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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  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 +1,383 @@
1
+ """Proof-bearing stereo refinements of immutable graph morphisms."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from dataclasses import dataclass, replace
6
+ from typing import Any, Hashable, Mapping
7
+
8
+ import networkx as nx
9
+
10
+ from synkit.Graph.Stereo.identity import StereoIdentityError
11
+
12
+ from .morphism import GraphMorphism
13
+ from .stereo_morphism_helpers import (
14
+ _build_certificates,
15
+ _frame_profile,
16
+ _transport_configuration,
17
+ _validate_stereo_port_bindings,
18
+ _validate_stored_port_bindings,
19
+ )
20
+ from .stereo_morphism_types import (
21
+ LocalStereoCertificate,
22
+ StereoCertificateStatus,
23
+ StereoInformationPolicy,
24
+ StereoMorphismError,
25
+ StereoMorphismIssue,
26
+ StereoMorphismIssueCode,
27
+ StereoPresenceMode,
28
+ )
29
+
30
+
31
+ @dataclass(frozen=True)
32
+ class StereoMorphism:
33
+ """A graph morphism refined by complete endpoint-local stereo evidence."""
34
+
35
+ graph_morphism: GraphMorphism
36
+ presence_mode: StereoPresenceMode
37
+ information_policy: StereoInformationPolicy
38
+ certificates: tuple[LocalStereoCertificate, ...] = ()
39
+
40
+ def __post_init__(self) -> None:
41
+ if not isinstance(self.presence_mode, StereoPresenceMode):
42
+ object.__setattr__(
43
+ self,
44
+ "presence_mode",
45
+ StereoPresenceMode(self.presence_mode),
46
+ )
47
+ if not isinstance(self.information_policy, StereoInformationPolicy):
48
+ object.__setattr__(
49
+ self,
50
+ "information_policy",
51
+ StereoInformationPolicy(self.information_policy),
52
+ )
53
+ certificates = tuple(
54
+ sorted(
55
+ self.certificates,
56
+ key=lambda item: (
57
+ item.layer,
58
+ repr(item.source_configuration.canonical_form()),
59
+ ),
60
+ )
61
+ )
62
+ object.__setattr__(self, "certificates", certificates)
63
+ _validate_stored_port_bindings(self.graph_morphism, certificates)
64
+ for certificate in certificates:
65
+ if certificate.status is not StereoCertificateStatus.MATCHED:
66
+ continue
67
+ transported = _transport_configuration(
68
+ certificate.source_configuration,
69
+ self.graph_morphism.mapping,
70
+ self.graph_morphism.substitutions,
71
+ )
72
+ target = certificate.target_configuration
73
+ witness = certificate.witness
74
+ relation = certificate.relation
75
+ assert target is not None and witness is not None and relation is not None
76
+ if relation.witness != witness:
77
+ raise StereoMorphismError(
78
+ StereoMorphismIssue(
79
+ StereoMorphismIssueCode.WITNESS_MISMATCH,
80
+ "The relation and local certificate store different witnesses.",
81
+ )
82
+ )
83
+ if witness.apply(transported.frame) != target.frame:
84
+ raise StereoMorphismError(
85
+ StereoMorphismIssue(
86
+ StereoMorphismIssueCode.WITNESS_MISMATCH,
87
+ "A local witness does not replay the transported frame.",
88
+ {"layer": certificate.layer, "shape": transported.shape},
89
+ )
90
+ )
91
+ direct = transported.relation_to(target)
92
+ if direct.kind is not relation.kind or direct.class_id != relation.class_id:
93
+ raise StereoMorphismError(
94
+ StereoMorphismIssue(
95
+ StereoMorphismIssueCode.INVALID_CERTIFICATE,
96
+ "A stored stereo relation disagrees with endpoint classification.",
97
+ )
98
+ )
99
+
100
+ @classmethod
101
+ def from_graphs(
102
+ cls,
103
+ graph_morphism: GraphMorphism,
104
+ source_graph: nx.Graph,
105
+ target_graph: nx.Graph,
106
+ *,
107
+ presence_mode: StereoPresenceMode | str = StereoPresenceMode.REQUIRE,
108
+ information_policy: StereoInformationPolicy | str = (
109
+ StereoInformationPolicy.EXACT
110
+ ),
111
+ information_policies: (
112
+ Mapping[
113
+ str,
114
+ StereoInformationPolicy | str,
115
+ ]
116
+ | None
117
+ ) = None,
118
+ ) -> "StereoMorphism":
119
+ """Construct and validate stereo evidence without retaining either graph."""
