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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  308. synkit/Chem/Molecule/derived_stereo_naming.py +165 -0
  309. synkit/Chem/Molecule/descriptors.py +452 -0
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  311. synkit/Chem/Molecule/global_stereo.py +175 -0
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  313. synkit/Chem/Molecule/standardize.py +817 -0
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  316. synkit/Chem/Molecule/valence.py +123 -0
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  318. synkit/Chem/Reaction/__init__.py +20 -0
  319. synkit/Chem/Reaction/aam_validator.py +5 -0
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  324. synkit/Chem/Reaction/explicit_h_audit.py +232 -0
  325. synkit/Chem/Reaction/fix_aam.py +64 -0
  326. synkit/Chem/Reaction/neutralize.py +207 -0
  327. synkit/Chem/Reaction/radical_wildcard.py +224 -0
  328. synkit/Chem/Reaction/standardize.py +203 -0
  329. synkit/Chem/Reaction/tautomerize.py +205 -0
  330. synkit/Chem/__init__.py +1 -0
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  332. synkit/Data/__init__.py +0 -0
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  343. synkit/Graph/Canon/canon_algs.py +228 -0
  344. synkit/Graph/Canon/canon_graph.py +531 -0
  345. synkit/Graph/Canon/cpp/CMakeLists.txt +42 -0
  346. synkit/Graph/Canon/cpp/README.md +123 -0
  347. synkit/Graph/Canon/cpp/examples/canonical_graph.cpp +16 -0
  348. synkit/Graph/Canon/cpp/include/synkit_canon/canon.h +85 -0
  349. synkit/Graph/Canon/cpp/src/canonical.cpp +391 -0
  350. synkit/Graph/Canon/cpp/src/symmetry.h +83 -0
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  367. synkit/Graph/Feature/Fingerprint/__init__.py +0 -0
  368. synkit/Graph/Feature/Fingerprint/wl_rxn_fps.py +222 -0
  369. synkit/Graph/Feature/__init__.py +5 -0
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  372. synkit/Graph/Feature/graph_signature.py +239 -0
  373. synkit/Graph/Feature/hash_fps.py +133 -0
  374. synkit/Graph/Feature/morgan_fps.py +88 -0
  375. synkit/Graph/Feature/path_fps.py +81 -0
  376. synkit/Graph/Feature/wl_hash.py +134 -0
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  378. synkit/Graph/Fusion/candidate.py +559 -0
  379. synkit/Graph/Fusion/constructor.py +877 -0
  380. synkit/Graph/Fusion/identity.py +184 -0
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  388. synkit/Graph/Hyrogen/hextend.py +570 -0
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  393. synkit/Graph/ITS/its_decompose.py +572 -0
  394. synkit/Graph/ITS/its_destruction.py +331 -0
  395. synkit/Graph/ITS/its_expand.py +1251 -0
  396. synkit/Graph/ITS/its_relabel.py +187 -0
  397. synkit/Graph/ITS/its_reverter.py +356 -0
  398. synkit/Graph/ITS/normalize_aam.py +145 -0
  399. synkit/Graph/ITS/partial_its.py +238 -0
  400. synkit/Graph/ITS/rc_extractor.py +656 -0
  401. synkit/Graph/ITS/stereo.py +74 -0
  402. synkit/Graph/MTG/__init__.py +107 -0
  403. synkit/Graph/MTG/gluing.py +451 -0
  404. synkit/Graph/MTG/history.py +928 -0
  405. synkit/Graph/MTG/inventory.py +118 -0
  406. synkit/Graph/MTG/local.py +447 -0
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  408. synkit/Graph/MTG/mtg.py +611 -0
  409. synkit/Graph/MTG/mtg_explore.py +74 -0
  410. synkit/Graph/MTG/observation.py +209 -0
  411. synkit/Graph/MTG/process.py +577 -0
  412. synkit/Graph/MTG/queries.py +66 -0
  413. synkit/Graph/MTG/realization.py +95 -0
  414. synkit/Graph/MTG/series_parallel.py +107 -0
  415. synkit/Graph/MTG/utils.py +424 -0
  416. synkit/Graph/Matcher/__init__.py +10 -0
  417. synkit/Graph/Matcher/approx_mcs.py +1264 -0
  418. synkit/Graph/Matcher/auto_est.py +736 -0
  419. synkit/Graph/Matcher/automorphism.py +314 -0
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  421. synkit/Graph/Matcher/dedup_matches.py +247 -0
  422. synkit/Graph/Matcher/graph_cluster.py +191 -0
  423. synkit/Graph/Matcher/graph_matcher.py +312 -0
