = forward
452
+ elif forward_wc and not backward_wc:
453
+ preferred = backward
454
+ elif backward_wc and not forward_wc:
455
+ preferred = forward
456
+ else:
457
+ preferred = forward
458
+ merged = copy.deepcopy(dict(preferred))
459
+ wildcard_only_keys = {
460
+ "wildcard_role",
461
+ "owner",
462
+ "elements",
463
+ "charges",
464
+ "radicals",
465
+ "bond_orders",
466
+ "side",
467
+ "capacity",
468
+ "resource_budget",
469
+ "stereo_slot",
470
+ "virtual_kind",
471
+ "mapped_identity",
472
+ "materialization",
473
+ }
474
+ resolving_to_concrete = forward_wc != backward_wc
475
+ for key, value in backward.items():
476
+ # The constraint is retained in the interface/provenance proof. Once
477
+ # its wildcard node is identified with a concrete atom, wildcard-only
478
+ # metadata must not leak onto that concrete quotient node.
479
+ if resolving_to_concrete and key in wildcard_only_keys:
480
+ continue
481
+ merged.setdefault(key, copy.deepcopy(value))
482
+ return merged
483
+
484
+
485
+ def _merge_graph_stereo(
486
+ fused: nx.Graph,
487
+ forward: nx.Graph,
488
+ backward: nx.Graph,
489
+ interface: FusionInterface,
490
+ forward_inclusion: Mapping[Hashable, int],
491
+ backward_inclusion: Mapping[Hashable, int],
492
+ *,
493
+ semantics: str = "orbit",
494
+ ) -> tuple[
495
+ tuple[FusionStereoEvidence, ...],
496
+ tuple[StereoSemanticComparison, ...],
497
+ ]:
498
+ """Merge already map-stable descriptor registries without inference."""
499
+ combined: dict[str, dict[str, Any]] = {}
500
+ proof: list[FusionStereoEvidence] = []
501
+ consumed_effects: set[tuple[str, str, str]] = set()
502
+ comparisons: list[StereoSemanticComparison] = []
503
+ semantics_mode = StereoSemanticsMode(semantics)
504
+ effects = {
505
+ (side, layer, descriptor_id): effect
506
+ for side, layer, descriptor_id, effect in interface.stereo_effects
507
+ }
508
+ for side, graph, inclusion in (
509
+ ("forward", forward, forward_inclusion),
510
+ ("backward", backward, backward_inclusion),
511
+ ):
512
+ for layer, registry in stereo_registry_layers(graph).items():
513
+ reference_mapping = _stereo_reference_mapping(
514
+ graph, fused, inclusion, layer
515
+ )
516
+ deltas = {
517
+ descriptor_key: StereoReferenceDelta(
518
+ effect=effects.get(
519
+ (side, layer, descriptor_key), StereoEffect.RETAIN
520
+ )
521
+ )
522
+ for descriptor_key in registry
523
+ }
524
+ try:
525
+ transport_stereo_registry(registry, reference_mapping, deltas)
526
+ except StereoTransportError as exc:
527
+ raise FusionConstructionError(
528
+ FusionConstructionIssue(
529
+ FusionConstructionIssueCode.STEREO_CONFLICT,
530
+ "A source stereo frame cannot be transported into the quotient.",
531
+ {"side": side, "layer": layer, "reason": str(exc)},
532
+ )
533
+ ) from exc
534
+ target = combined.setdefault(layer, {})
535
+ for source_key in sorted(registry):
536
+ source_descriptor = registry[source_key]
537
+ delta = deltas[source_key]
538
+ interface_descriptor = transport_stereo_descriptor(
539
+ source_descriptor,
540
+ reference_mapping,
541
+ StereoReferenceDelta(effect=StereoEffect.RETAIN),
542
+ )
543
+ orbit_descriptor = transport_stereo_descriptor(
544
+ source_descriptor,
545
+ reference_mapping,
546
+ delta,
547
+ )
548
+ legacy_descriptor = _legacy_transport_stereo_descriptor(
549
+ source_descriptor,
550
+ reference_mapping,
551
+ delta.effect,
552
+ )
553
+ descriptor = (
554
+ legacy_descriptor
555
+ if semantics_mode is StereoSemanticsMode.LEGACY
556
+ else orbit_descriptor
557
+ )
558
+ descriptor_key = descriptor_id(descriptor)
559
+ if (side, layer, source_key) in effects:
560
+ consumed_effects.add((side, layer, source_key))
561