120
+ mode = StereoPresenceMode(presence_mode)
121
+ policy = StereoInformationPolicy(information_policy)
122
+ if graph_morphism.source_nodes != frozenset(source_graph.nodes) or (
123
+ graph_morphism.target_nodes != frozenset(target_graph.nodes)
124
+ ):
125
+ raise StereoMorphismError(
126
+ StereoMorphismIssue(
127
+ StereoMorphismIssueCode.GRAPH_NODE_MISMATCH,
128
+ "GraphMorphism endpoint node sets must equal the supplied graphs.",
129
+ )
130
+ )
131
+ try:
132
+ _validate_stereo_port_bindings(
133
+ graph_morphism,
134
+ source_graph,
135
+ target_graph,
136
+ )
137
+ certificates = _build_certificates(
138
+ graph_morphism,
139
+ source_graph,
140
+ target_graph,
141
+ mode,
142
+ policy,
143
+ information_policies or {},
144
+ )
145
+ except StereoIdentityError as exc:
146
+ raise StereoMorphismError(
147
+ StereoMorphismIssue(
148
+ StereoMorphismIssueCode.INVALID_REFERENCE,
149
+ str(exc),
150
+ )
151
+ ) from exc
152
+ return cls(graph_morphism, mode, policy, certificates)
153
+
154
+ @classmethod
155
+ def identity(
156
+ cls,
157
+ object_id: Hashable,
158
+ graph: nx.Graph,
159
+ *,
160
+ presence_mode: StereoPresenceMode | str = StereoPresenceMode.REQUIRE,
161
+ information_policy: StereoInformationPolicy | str = (
162
+ StereoInformationPolicy.EXACT
163
+ ),
164
+ information_policies: (
165
+ Mapping[
166
+ str,
167
+ StereoInformationPolicy | str,
168
+ ]
169
+ | None
170
+ ) = None,
171
+ ) -> "StereoMorphism":
172
+ graph_morphism = GraphMorphism.identity(object_id, frozenset(graph.nodes))
173
+ return cls.from_graphs(
174
+ graph_morphism,
175
+ graph,
176
+ graph,
177
+ presence_mode=presence_mode,
178
+ information_policy=information_policy,
179
+ information_policies=information_policies,
180
+ )
181
+
182
+ def then(self, after: "StereoMorphism") -> "StereoMorphism":
183
+ """Return ``after ∘ self`` and reclassify every endpoint relation."""
184
+ if self.presence_mode is not after.presence_mode or (
185
+ self.information_policy is not after.information_policy
186
+ ):
187
+ raise StereoMorphismError(
188
+ StereoMorphismIssue(
189
+ StereoMorphismIssueCode.POLICY_MISMATCH,
190
+ "Composable stereo morphisms must use identical policies.",
191
+ )
192
+ )
193
+ graph_morphism = self.graph_morphism.then(after.graph_morphism)
194
+ remaining = list(after.certificates)
195
+ composed_certificates = []
196
+ for first in self.certificates:
197
+ if first.status is not StereoCertificateStatus.MATCHED:
198
+ composed_certificates.append(
199
+ replace(
200
+ first, target_configuration=None, relation=None, witness=None
201
+ )
202
+ )
203
+ continue
204
+ intermediate = first.target_configuration
205
+ assert intermediate is not None
206
+ match_index = next(
207
+ (
208
+ index
209
+ for index, candidate in enumerate(remaining)
210
+ if candidate.layer == first.layer
211
+ and candidate.source_configuration.same_configuration(intermediate)
212
+ ),
213
+ None,
214
+ )
215
+ if match_index is None:
216
+ raise StereoMorphismError(
217
+ StereoMorphismIssue(
218
+ StereoMorphismIssueCode.INTERMEDIATE_MISMATCH,
219
+ "A matched intermediate descriptor has no continuation.",
220
+ {"layer": first.layer, "shape": intermediate.shape},
221
+ )
222
+ )
223
+ second = remaining.pop(match_index)
224
+ if second.status is not StereoCertificateStatus.MATCHED:
225
+ composed_certificates.append(
226
+ LocalStereoCertificate(
227
+ first.layer,
228
+ first.source_configuration,
229
+ None,
230
+ None,
231
+ None,
232
+ second.status,
233
+ first.information_policy,
234
+ )
235
+ )
236
+ continue
237
+ target = second.target_configuration
238
+ assert target is not None and first.witness is not None
239
+ assert second.witness is not None
240
+ transported = _transport_configuration(
241
+ first.source_configuration,
242
+ graph_morphism.mapping,
243
+ graph_morphism.substitutions,
244
+ )
245
+ direct = transported.relation_to(target)