  424. synkit/Graph/Matcher/graph_morphism.py +421 -0
  425. synkit/Graph/Matcher/mcs_matcher.py +804 -0
  426. synkit/Graph/Matcher/multi_turbo_iso.py +186 -0
  427. synkit/Graph/Matcher/orbit.py +284 -0
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  429. synkit/Graph/Matcher/sing.py +544 -0
  430. synkit/Graph/Matcher/subgraph_matcher.py +812 -0
  431. synkit/Graph/Matcher/turbo_iso.py +272 -0
  432. synkit/Graph/Matcher/wl_sel.py +537 -0
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  434. synkit/Graph/Mech/conversion.py +1466 -0
  435. synkit/Graph/Mech/conversion_debug.py +237 -0
  436. synkit/Graph/Mech/electron_accounting.py +200 -0
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  449. synkit/Graph/Stereo/_descriptor_serialization.py +138 -0
  450. synkit/Graph/Stereo/canonical.py +648 -0
  451. synkit/Graph/Stereo/changes.py +964 -0
  452. synkit/Graph/Stereo/composition.py +391 -0
  453. synkit/Graph/Stereo/configured.py +946 -0
  454. synkit/Graph/Stereo/couplings.py +245 -0
  455. synkit/Graph/Stereo/descriptors.py +1030 -0
  456. synkit/Graph/Stereo/enumeration.py +597 -0
  457. synkit/Graph/Stereo/extended_descriptors.py +406 -0
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  461. synkit/Graph/Stereo/interchange.py +496 -0
  462. synkit/Graph/Stereo/legacy.py +460 -0
  463. synkit/Graph/Stereo/matching.py +899 -0
  464. synkit/Graph/Stereo/native.py +154 -0
  465. synkit/Graph/Stereo/orbits.py +668 -0
  466. synkit/Graph/Stereo/outcomes.py +99 -0
  467. synkit/Graph/Stereo/pairwise.py +350 -0
  468. synkit/Graph/Stereo/rdkit_adapter.py +662 -0
  469. synkit/Graph/Stereo/rdkit_identity.py +118 -0
  470. synkit/Graph/Stereo/rdkit_resonance.py +140 -0
  471. synkit/Graph/Stereo/reaction_interchange.py +266 -0
  472. synkit/Graph/Stereo/semantics.py +296 -0
  473. synkit/Graph/Stereo/supports.py +257 -0
  474. synkit/Graph/Stereo/wire.py +339 -0
  475. synkit/Graph/Wildcard/__init__.py +0 -0
  476. synkit/Graph/Wildcard/fuse_graph.py +156 -0
  477. synkit/Graph/Wildcard/graph_wc.py +303 -0
  478. synkit/Graph/Wildcard/its_merge.py +857 -0
  479. synkit/Graph/Wildcard/radwc.py +114 -0
  480. synkit/Graph/Wildcard/wc_matcher.py +576 -0
  481. synkit/Graph/Wildcard/wildcard.py +225 -0
  482. synkit/Graph/__init__.py +17 -0
  483. synkit/Graph/canon_graph.py +14 -0
  484. synkit/Graph/syn_graph.py +199 -0
  485. synkit/Graph/utils.py +324 -0
  486. synkit/IO/__init__.py +4 -0
  487. synkit/IO/chem_converter.py +1059 -0
  488. synkit/IO/combinatorial/__init__.py +8 -0
  489. synkit/IO/combinatorial/gml_to_graph.py +223 -0
  490. synkit/IO/combinatorial/graph_to_gml.py +280 -0
  491. synkit/IO/combinatorial/graph_to_smarts.py +186 -0
  492. synkit/IO/combinatorial/smarts_expander.py +147 -0
  493. synkit/IO/combinatorial/smarts_generalizer.py +133 -0
  494. synkit/IO/combinatorial/smarts_to_graph.py +179 -0
  495. synkit/IO/conversion.py +42 -0
  496. synkit/IO/data_io.py +269 -0
  497. synkit/IO/data_process.py +143 -0
  498. synkit/IO/debug.py +73 -0
  499. synkit/IO/gml_to_nx.py +150 -0
  500. synkit/IO/graph_to_mol.py +199 -0
  501. synkit/IO/mol_to_graph.py +1105 -0
  502. synkit/IO/mol_to_graph_chemistry.py +545 -0
  503. synkit/IO/nx_to_gml.py +209 -0
  504. synkit/IO/smiles_to_id.py +123 -0
  505. synkit/Mechanism/__init__.py +151 -0
  506. synkit/Mechanism/adapters.py +136 -0
  507. synkit/Mechanism/audit.py +323 -0
  508. synkit/Mechanism/benchmark.py +638 -0
  509. synkit/Mechanism/compatibility.py +13 -0
  510. synkit/Mechanism/drawing.py +85 -0
  511. synkit/Mechanism/electron_models.py +725 -0
  512. synkit/Mechanism/equivalence.py +521 -0
  513. synkit/Mechanism/evidence.py +262 -0
  514. synkit/Mechanism/interchange.py +141 -0
  515. synkit/Mechanism/model.py +918 -0
  516. synkit/Mechanism/neighbor_stereo.py +312 -0
  517. synkit/Mechanism/radical_data.py +740 -0
  518. synkit/Mechanism/replay.py +986 -0
  519. synkit/Mechanism/schema.py +264 -0
