synkit 1.6.3__tar.gz → 1.6.5__tar.gz

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 (717) hide show
  1. {synkit-1.6.3 → synkit-1.6.5}/.gitignore +20 -0
  2. synkit-1.6.5/CMakeLists.txt +23 -0
  3. synkit-1.6.5/Data/Figure/synkit_graphical_abstract.svg +203 -0
  4. synkit-1.6.5/Experiment/CRN/AGENTS.md +13 -0
  5. synkit-1.6.5/Experiment/CRN/__init__.py +6 -0
  6. {synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/__init__.py +6 -6
  7. synkit-1.6.5/Experiment/CRN/benchmarks/backends.py +332 -0
  8. {synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/crosschecks.py +15 -18
  9. synkit-1.6.5/Experiment/CRN/benchmarks/glycolysis.py +27 -0
  10. {synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/kegg.py +72 -39
  11. {synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/networks.py +16 -20
  12. {synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/scaling.py +124 -110
  13. {synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/validate.py +28 -17
  14. synkit-1.6.5/Experiment/CRN/data/biomodels_manifest.json +50 -0
  15. synkit-1.6.5/Experiment/CRN/data/glycolysis_routes.json +367 -0
  16. synkit-1.6.5/Experiment/CRN/environments/crnt4sbml-requirements.txt +26 -0
  17. synkit-1.6.5/Experiment/CRN/notebooks/crn_glycolysis_case_study.ipynb +226 -0
  18. synkit-1.6.5/Experiment/CRN/run_all.py +272 -0
  19. synkit-1.6.5/Experiment/CRN/studies/__init__.py +1 -0
  20. synkit-1.6.5/Experiment/CRN/studies/biomodels.py +405 -0
  21. synkit-1.6.5/Experiment/CRN/studies/external_crnt4sbml.py +198 -0
  22. synkit-1.6.5/Experiment/CRN/studies/formose_case_study.py +276 -0
  23. synkit-1.6.5/Experiment/CRN/studies/glycolysis_donors.py +126 -0
  24. synkit-1.6.5/Experiment/CRN/studies/kegg_case_study.py +177 -0
  25. synkit-1.6.5/Experiment/CRN/studies/representation.py +239 -0
  26. synkit-1.6.5/Experiment/CRN/studies/scaling.py +166 -0
  27. synkit-1.6.5/Experiment/CRN/studies/supplementary.py +249 -0
  28. synkit-1.6.5/Experiment/CRN/studies/validation.py +123 -0
  29. synkit-1.6.5/Experiment/CRN/tools/__init__.py +1 -0
  30. synkit-1.6.5/Experiment/CRN/tools/check_reports.py +100 -0
  31. synkit-1.6.5/Experiment/CRN/tools/common.py +271 -0
  32. synkit-1.6.5/Experiment/CRN/tools/crnt4sbml_worker.py +76 -0
  33. synkit-1.6.5/Experiment/CRN/tools/refresh_kegg_cache.py +136 -0
  34. {synkit-1.6.3 → synkit-1.6.5}/PKG-INFO +37 -3
  35. {synkit-1.6.3 → synkit-1.6.5}/README.md +30 -1
  36. synkit-1.6.5/doc/_static/custom.css +488 -0
  37. synkit-1.6.5/doc/_static/favicon.svg +13 -0
  38. synkit-1.6.5/doc/_static/logo-dark.svg +19 -0
  39. synkit-1.6.5/doc/_static/logo.svg +23 -0
  40. synkit-1.6.5/doc/_static/navigation.js +58 -0
  41. synkit-1.6.5/doc/_templates/sidebar-globaltoc.html +33 -0
  42. synkit-1.6.5/doc/api/chem.rst +236 -0
  43. synkit-1.6.5/doc/api/crn.rst +248 -0
  44. synkit-1.6.5/doc/api/graph.rst +282 -0
  45. synkit-1.6.5/doc/api/index.rst +85 -0
  46. synkit-1.6.5/doc/api/io.rst +34 -0
  47. synkit-1.6.5/doc/api/rule.rst +65 -0
  48. synkit-1.6.5/doc/api/synthesis.rst +97 -0
  49. synkit-1.6.5/doc/api/vis.rst +79 -0
  50. synkit-1.6.5/doc/changelog.rst +447 -0
  51. synkit-1.6.5/doc/chem/molecule.rst +277 -0
  52. synkit-1.6.5/doc/chem/reaction.rst +132 -0
  53. synkit-1.6.5/doc/chem.rst +31 -0
  54. synkit-1.6.5/doc/conf.py +221 -0
  55. synkit-1.6.5/doc/crn.rst +512 -0
  56. synkit-1.6.5/doc/figures/aldol.png +0 -0
  57. synkit-1.6.5/doc/figures/aldol_its.png +0 -0
  58. synkit-1.6.5/doc/figures/context.png +0 -0
  59. synkit-1.6.5/doc/figures/epd_sn2.png +0 -0
  60. synkit-1.6.5/doc/figures/mtg.png +0 -0
  61. synkit-1.6.5/doc/figures/mtg_lsg_changed_core.png +0 -0
  62. synkit-1.6.5/doc/figures/mtg_mechanism.png +0 -0
  63. synkit-1.6.5/doc/figures/vis_lsg_sn2.png +0 -0
  64. synkit-1.6.5/doc/figures/vis_molecule_aspirin.png +0 -0
  65. synkit-1.6.5/doc/figures/vis_mtg_steps.png +0 -0
  66. synkit-1.6.5/doc/figures/vis_mtg_timeline.png +0 -0
  67. synkit-1.6.5/doc/figures/vis_reaction_sn2.png +0 -0
  68. synkit-1.6.5/doc/getting_started.rst +190 -0
  69. synkit-1.6.5/doc/graph.rst +541 -0
  70. synkit-1.6.5/doc/index.rst +157 -0
  71. synkit-1.6.5/doc/io.rst +239 -0
  72. synkit-1.6.5/doc/mapper/advanced.rst +516 -0
  73. synkit-1.6.5/doc/mapper/implementation.rst +74 -0
  74. synkit-1.6.5/doc/mapper.rst +350 -0
  75. synkit-1.6.5/doc/reference.rst +11 -0