246
+ witness = first.witness.then(second.witness)
247
+ if witness.apply(transported.frame) != target.frame:
248
+ raise StereoMorphismError(
249
+ StereoMorphismIssue(
250
+ StereoMorphismIssueCode.WITNESS_MISMATCH,
251
+ "Composed local witnesses do not replay the endpoint frame.",
252
+ )
253
+ )
254
+ relation = replace(direct, witness=witness)
255
+ composed_certificates.append(
256
+ LocalStereoCertificate(
257
+ first.layer,
258
+ first.source_configuration,
259
+ target,
260
+ relation,
261
+ witness,
262
+ StereoCertificateStatus.MATCHED,
263
+ first.information_policy,
264
+ )
265
+ )
266
+ return StereoMorphism(
267
+ graph_morphism,
268
+ self.presence_mode,
269
+ self.information_policy,
270
+ tuple(composed_certificates),
271
+ )
272
+
273
+ def compose(self, after: "StereoMorphism") -> "StereoMorphism":
274
+ return self.then(after)
275
+
276
+ def relabel(
277
+ self,
278
+ source_labels: Mapping[Hashable, Hashable],
279
+ target_labels: Mapping[Hashable, Hashable],
280
+ *,
281
+ source: Hashable | None = None,
282
+ target: Hashable | None = None,
283
+ ) -> "StereoMorphism":
284
+ graph_morphism = self.graph_morphism.relabel(
285
+ source_labels,
286
+ target_labels,
287
+ source=source,
288
+ target=target,
289
+ )
290
+ certificates = []
291
+ for certificate in self.certificates:
292
+ source_configuration = _transport_configuration(
293
+ certificate.source_configuration,
294
+ source_labels,
295
+ )
296
+ target_configuration = (
297
+ None
298
+ if certificate.target_configuration is None
299
+ else _transport_configuration(
300
+ certificate.target_configuration,
301
+ target_labels,
302
+ )
303
+ )
304
+ relation = certificate.relation
305
+ if target_configuration is not None:
306
+ transported = _transport_configuration(
307
+ source_configuration,
308
+ graph_morphism.mapping,
309
+ graph_morphism.substitutions,
310
+ )
311
+ direct = transported.relation_to(target_configuration)
312
+ relation = replace(direct, witness=certificate.witness)
313
+ certificates.append(
314
+ replace(
315
+ certificate,
316
+ source_configuration=source_configuration,
317
+ target_configuration=target_configuration,
318
+ relation=relation,
319
+ )
320
+ )
321
+ return StereoMorphism(
322
+ graph_morphism,
323
+ self.presence_mode,
324
+ self.information_policy,
325
+ tuple(certificates),
326
+ )
327
+
328
+ def canonical_signature(self) -> tuple[Any, ...]:
329
+ """Return a numbering-independent structural/stereo proof signature."""
330
+ wildcard_nodes = frozenset(self.graph_morphism.substitutions)
331
+ records = (
332
+ (
333
+ certificate.layer,
334
+ certificate.status.value,
335
+ certificate.information_policy.value,
336
+ certificate.source_configuration.shape,
337
+ certificate.source_configuration.specification.value,
338
+ (
339
+ None
340
+ if certificate.target_configuration is None
341
+ else certificate.target_configuration.specification.value
342
+ ),
343
+ (
344
+ None
345
+ if certificate.relation is None
346
+ else certificate.relation.kind.value
347
+ ),
348
+ (
349
+ None
350
+ if certificate.relation is None
351
+ else certificate.relation.class_id
352
+ ),
353
+ (
354
+ None
355
+ if certificate.witness is None
356
+ else certificate.witness.permutation.image
357
+ ),
358
+ _frame_profile(
359
+ certificate.source_configuration,
360
+ wildcard_nodes,
361
+ ),
362
+ )
363
+ for certificate in self.certificates
364
+ )
365
+ evidence = tuple(sorted(records, key=repr))
366
+ return (
367
+ self.graph_morphism.canonical_signature(),
368
+ self.presence_mode.value,
369
+ self.information_policy.value,
370
+ evidence,
371
+ )
372
+
373
+
374
+ __all__ = [
375
+ "LocalStereoCertificate",
376
+ "StereoCertificateStatus",
377
+ "StereoInformationPolicy",
378
+ "StereoMorphism",
379
+ "StereoMorphismError",
380
+ "StereoMorphismIssue",
381
+ "StereoMorphismIssueCode",
382
+ "StereoPresenceMode",
383
+ ]