  520. synkit/Mechanism/stereo_state.py +416 -0
  521. synkit/Mechanism/symbols.py +91 -0
  522. synkit/Rule/Apply/__init__.py +35 -0
  523. synkit/Rule/Apply/conditions.py +45 -0
  524. synkit/Rule/Apply/dpo.py +998 -0
  525. synkit/Rule/Apply/rule_matcher.py +218 -0
  526. synkit/Rule/Apply/validation.py +354 -0
  527. synkit/Rule/Compose/__init__.py +106 -0
  528. synkit/Rule/Compose/_identity.py +43 -0
  529. synkit/Rule/Compose/composition.py +976 -0
  530. synkit/Rule/Compose/laws.py +439 -0
  531. synkit/Rule/Compose/search.py +771 -0
  532. synkit/Rule/Compose/synrule.py +170 -0
  533. synkit/Rule/Modify/__init__.py +0 -0
  534. synkit/Rule/Modify/implict_rule.py +56 -0
  535. synkit/Rule/Modify/longest_path.py +92 -0
  536. synkit/Rule/Modify/molecule_rule.py +115 -0
  537. synkit/Rule/Modify/prune_templates.py +78 -0
  538. synkit/Rule/Modify/rule_utils.py +194 -0
  539. synkit/Rule/Modify/strip_rule.py +97 -0
  540. synkit/Rule/__init__.py +28 -0
  541. synkit/Rule/generic_stereo.py +884 -0
  542. synkit/Rule/stereo_identity.py +271 -0
  543. synkit/Rule/syn_rule.py +1090 -0
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  553. synkit/Synthesis/RBL/overlap.py +336 -0
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  556. synkit/Synthesis/RBL/proof.py +370 -0
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  558. synkit/Synthesis/RBL/state.py +169 -0
  559. synkit/Synthesis/RBL/validation.py +1060 -0
  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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  572. synkit/Synthesis/Reactor/output/policy.py +16 -0
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  574. synkit/Synthesis/Reactor/output/structural.py +893 -0
  575. synkit/Synthesis/Reactor/stereo/__init__.py +1 -0
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  577. synkit/Synthesis/Reactor/stereo/mixin.py +780 -0
  578. synkit/Synthesis/Reactor/variants/__init__.py +1 -0
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  580. synkit/Synthesis/Reactor/variants/partial.py +84 -0
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  583. synkit/Synthesis/Reactor/workflow/benchmark.py +143 -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 +1,732 @@
1
+ /*****************************************************************************
2
+ * *
3
+ * Graph-specific auxiliary source file for version 2.9 of nauty. *
4
+ * *
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+ * Subject to conditions and disclaimers in the file COPYRIGHT. *
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+ * *
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+ * CHANGE HISTORY *
8
+ * 16-Nov-00 : initial creation out of nautil.c *
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+ * 22-Apr-01 : added aproto line for Magma *
10
+ * EXTDEFS is no longer required *
11
+ * removed dynamic allocation from refine1() *
12
+ * 21-Nov-01 : use NAUTYREQUIRED in naugraph_check() *
13
+ * 23-Nov-06 : add targetcell(); make bestcell() local *
14
+ * 10-Dec-06 : remove BIGNAUTY *
15
+ * 10-Nov-09 : remove shortish and permutation types *
16
+ * 23-May-10 : add densenauty() *
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+ * 15-Jan-12 : add TLS_ATTR attributes *
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+ * 23-Jan-13 : add some parens to make icc happy *
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+ * 15-Oct-19 : fix default size of dnwork[] to match densenauty() *
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+ * 6-Apr-21 : increase work space in densenauty() *
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+ * *
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+ *****************************************************************************/
23
+
24
+ #define ONE_WORD_SETS
25
+ #include "nauty.h"
26
+
27
+ /* macros for hash-codes: */
28
+ #define MASH(l,i) ((((l) ^ 065435) + (i)) & 077777)
29
+ /* : expression whose long value depends only on long l and int/long i.