  76. synkit-1.6.5/doc/refs.bib +31 -0
  77. synkit-1.6.5/doc/rule.rst +106 -0
  78. synkit-1.6.5/doc/stereo_reactions.rst +174 -0
  79. synkit-1.6.5/doc/synthesis.rst +432 -0
  80. synkit-1.6.5/doc/vis.rst +379 -0
  81. synkit-1.6.5/hatch_build.py +138 -0
  82. {synkit-1.6.3 → synkit-1.6.5}/pyproject.toml +36 -9
  83. synkit-1.6.5/scripts/check_package_artifacts.py +385 -0
  84. synkit-1.6.5/scripts/smoke_native_wheel.py +191 -0
  85. synkit-1.6.5/synkit/CRN/Benchmark/__init__.py +53 -0
  86. synkit-1.6.5/synkit/CRN/Benchmark/crosschecks.py +13 -0
  87. synkit-1.6.5/synkit/CRN/Benchmark/kegg.py +12 -0
  88. synkit-1.6.5/synkit/CRN/Benchmark/networks.py +13 -0
  89. synkit-1.6.5/synkit/CRN/Benchmark/scaling.py +13 -0
  90. synkit-1.6.5/synkit/CRN/Benchmark/validate.py +13 -0
  91. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Construct/builder.py +12 -2
  92. synkit-1.6.5/synkit/CRN/Construct/rdkit_worker.py +69 -0
  93. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/IO/sbml.py +38 -0
  94. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Pathway/realizability.py +30 -3
  95. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Petrinet/__init__.py +2 -0
  96. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Petrinet/analyzer.py +57 -13
  97. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Petrinet/minimal_semiflows.py +62 -14
  98. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Petrinet/persistence.py +27 -5
  99. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Petrinet/semiflows.py +17 -29
  100. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Petrinet/structure.py +42 -0
  101. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Props/__init__.py +4 -0
  102. synkit-1.6.5/synkit/CRN/Props/_rank.py +29 -0
  103. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Props/deficiency.py +29 -8
  104. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Props/stoich.py +94 -67
  105. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Props/thermo.py +53 -21
  106. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Query/__init__.py +4 -0
  107. synkit-1.6.5/synkit/CRN/Query/cache.py +41 -0
  108. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Query/to_syncrn.py +3 -7
  109. synkit-1.6.5/synkit/CRN/README.md +234 -0
  110. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Structure/_graph_io.py +14 -7
  111. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Symmetry/automorphism.py +32 -0
  112. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/Symmetry/canon.py +26 -0
  113. {synkit-1.6.3 → synkit-1.6.5}/synkit/CRN/__init__.py +30 -0
  114. synkit-1.6.5/synkit/CRN/_build.py +50 -0
  115. synkit-1.6.5/synkit/CRN/_native_build.py +175 -0
  116. synkit-1.6.5/synkit/CRN/analysis.py +629 -0
  117. synkit-1.6.5/synkit/CRN/backend.py +74 -0
  118. synkit-1.6.5/synkit/CRN/cpp/CMakeLists.txt +58 -0
  119. synkit-1.6.5/synkit/CRN/cpp/algebra.cpp +46 -0
  120. synkit-1.6.5/synkit/CRN/cpp/closure.cpp +29 -0
  121. synkit-1.6.5/synkit/CRN/cpp/exact.h +55 -0
  122. synkit-1.6.5/synkit/CRN/cpp/pathway.cpp +46 -0
  123. synkit-1.6.5/synkit/CRN/cpp/semiflows.cpp +209 -0
  124. synkit-1.6.5/synkit/CRN/cpp/structural.cpp +240 -0
  125. synkit-1.6.5/synkit/CRN/cpp/symmetry.cpp +45 -0
  126. synkit-1.6.5/synkit/CRN/cpp/write_manifest.cmake +28 -0
  127. synkit-1.6.5/synkit/CRN/native.py +388 -0
  128. synkit-1.6.5/synkit/CRN/native_analysis.py +459 -0
  129. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Fingerprint/fp_calculator.py +1 -1
  130. synkit-1.6.5/synkit/Chem/Mapper/README.rst +43 -0
  131. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/__init__.py +121 -98
  132. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/_compat.py +53 -0
  133. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/adapters/prediction.py +1 -1
  134. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/chem/aam.py +12 -12
  135. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/mapper.py +269 -35
  136. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/reaction_search.py +132 -77
  137. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/reporting/alternatives.py +3 -3
  138. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/reporting/analysis.py +10 -10
  139. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/reporting/native_analysis.py +7 -7