+ previous = target.get(descriptor_key)
562
+ if previous is not None and previous != descriptor:
563
+ raise FusionConstructionError(
564
+ FusionConstructionIssue(
565
+ FusionConstructionIssueCode.STEREO_CONFLICT,
566
+ "Source stereo descriptors disagree in the quotient.",
567
+ {"descriptor_id": descriptor_key, "layer": layer},
568
+ )
569
+ )
570
+ target[descriptor_key] = descriptor
571
+ evidence = FusionStereoEvidence.create(
572
+ side=side,
573
+ layer=layer,
574
+ source_descriptor_id=source_key,
575
+ target_descriptor_id=descriptor_key,
576
+ effect=delta.effect,
577
+ source_configuration=source_descriptor.configuration,
578
+ interface_configuration=interface_descriptor.configuration,
579
+ target_configuration=descriptor.configuration,
580
+ reference_mapping=reference_mapping,
581
+ )
582
+ proof.append(evidence)
583
+ if semantics_mode is StereoSemanticsMode.COMPARE:
584
+ comparisons.append(
585
+ StereoSemanticComparison.create(
586
+ "fusion_stereo_transport",
587
+ legacy_canonical_form(orbit_descriptor),
588
+ legacy_canonical_form(legacy_descriptor),
589
+ )
590
+ )
591
+ legacy_projection = legacy_classify_stereo_change(
592
+ interface_descriptor,
593
+ legacy_descriptor,
594
+ )
595
+ legacy_relation = {
596
+ "RETAINED": "equivalent",
597
+ "INVERTED": "opposite",
598
+ }.get(legacy_projection, "unspecified")
599
+ expected_divergence = None
600
+ if (
601
+ evidence.interface_to_candidate.kind.value == "reconfigured"
602
+ and evidence.interface_to_candidate.shape
603
+ in {"trigonal_bipyramidal", "octahedral"}
604
+ and delta.effect is StereoEffect.INVERT
605
+ ):
606
+ expected_divergence = "nonbinary_orbit_reconfiguration"
607
+ comparisons.append(
608
+ StereoSemanticComparison.create(
609
+ "fusion_stereo_relation",
610
+ evidence.interface_to_candidate.kind.value,
611
+ legacy_relation,
612
+ expected_divergence=expected_divergence,
613
+ )
614
+ )
615
+ if combined:
616
+ fused.graph["stereo_descriptors"] = combined
617
+ unknown_effects = set(effects) - consumed_effects
618
+ if unknown_effects:
619
+ raise FusionConstructionError(
620
+ FusionConstructionIssue(
621
+ FusionConstructionIssueCode.STEREO_CONFLICT,
622
+ "A declared fusion stereo effect has no source descriptor.",
623
+ {"effects": tuple(sorted(unknown_effects))},
624
+ )
625
+ )
626
+ return (
627
+ tuple(
628
+ sorted(
629
+ proof,
630
+ key=lambda evidence: (
631
+ evidence.canonical_signature(),
632
+ evidence.side,
633
+ evidence.layer,
634
+ evidence.source_descriptor_id,
635
+ ),
636
+ )
637
+ ),
638
+ tuple(comparisons),
639
+ )
640
+
641
+
642
+ def _layer_reference(
643
+ graph: nx.Graph,
644
+ node: Hashable,
645
+ layer: str,
646
+ ) -> Hashable:
647
+ atom_map = graph.nodes[node].get("atom_map")
648
+ if isinstance(atom_map, (tuple, list)) and len(atom_map) == 2:
649
+ index = {"reactant": 0, "product": 1}.get(layer)
650
+ if index is not None and type(atom_map[index]) is int:
651
+ return atom_map[index]
652
+ if type(atom_map) is int:
653
+ return atom_map
654
+ return node
655
+
656
+
657
+ def _stereo_reference_mapping(
658
+ source: nx.Graph,
659
+ fused: nx.Graph,
660
+ inclusion: Mapping[Hashable, int],
661
+ layer: str,
662
+ ) -> dict[int, int]:
663
+ mapping: dict[int, int] = {}
664
+ for source_node, fused_node in inclusion.items():
665
+ source_reference = _layer_reference(source, source_node, layer)
666
+ target_reference = _layer_reference(fused, fused_node, layer)
667
+ if type(source_reference) is not int or type(target_reference) is not int:
668
+ continue
669
+ previous = mapping.get(source_reference)
670
+ if previous is not None and previous != target_reference:
671
+ raise FusionConstructionError(
672