30
+ Anything goes, preferably non-commutative. */
31
+
32
+ #define CLEANUP(l) ((int)((l) % 077777))
33
+ /* : expression whose value depends on long l and is less than 077777
34
+ when converted to int then short. Anything goes. */
35
+
36
+ #if MAXM==1
37
+ #define M 1
38
+ #else
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+ #define M m
40
+ #endif
41
+
42
+ /* aproto: header new_nauty_protos.h */
43
+
44
+ dispatchvec dispatch_graph =
45
+ {isautom,testcanlab,updatecan,refine,refine1,cheapautom,targetcell,
46
+ naugraph_freedyn,naugraph_check,NULL,NULL};
47
+
48
+ #if !MAXN
49
+ DYNALLSTAT(set,workset,workset_sz);
50
+ DYNALLSTAT(int,workperm,workperm_sz);
51
+ DYNALLSTAT(int,bucket,bucket_sz);
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+ DYNALLSTAT(set,dnwork,dnwork_sz);
53
+ #else
54
+ static TLS_ATTR set workset[MAXM]; /* used for scratch work */
55
+ static TLS_ATTR int workperm[MAXN];
56
+ static TLS_ATTR int bucket[MAXN+2];
57
+ static TLS_ATTR set dnwork[2*500*MAXM];
58
+ #endif
59
+
60
+ /*****************************************************************************
61
+ * *
62
+ * isautom(g,perm,digraph,m,n) = TRUE iff perm is an automorphism of g *
63
+ * (i.e., g^perm = g). Symmetry is assumed unless digraph = TRUE. *
64
+ * *
65
+ *****************************************************************************/
66
+
67
+ boolean
68
+ isautom(graph *g, int *perm, boolean digraph, int m, int n)
69
+ {
70
+ set *pg;
71
+ int pos;
72
+ set *pgp;
73
+ int posp,i;
74
+
75
+ for (pg = g, i = 0; i < n; pg += M, ++i)
76
+ {
77
+ pgp = GRAPHROW(g,perm[i],M);
78
+ pos = (digraph ? -1 : i);
79
+
80
+ while ((pos = nextelement(pg,M,pos)) >= 0)
81
+ {
82
+ posp = perm[pos];
83
+ if (!ISELEMENT(pgp,posp)) return FALSE;
84
+ }
85
+ }
86
+ return TRUE;
87
+ }
88
+
89
+ /*****************************************************************************
90
+ * *
91
+ * testcanlab(g,canong,lab,samerows,m,n) compares g^lab to canong, *
92
+ * using an ordering which is immaterial since it's only used here. The *
93
+ * value returned is -1,0,1 if g^lab <,=,> canong. *samerows is set to *
94
+ * the number of rows (0..n) of canong which are the same as those of g^lab. *
95
+ * *
96
+ * GLOBALS ACCESSED: workset<rw>,permset(),workperm<rw> *
97
+ * *
98
+ *****************************************************************************/
99
+
100
+ int
101
+ testcanlab(graph *g, graph *canong, int *lab, int *samerows, int m, int n)
102
+ {
103
+ int i,j;
104
+ set *ph;
105
+
106
+ #if !MAXN
107
+ DYNALLOC1(int,workperm,workperm_sz,n,"testcanlab");
108
+ DYNALLOC1(set,workset,workset_sz,m,"testcanlab");
109
+ #endif
110
+
111
+ for (i = 0; i < n; ++i) workperm[lab[i]] = i;
112
+
113
+ for (i = 0, ph = canong; i < n; ++i, ph += M)
114
+ {
115
+ permset(GRAPHROW(g,lab[i],M),workset,M,workperm);
116
+ for (j = 0; j < M; ++j)
117
+ if (workset[j] < ph[j])
118
+ {
119
+ *samerows = i;
120
+ return -1;
121
+ }
122
+ else if (workset[j] > ph[j])
123
+ {
124
+ *samerows = i;
125
+ return 1;
126
+ }
127
+ }
128
+
129
+ *samerows = n;
130
+ return 0;
131
+ }
132
+
133
+ /*****************************************************************************
134
+ * *
135
+ * updatecan(g,canong,lab,samerows,m,n) sets canong = g^lab, assuming *
136
+ * the first samerows of canong are ok already. *
137
+ * *
138
+ * GLOBALS ACCESSED: permset(),workperm<rw> *
139
+ * *
140
+ *****************************************************************************/
141
+
142
+ void
143
+ updatecan(graph *g, graph *canong, int *lab, int samerows, int m, int n)
144
+ {
145
+ int i;
146
+ set *ph;
147
+
148
+ #if !MAXN
149
+ DYNALLOC1(int,workperm,workperm_sz,n,"updatecan");
150
+ #endif
151
+
152
+ for (i = 0; i < n; ++i) workperm[lab[i]] = i;
153
+
154
+ for (i = samerows, ph = GRAPHROW(canong,samerows,M);
155
+ i < n; ++i, ph += M)
156
+ permset(GRAPHROW(g,lab[i],M),ph,M,workperm);
157
+ }
158
+
159
+ /*****************************************************************************
160
+ * *
161