  140. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/reporting/spectrum.py +1 -1
  141. synkit-1.6.5/synkit/Chem/Mapper/solvers/__init__.py +1 -0
  142. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/__init__.py +1 -1
  143. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/core.py +1 -1
  144. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/distance_search/exhaustive.py +1 -1
  145. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/distance_search/records.py +1 -1
  146. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/distance_search/search.py +1 -1
  147. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/kernel_solvers/enumerate.py +4 -4
  148. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/candidates.py +249 -5
  149. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/canonical.py +2 -2
  150. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/disk_frontier.py +2 -2
  151. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/frontier.py +2 -2
  152. synkit-1.6.5/synkit/Chem/Mapper/solvers/exact/native/hydrogen_quotient.py +213 -0
  153. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/its.py +1 -1
  154. synkit-1.6.5/synkit/Chem/Mapper/solvers/exact/native/native_distance.cpp +2803 -0
  155. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/orbit_aggregation.py +2 -2
  156. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native/parallel.py +3 -3
  157. synkit-1.6.5/synkit/Chem/Mapper/solvers/exact/native/pmcd.py +203 -0
  158. synkit-1.6.5/synkit/Chem/Mapper/solvers/exact/native/search.py +294 -0
  159. synkit-1.6.5/synkit/Chem/Mapper/solvers/exact/native/separator.py +224 -0
  160. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/native_build.py +1 -1
  161. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/exact/pabs/propagation.py +1 -1
  162. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/__init__.py +4 -0
  163. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/assignment.py +99 -0
  164. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/astar.py +22 -0
  165. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/build.py +385 -0
  166. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/classification.py +641 -0
  167. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/core.py +378 -0
  168. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/CMakeLists.txt +120 -0
  169. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/examples/map_reaction.cpp +29 -0
  170. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/examples/slap_graph.cpp +63 -0
  171. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/assignment/assignment.h +18 -0
  172. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/astar/astar.h +18 -0
  173. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/astar/bound.h +33 -0
  174. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/core/pmcd_witness.h +16 -0
  175. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/core/runtime.h +130 -0
  176. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/hydrogen/hydrogen.h +73 -0
  177. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/mapper.h +175 -0
  178. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/mces/mces.h +9 -0
  179. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/pabs/seed.h +34 -0
  180. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/reaction/reaction.h +30 -0
  181. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/sepdp/sepdp.h +21 -0
  182. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/slap.h +72 -0
  183. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/solvers/solvers.h +16 -0
  184. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/symmetry/classification.h +140 -0
  185. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/include/synkit_mapper/symmetry/cpabs.h +33 -0
  186. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/assignment/abb.cpp +302 -0
  187. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/astar/CMakeLists.txt +12 -0
  188. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/astar/README.md +47 -0
  189. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/astar/astar.cpp +228 -0
  190. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/astar/astar_graph.cpp +37 -0
  191. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/astar/bound.cpp +212 -0
  192. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/core/dispatch.cpp +272 -0