+ FusionConstructionIssue(
673
+ FusionConstructionIssueCode.STEREO_CONFLICT,
674
+ "A stereo reference has ambiguous quotient images.",
675
+ {"reference": source_reference},
676
+ )
677
+ )
678
+ mapping[source_reference] = target_reference
679
+ return mapping
680
+
681
+
682
+ def _verify_endpoint(
683
+ source: nx.Graph,
684
+ fused: nx.Graph,
685
+ inclusion: Mapping[Hashable, int],
686
+ ) -> tuple[int, int]:
687
+ if set(inclusion) != set(source.nodes):
688
+ raise FusionConstructionError(
689
+ FusionConstructionIssue(
690
+ FusionConstructionIssueCode.ENDPOINT_NONCOMMUTATIVE,
691
+ "Endpoint inclusion is not total.",
692
+ )
693
+ )
694
+ for left, right in source.edges:
695
+ if not fused.has_edge(inclusion[left], inclusion[right]):
696
+ raise FusionConstructionError(
697
+ FusionConstructionIssue(
698
+ FusionConstructionIssueCode.ENDPOINT_NONCOMMUTATIVE,
699
+ "A source edge is absent from the fused quotient.",
700
+ {"edge": (repr(left), repr(right))},
701
+ )
702
+ )
703
+ return source.number_of_nodes(), source.number_of_edges()
704
+
705
+
706
+ def _publish_stereo_diagnostics(
707
+ target: list[StereoSemanticComparison] | None,
708
+ values: tuple[StereoSemanticComparison, ...],
709
+ ) -> None:
710
+ if target is not None:
711
+ target.extend(values)
712
+
713
+
714
+ def construct_pushout(
715
+ forward_graph: nx.Graph,
716
+ backward_graph: nx.Graph,
717
+ interface: FusionInterface,
718
+ *,
719
+ node_keys: Sequence[str] = DEFAULT_INTERFACE_NODE_KEYS,
720
+ edge_keys: Sequence[str] = DEFAULT_INTERFACE_EDGE_KEYS,
721
+ element_key: str = "element",
722
+ wildcard_element: Any = "*",
723
+ replay_status: str = "not_requested",
724
+ replay_reason: str | None = None,
725
+ stereo_semantics: str = "orbit",
726
+ stereo_diagnostics: list[StereoSemanticComparison] | None = None,
727
+ ) -> FusionConstruction:
728
+ """Construct a pushout-like quotient after all interface checks pass."""
729
+ if any(
730
+ isinstance(graph, (nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph))
731
+ for graph in (forward_graph, backward_graph)
732
+ ):
733
+ raise FusionConstructionError(
734
+ FusionConstructionIssue(
735
+ FusionConstructionIssueCode.UNSUPPORTED_GRAPH,
736
+ "Sprint 15 verified fusion currently requires simple undirected graphs.",
737
+ )
738
+ )
739
+ if interface.forward_morphism.target_nodes != frozenset(forward_graph.nodes) or (
740
+ interface.backward_morphism.target_nodes != frozenset(backward_graph.nodes)
741
+ ):
742
+ raise FusionConstructionError(
743
+ FusionConstructionIssue(
744
+ FusionConstructionIssueCode.TARGET_MISMATCH,
745
+ "Interface arms do not target the supplied source graphs.",
746
+ )
747
+ )
748
+
749
+ forward_snapshot = copy.deepcopy(forward_graph)
750
+ backward_snapshot = copy.deepcopy(backward_graph)
751
+ forward_arm = interface.forward_morphism.mapping
752
+ backward_arm = interface.backward_morphism.mapping
753
+ fused = nx.Graph()
754
+ forward_inclusion: dict[Hashable, int] = {}
755
+ backward_inclusion: dict[Hashable, int] = {}
756
+ node_sources: dict[int, list[tuple[str, Hashable]]] = {}
757
+ next_node = 1
758
+
759
+ for interface_node in sorted(interface.interface_nodes, key=repr):
760
+ forward_node = forward_arm[interface_node]
761
+ backward_node = backward_arm[interface_node]
762
+ attributes = _merge_node_attributes(
763
+ forward_graph.nodes[forward_node],
764
+ backward_graph.nodes[backward_node],
765
+ node_keys=node_keys,
766
+ element_key=element_key,
767
+ wildcard_element=wildcard_element,
768
+ )
769
+ fused.add_node(next_node, **attributes)
770
+ forward_inclusion[forward_node] = next_node
771
+ backward_inclusion[backward_node] = next_node
772