+ * refine(g,lab,ptn,level,numcells,count,active,code,m,n) performs a *
162
+ * refinement operation on the partition at the specified level of the *
163
+ * partition nest (lab,ptn). *numcells is assumed to contain the number of *
164
+ * cells on input, and is updated. The initial set of active cells (alpha *
165
+ * in the paper) is specified in the set active. Precisely, x is in active *
166
+ * iff the cell starting at index x in lab is active. *
167
+ * The resulting partition is equitable if active is correct (see the paper *
168
+ * and the Guide). *
169
+ * *code is set to a value which depends on the fine detail of the *
170
+ * algorithm, but which is independent of the labelling of the graph. *
171
+ * count is used for work space. *
172
+ * *
173
+ * GLOBALS ACCESSED: workset<w>,bit<r>,nextelement(),bucket<w>,workperm<w> *
174
+ * *
175
+ *****************************************************************************/
176
+
177
+ void
178
+ refine(graph *g, int *lab, int *ptn, int level, int *numcells,
179
+ int *count, set *active, int *code, int m, int n)
180
+ {
181
+
182
+ #if MAXM==1
183
+ refine1(g,lab,ptn,level,numcells,count,active,code,m,n);
184
+ }
185
+ #else
186
+
187
+ int i,c1,c2,labc1;
188
+ setword x;
189
+ set *set1,*set2;
190
+ int split1,split2,cell1,cell2;
191
+ int cnt,bmin,bmax;
192
+ long longcode;
193
+ set *gptr;
194
+ int maxcell,maxpos,hint;
195
+
196
+ #if !MAXN
197
+ DYNALLOC1(int,workperm,workperm_sz,n,"refine");
198
+ DYNALLOC1(set,workset,workset_sz,m,"refine");
199
+ DYNALLOC1(int,bucket,bucket_sz,n+2,"refine");
200
+ #endif
201
+
202
+ longcode = *numcells;
203
+ split1 = -1;
204
+ hint = 0;
205
+ maxpos = 0;
206
+ while (*numcells < n && ((split1 = hint, ISELEMENT(active,split1))
207
+ || (split1 = nextelement(active,M,split1)) >= 0
208
+ || (split1 = nextelement(active,M,-1)) >= 0))
209
+ {
210
+ DELELEMENT(active,split1);
211
+ for (split2 = split1; ptn[split2] > level; ++split2) {}
212
+ longcode = MASH(longcode,split1+split2);
213
+ if (split1 == split2) /* trivial splitting cell */
214
+ {
215
+ gptr = GRAPHROW(g,lab[split1],M);
216
+ for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
217
+ {
218
+ for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
219
+ if (cell1 == cell2) continue;
220
+ c1 = cell1;
221
+ c2 = cell2;
222
+ while (c1 <= c2)
223
+ {
224
+ labc1 = lab[c1];
225
+ if (ISELEMENT(gptr,labc1))
226
+ ++c1;
227
+ else
228
+ {
229
+ lab[c1] = lab[c2];
230
+ lab[c2] = labc1;
231
+ --c2;
232
+ }
233
+ }
234
+ if (c2 >= cell1 && c1 <= cell2)
235
+ {
236
+ ptn[c2] = level;
237
+ longcode = MASH(longcode,c2);
238
+ ++*numcells;
239
+ if (ISELEMENT(active,cell1) || c2-cell1 >= cell2-c1)
240
+ {
241
+ ADDELEMENT(active,c1);
242
+ if (c1 == cell2) hint = c1;
243
+ }
244
+ else
245
+ {
246
+ ADDELEMENT(active,cell1);
247
+ if (c2 == cell1) hint = cell1;
248
+ }
249
+ }
250
+ }
251
+ }
252
+
253
+ else /* nontrivial splitting cell */
254
+ {
255
+ EMPTYSET(workset,m);
256
+ for (i = split1; i <= split2; ++i)
257
+ ADDELEMENT(workset,lab[i]);
258
+ longcode = MASH(longcode,split2-split1+1);
259
+
260
+ for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
261
+ {
262
+ for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
263
+ if (cell1 == cell2) continue;
264
+ i = cell1;
265
+ set1 = workset;
266
+ set2 = GRAPHROW(g,lab[i],m);
267
+ cnt = 0;
268
+ for (c1 = m; --c1 >= 0;)
269
+ if ((x = ((*set1++) & (*set2++))) != 0)
270
+ cnt += POPCOUNT(x);
271
+
272
+ count[i] = bmin = bmax = cnt;
273
+ bucket[cnt] = 1;
274
+ while (++i <= cell2)
275
+ {
276
+ set1 = workset;
277
+ set2 = GRAPHROW(g,lab[i],m);
278
+ cnt = 0;
279
+ for (c1 = m; --c1 >= 0;)
280
+ if ((x = ((*set1++) & (*set2++))) != 0)
281
+ cnt += POPCOUNT(x);
282
+
283
+ while (bmin > cnt) bucket[--bmin] = 0;
284
+ while (bmax < cnt) bucket[++bmax] = 0;
285
+ ++bucket[cnt];
286
+ count[i] = cnt;
287
+ }
288
+ if (bmin == bmax)
289
+ {
290
+ longcode = MASH(longcode,bmin+cell1);
291
+ continue;
292
+ }
293
+ c1 = cell1;
294
+ maxcell = -1;
295