  193. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/core/pmcd_witness.cpp +36 -0
  194. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/hydrogen/hydrogen.cpp +380 -0
  195. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/mces/README.md +57 -0
  196. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/mces/mces.cpp +287 -0
  197. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/bridge.cpp +334 -0
  198. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/chemical_floor.inc +181 -0
  199. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/endpoint_symmetry.inc +104 -0
  200. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/exact_helpers.h +20 -0
  201. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_assignment_certificate.h +165 -0
  202. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_certificate.h +125 -0
  203. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_model.h +365 -0
  204. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_provider.inc +319 -0
  205. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_rounding.inc +170 -0
  206. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/lp_test_hooks.h +342 -0
  207. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/objective_reduction.inc +137 -0
  208. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/overlap_dual.inc +351 -0
  209. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/profile_seed.inc +214 -0
  210. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/seed_heuristics.inc +640 -0
  211. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/sparse_embedding.cpp +430 -0
  212. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/sparse_root_lp.h +176 -0
  213. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/pabs/test_hooks.inc +262 -0
  214. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/reaction/reaction.cpp +611 -0
  215. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/sepdp/README.md +61 -0
  216. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/sepdp/sepdp.cpp +253 -0
  217. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/slap.cpp +810 -0
  218. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/solvers/formulation.h +138 -0
  219. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/solvers/maxsat.cpp +526 -0
  220. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/solvers/ortools.cpp +475 -0
  221. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/solvers/seed.h +80 -0
  222. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/solvers/weighted_cnf.h +256 -0
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  232. synkit-1.6.5/synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt +202 -0
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  260. {synkit-1.6.3/synkit/Chem/Mapper → synkit-1.6.5/synkit/Chem/Mapper/solvers}/slap/sequential.py +2 -2
  261. {synkit-1.6.3 → synkit-1.6.5}/synkit/Chem/Mapper/validation/annotations.py +1 -1
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  277. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/pipeline.py +6 -1
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  281. synkit-1.6.3/synkit/Chem/Mapper/README.rst +0 -281
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  608. {synkit-1.6.3 → synkit-1.6.5}/synkit/Mechanism/radical_data.py +0 -0
  609. {synkit-1.6.3 → synkit-1.6.5}/synkit/Mechanism/replay.py +0 -0
  610. {synkit-1.6.3 → synkit-1.6.5}/synkit/Mechanism/schema.py +0 -0
  611. {synkit-1.6.3 → synkit-1.6.5}/synkit/Mechanism/stereo_state.py +0 -0
  612. {synkit-1.6.3 → synkit-1.6.5}/synkit/Mechanism/symbols.py +0 -0
  613. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Apply/__init__.py +0 -0
  614. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Apply/conditions.py +0 -0
  615. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Apply/dpo.py +0 -0
  616. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Apply/rule_matcher.py +0 -0
  617. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Apply/validation.py +0 -0
  618. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Compose/__init__.py +0 -0
  619. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Compose/_identity.py +0 -0
  620. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Compose/composition.py +0 -0
  621. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Compose/laws.py +0 -0