+ node_sources[next_node] = [
773
+ ("forward", forward_node),
774
+ ("backward", backward_node),
775
+ ]
776
+ next_node += 1
777
+
778
+ for side, graph, inclusion in (
779
+ ("forward", forward_graph, forward_inclusion),
780
+ ("backward", backward_graph, backward_inclusion),
781
+ ):
782
+ for source_node in sorted(graph.nodes, key=repr):
783
+ if source_node in inclusion:
784
+ continue
785
+ fused.add_node(next_node, **copy.deepcopy(graph.nodes[source_node]))
786
+ inclusion[source_node] = next_node
787
+ node_sources[next_node] = [(side, source_node)]
788
+ next_node += 1
789
+
790
+ edge_sources: dict[tuple[int, int], list[tuple[str, Hashable, Hashable]]] = {}
791
+ for side, graph, inclusion in (
792
+ ("forward", forward_graph, forward_inclusion),
793
+ ("backward", backward_graph, backward_inclusion),
794
+ ):
795
+ for left, right, attributes in graph.edges(data=True):
796
+ fused_left, fused_right = inclusion[left], inclusion[right]
797
+ edge = tuple(sorted((fused_left, fused_right)))
798
+ if fused.has_edge(*edge):
799
+ existing = fused.edges[edge]
800
+ if _attribute_signature(existing, edge_keys) != _attribute_signature(
801
+ attributes, edge_keys
802
+ ):
803
+ raise FusionConstructionError(
804
+ FusionConstructionIssue(
805
+ FusionConstructionIssueCode.EDGE_CONFLICT,
806
+ "Quotient edge attributes conflict across sources.",
807
+ {"edge": edge},
808
+ )
809
+ )
810
+ for key, value in attributes.items():
811
+ existing.setdefault(key, copy.deepcopy(value))
812
+ else:
813
+ fused.add_edge(*edge, **copy.deepcopy(attributes))
814
+ edge_sources.setdefault(edge, []).append((side, left, right))
815
+
816
+ stereo_evidence, stereo_comparisons = _merge_graph_stereo(
817
+ fused,
818
+ forward_graph,
819
+ backward_graph,
820
+ interface,
821
+ forward_inclusion,
822
+ backward_inclusion,
823
+ semantics=stereo_semantics,
824
+ )
825
+ _publish_stereo_diagnostics(stereo_diagnostics, stereo_comparisons)
826
+ forward_counts = _verify_endpoint(forward_graph, fused, forward_inclusion)
827
+ backward_counts = _verify_endpoint(backward_graph, fused, backward_inclusion)
828
+ if not nx.utils.graphs_equal(
829
+ forward_graph, forward_snapshot
830
+ ) or not nx.utils.graphs_equal(backward_graph, backward_snapshot):
831
+ raise FusionConstructionError(
832
+ FusionConstructionIssue(
833
+ FusionConstructionIssueCode.SOURCE_MUTATED,
834
+ "Fusion construction mutated a source graph.",
835
+ )
836
+ )
837
+
838
+ substitutions = tuple(
839
+ sorted(
840
+ (
841
+ (node, constraint.normalized())
842
+ for node, constraint in interface.substitutions.items()
843
+ ),
844
+ key=lambda item: repr(item[0]),
845
+ )
846
+ )
847
+ provenance = FusionProvenance(
848
+ tuple((node, tuple(sources)) for node, sources in sorted(node_sources.items())),
849
+ tuple((edge, tuple(sources)) for edge, sources in sorted(edge_sources.items())),
850
+ substitutions,
851
+ stereo_evidence,
852
+ stereo_comparisons,
853
+ )
854
+ certificate = EndpointCertificate(
855
+ tuple(sorted(forward_inclusion.items(), key=lambda item: repr(item[0]))),
856
+ tuple(sorted(backward_inclusion.items(), key=lambda item: repr(item[0]))),
857
+ forward_counts[0],
858
+ backward_counts[0],
859
+ forward_counts[1],
860
+ backward_counts[1],
861
+ replay_status,
862
+ replay_reason,
863
+ )
864
+ return FusionConstruction(fused, interface, provenance, certificate)
865
+
866
+
867
+ __all__ = [
868
+ "EndpointCertificate",
869
+ "FusionConstruction",
870
+ "FusionConstructionError",
871
+ "FusionConstructionIssue",
872
+ "FusionConstructionIssueCode",
873
+ "FusionProvenance",
874
+ "FusionStereoEvidence",
875
+ "FusionStereoReplay",
876
+ "construct_pushout",
877
+ ]