+ for (i = bmin; i <= bmax; ++i)
296
+ if (bucket[i])
297
+ {
298
+ c2 = c1 + bucket[i];
299
+ bucket[i] = c1;
300
+ longcode = MASH(longcode,i+c1);
301
+ if (c2-c1 > maxcell)
302
+ {
303
+ maxcell = c2-c1;
304
+ maxpos = c1;
305
+ }
306
+ if (c1 != cell1)
307
+ {
308
+ ADDELEMENT(active,c1);
309
+ if (c2-c1 == 1) hint = c1;
310
+ ++*numcells;
311
+ }
312
+ if (c2 <= cell2) ptn[c2-1] = level;
313
+ c1 = c2;
314
+ }
315
+ for (i = cell1; i <= cell2; ++i)
316
+ workperm[bucket[count[i]]++] = lab[i];
317
+ for (i = cell1; i <= cell2; ++i) lab[i] = workperm[i];
318
+ if (!ISELEMENT(active,cell1))
319
+ {
320
+ ADDELEMENT(active,cell1);
321
+ DELELEMENT(active,maxpos);
322
+ }
323
+ }
324
+ }
325
+ }
326
+
327
+ longcode = MASH(longcode,*numcells);
328
+ *code = CLEANUP(longcode);
329
+ }
330
+ #endif /* else case of MAXM==1 */
331
+
332
+ /*****************************************************************************
333
+ * *
334
+ * refine1(g,lab,ptn,level,numcells,count,active,code,m,n) is the same as *
335
+ * refine(g,lab,ptn,level,numcells,count,active,code,m,n), except that *
336
+ * m==1 is assumed for greater efficiency. The results are identical in all *
337
+ * respects. See refine (above) for the specs. *
338
+ * *
339
+ *****************************************************************************/
340
+
341
+ void
342
+ refine1(graph *g, int *lab, int *ptn, int level, int *numcells,
343
+ int *count, set *active, int *code, int m, int n)
344
+ {
345
+ int i,c1,c2,labc1;
346
+ setword x;
347
+ int split1,split2,cell1,cell2;
348
+ int cnt,bmin,bmax;
349
+ long longcode;
350
+ set *gptr,workset0;
351
+ int maxcell,maxpos,hint;
352
+
353
+ #if !MAXN
354
+ DYNALLOC1(int,workperm,workperm_sz,n,"refine1");
355
+ DYNALLOC1(int,bucket,bucket_sz,n+2,"refine1");
356
+ #endif
357
+
358
+ longcode = *numcells;
359
+ split1 = -1;
360
+ maxpos = 0;
361
+
362
+ hint = 0;
363
+ while (*numcells < n && ((split1 = hint, ISELEMENT1(active,split1))
364
+ || (split1 = nextelement(active,1,split1)) >= 0
365
+ || (split1 = nextelement(active,1,-1)) >= 0))
366
+ {
367
+ DELELEMENT1(active,split1);
368
+ for (split2 = split1; ptn[split2] > level; ++split2) {}
369
+ longcode = MASH(longcode,split1+split2);
370
+ if (split1 == split2) /* trivial splitting cell */
371
+ {
372
+ gptr = GRAPHROW(g,lab[split1],1);
373
+ for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
374
+ {
375
+ for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
376
+ if (cell1 == cell2) continue;
377
+ c1 = cell1;
378
+ c2 = cell2;
379
+ while (c1 <= c2)
380
+ {
381
+ labc1 = lab[c1];
382
+ if (ISELEMENT1(gptr,labc1))
383
+ ++c1;
384
+ else
385
+ {
386
+ lab[c1] = lab[c2];
387
+ lab[c2] = labc1;
388
+ --c2;
389
+ }
390
+ }
391
+ if (c2 >= cell1 && c1 <= cell2)
392
+ {
393
+ ptn[c2] = level;
394
+ longcode = MASH(longcode,c2);
395
+ ++*numcells;
396
+ if (ISELEMENT1(active,cell1) || c2-cell1 >= cell2-c1)
397
+ {
398
+ ADDELEMENT1(active,c1);
399
+ if (c1 == cell2) hint = c1;
400
+ }
401
+ else
402
+ {
403
+ ADDELEMENT1(active,cell1);
404
+ if (c2 == cell1) hint = cell1;
405
+ }
406
+ }
407
+ }
408
+ }
409
+
410
+ else /* nontrivial splitting cell */
411
+ {
412
+ workset0 = 0;
413
+ for (i = split1; i <= split2; ++i)
414
+ ADDELEMENT1(&workset0,lab[i]);
415
+ longcode = MASH(longcode,split2-split1+1);
416
+
417
+ for (cell1 = 0; cell1 < n; cell1 = cell2 + 1)
418
+ {
419
+ for (cell2 = cell1; ptn[cell2] > level; ++cell2) {}
420
+ if (cell1 == cell2) continue;
421
+ i = cell1;
422
+ if ((x = workset0 & g[lab[i]]) != 0)
423
+ cnt = POPCOUNT(x);
424
+ else
425
+ cnt = 0;
426
+ count[i] = bmin = bmax = cnt;
427
+ bucket[cnt] = 1;
428
+ while (++i <= cell2)
429
+ {
430
+ if ((x = workset0 & g[lab[i]]) != 0)
431
+ cnt = POPCOUNT(x);
432
+ else
433
+ cnt = 0;
434
+ while (bmin > cnt) bucket[--bmin] = 0;
435
+ while (bmax < cnt) bucket[++bmax] = 0;
436
+ ++bucket[cnt];
437
+ count[i] = cnt;
438
+ }
439
+ if (bmin == bmax)
440
+ {
441
+ longcode = MASH(longcode,bmin+cell1);
442
+ continue;
443
+ }
444
+ c1 = cell1;
445
+ maxcell = -1;
446
+ for (i = bmin; i <= bmax; ++i)
447
+ if (bucket[i])
448
+ {
449
+ c2 = c1 + bucket[i];
450
+ bucket[i] = c1;
451
+ longcode = MASH(longcode,i+c1);
452
+ if (c2-c1 > maxcell)
453
+ {
454
+ maxcell = c2-c1;
455
+ maxpos = c1;
456
+ }
457
+ if (c1 != cell1)
458
+ {
459
+ ADDELEMENT1(active,c1);
460
+ if (c2-c1 == 1) hint = c1;
461
+ ++*numcells;
462
+ }
463
+ if (c2 <= cell2) ptn[c2-1] = level;
464
+ c1 = c2;
465
+ }
466
+ for (i = cell1; i <= cell2; ++i)
467
+ workperm[bucket[count[i]]++] = lab[i];
468
+ for (i = cell1; i <= cell2; ++i) lab[i] = workperm[i];
469
+ if (!ISELEMENT1(active,cell1))
470
+ {
471
+ ADDELEMENT1(active,cell1);
472
+ DELELEMENT1(active,maxpos);
473
+ }
474
+ }
475
+ }
476
+ }
477
+
478
+ longcode = MASH(longcode,*numcells);
479
+ *code = CLEANUP(longcode);
480
+ }
481
+
482
+ /*****************************************************************************
483
+ * *
484
+ * cheapautom(ptn,level,digraph,n) returns TRUE if the partition at the *
485
+ * specified level in the partition nest (lab,ptn) {lab is not needed here} *
486
+ * satisfies a simple sufficient condition for its cells to be the orbits of *
487
+ * some subgroup of the automorphism group. Otherwise it returns FALSE. *
488
+ * It always returns FALSE if digraph!=FALSE. *
489
+ * *
490
+ * nauty assumes that this function will always return TRUE for any *
491
+ * partition finer than one for which it returns TRUE. *
492
+ * *
493
+ *****************************************************************************/
494
+
495
+ boolean
496
+ cheapautom(int *ptn, int level, boolean digraph, int n)
497
+ {
498
+ int i,k,nnt;
499
+
500
+ if (digraph) return FALSE;
501
+
502
+ k = n;
503
+ nnt = 0;
504
+ for (i = 0; i < n; ++i)
505
+ {
506
+ --k;
507
+ if (ptn[i] > level)
508
+ {
509
+ ++nnt;
510
+ while (ptn[++i] > level) {}
511
+ }
512
+ }
513
+
514
+ return (k <= nnt + 1 || k <= 4);
515
+ }
516
+
517
+ /*****************************************************************************
518
+ * *
519
+ * bestcell(g,lab,ptn,level,tc_level,m,n) returns the index in lab of the *
520
+ * start of the "best non-singleton cell" for fixing. If there is no *
521
+ * non-singleton cell it returns n. *
522
+ * This implementation finds the first cell which is non-trivially joined *
523
+ * to the greatest number of other cells. *
524
+ * *
525
+ * GLOBALS ACCESSED: bit<r>,workperm<rw>,workset<rw>,bucket<rw> *
526
+ * *
527
+ *****************************************************************************/
528
+
529
+ static int
530
+ bestcell(const graph *g, const int *lab, const int *ptn, int level,
531
+ int tc_level, int m, int n)
532
+ {
533
+ int i;
534
+ set *gp;
535
+ setword setword1,setword2;
536
+ int v1,v2,nnt;
537
+
538
+ #if !MAXN
539
+ DYNALLOC1(int,workperm,workperm_sz,n,"bestcell");
540
+ DYNALLOC1(set,workset,workset_sz,m,"bestcell");
541
+ DYNALLOC1(int,bucket,bucket_sz,n+2,"bestcell");
542
+ #endif
543
+
544
+ /* find non-singleton cells: put starts in workperm[0..nnt-1] */
545
+
546
+ i = nnt = 0;
547
+
548
+ while (i < n)
549
+ {
550
+ if (ptn[i] > level)
551
+ {
552
+ workperm[nnt++] = i;
553
+ while (ptn[i] > level) ++i;
554
+ }
555
+ ++i;
556
+ }
557
+
558
+ if (nnt == 0) return n;
559
+
560
+ /* set bucket[i] to # non-trivial neighbours of n.s. cell i */
561
+
562
+ for (i = nnt; --i >= 0;) bucket[i] = 0;
563
+
564
+ for (v2 = 1; v2 < nnt; ++v2)
565
+ {
566
+ EMPTYSET(workset,m);
567
+ i = workperm[v2] - 1;
568
+ do
569
+ {
570
+ ++i;
571
+ ADDELEMENT(workset,lab[i]);
572
+ }
573
+ while (ptn[i] > level);
574
+ for (v1 = 0; v1 < v2; ++v1)
575
+ {
576
+ gp = GRAPHROW(g,lab[workperm[v1]],m);
577
+ #if MAXM==1
578
+ setword1 = *workset & *gp;
579
+ setword2 = *workset & ~*gp;
580
+ #else
581
+ setword1 = setword2 = 0;
582
+ for (i = m; --i >= 0;)
583
+ {
584
+ setword1 |= workset[i] & gp[i];
585
+ setword2 |= workset[i] & ~gp[i];
586
+ }
587
+ #endif
588
+ if (setword1 != 0 && setword2 != 0)
589
+ {
590
+ ++bucket[v1];
591
+ ++bucket[v2];
592
+ }
593
+ }
594
+ }
595
+
596
+ /* find first greatest bucket value */
597
+
598
+ v1 = 0;
599
+ v2 = bucket[0];
600
+ for (i = 1; i < nnt; ++i)
601
+ if (bucket[i] > v2)
602
+ {
603
+ v1 = i;
604
+ v2 = bucket[i];
605
+ }
606
+
607
+ return (int)workperm[v1];
608
+ }
609
+
610
+ /*****************************************************************************
611
+ * *
612
+ * targetcell(g,lab,ptn,level,tc_level,digraph,hint,m,n) returns the index *
613
+ * in lab of the next cell to split. *
614
+ * hint is a suggestion for the answer, which is obeyed if it is valid. *
615
+ * Otherwise we use bestcell() up to tc_level and the first non-trivial *
616
+ * cell after that. *
617
+ * *
618
+ *****************************************************************************/
619
+
620
+ int
621
+ targetcell(graph *g, int *lab, int *ptn, int level,
622
+ int tc_level, boolean digraph, int hint, int m, int n)
623
+ {
624
+ int i;
625
+
626
+ if (hint >= 0 && ptn[hint] > level &&
627
+ (hint == 0 || ptn[hint-1] <= level))
628
+ return hint;
629
+ else if (level <= tc_level)
630
+ return bestcell(g,lab,ptn,level,tc_level,m,n);
631
+ else
632
+ {
633
+ for (i = 0; i < n && ptn[i] <= level; ++i) {}
634
+ return (i == n ? 0 : i);
635
+ }
636
+ }
637
+
638
+ /*****************************************************************************
639
+ * *
640
+ * densenauty(g,lab,ptn,orbits,&options,&stats,m,n,h) *
641
+ * is a slightly simplified interface to nauty(). It allocates enough *
642
+ * workspace for 500 automorphisms and checks that the densegraph dispatch *
643
+ * vector is in use. *
644
+ * *
645
+ *****************************************************************************/
646
+
647
+ void
648
+ densenauty(graph *g, int *lab, int *ptn, int *orbits,
649
+ optionblk *options, statsblk *stats, int m, int n, graph *h)
650
+ {
651
+ int i;
652
+ boolean digraph;
653
+ graph *gi;
654
+
655
+ if (options->dispatch != &dispatch_graph)
656
+ {
657
+ fprintf(ERRFILE,"Error: densenauty() needs standard options block\n");
658
+ exit(1);
659
+ }
660
+
661
+ digraph = options->digraph;
662
+ if (!digraph)
663
+ {
664
+ for (i = 0, gi = g; i < n; ++i, gi += m)
665
+ if (ISELEMENT(gi,i)) break;
666
+
667
+ if (i < n) options->digraph = TRUE;
668
+ }
669
+
670
+ #if !MAXN
671
+ /* Don't increase 2*500*m in the next line unless you also increase
672
+ the default declaration of dnwork[] earlier. */
673
+ DYNALLOC1(set,dnwork,dnwork_sz,2*500*m,"densenauty malloc");
674
+ #endif
675
+
676
+ nauty(g,lab,ptn,NULL,orbits,options,stats,dnwork,2*500*m,m,n,h);
677
+ options->digraph = digraph;
678
+ }
679
+
680
+ /*****************************************************************************
681
+ * *
682
+ * naugraph_check() checks that this file is compiled compatibly with the *
683
+ * given parameters. If not, call exit(1). *
684
+ * *
685
+ *****************************************************************************/
686
+
687
+ void
688
+ naugraph_check(int wordsize, int m, int n, int version)
689
+ {
690
+ if (wordsize != WORDSIZE)
691
+ {
692
+ fprintf(ERRFILE,"Error: WORDSIZE mismatch in naugraph.c\n");
693
+ exit(1);
694
+ }
695
+
696
+ #if MAXN
697
+ if (m > MAXM)
698
+ {
699
+ fprintf(ERRFILE,"Error: MAXM inadequate in naugraph.c\n");
700
+ exit(1);
701
+ }
702
+
703
+ if (n > MAXN)
704
+ {
705
+ fprintf(ERRFILE,"Error: MAXN inadequate in naugraph.c\n");
706
+ exit(1);
707
+ }
708
+ #endif
709
+
710
+ if (version < NAUTYREQUIRED)
711
+ {
712
+ fprintf(ERRFILE,"Error: naugraph.c version mismatch\n");
713
+ exit(1);
714
+ }
715
+ }
716
+
717
+ /*****************************************************************************
718
+ * *
719
+ * naugraph_freedyn() - free the dynamic memory in this module *
720
+ * *
721
+ *****************************************************************************/
722
+
723
+ void
724
+ naugraph_freedyn(void)
725
+ {
726
+ #if !MAXN
727
+ DYNFREE(workset,workset_sz);
728
+ DYNFREE(workperm,workperm_sz);
729
+ DYNFREE(bucket,bucket_sz);
730
+ DYNFREE(dnwork,dnwork_sz);
731
+ #endif
732
+ }