  622. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Compose/search.py +0 -0
  623. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Compose/synrule.py +0 -0
  624. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/__init__.py +0 -0
  625. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/implict_rule.py +0 -0
  626. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/longest_path.py +0 -0
  627. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/molecule_rule.py +0 -0
  628. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/prune_templates.py +0 -0
  629. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/rule_utils.py +0 -0
  630. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/Modify/strip_rule.py +0 -0
  631. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/__init__.py +0 -0
  632. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/generic_stereo.py +0 -0
  633. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/stereo_identity.py +0 -0
  634. {synkit-1.6.3 → synkit-1.6.5}/synkit/Rule/syn_rule.py +0 -0
  635. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/MSR/__init__.py +0 -0
  636. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/MSR/path_finder.py +0 -0
  637. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Metrics/__init__.py +0 -0
  638. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Metrics/_base.py +0 -0
  639. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Metrics/_plot.py +0 -0
  640. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Metrics/_ranking.py +0 -0
  641. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/__init__.py +0 -0
  642. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/engine.py +0 -0
  643. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/matching.py +0 -0
  644. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/overlap.py +0 -0
  645. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/policy.py +0 -0
  646. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/proof.py +0 -0
  647. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/state.py +0 -0
  648. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/RBL/validation.py +0 -0
  649. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/__init__.py +0 -0
  650. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/core/__init__.py +0 -0
  651. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/core/engine.py +0 -0
  652. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/core/product.py +0 -0
  653. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/core/rewrite.py +0 -0
  654. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/core/strategy.py +0 -0
  655. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/matching/__init__.py +0 -0
  656. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/matching/mixin.py +0 -0
  657. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/matching/policy.py +0 -0
  658. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/matching/symmetry.py +0 -0
  659. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/output/__init__.py +0 -0
  660. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/output/deduplication.py +0 -0
  661. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/output/policy.py +0 -0
  662. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/output/serialization.py +0 -0
  663. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/output/structural.py +0 -0
  664. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/stereo/__init__.py +0 -0
  665. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/stereo/assignment.py +0 -0
  666. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/stereo/mixin.py +0 -0
  667. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/variants/__init__.py +0 -0
  668. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/variants/imbalanced.py +0 -0
  669. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/variants/partial.py +0 -0
  670. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/workflow/__init__.py +0 -0
  671. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/workflow/batch.py +0 -0
  672. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/workflow/benchmark.py +0 -0
  673. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/workflow/postprocess.py +0 -0
  674. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/Reactor/workflow/rule_filter.py +0 -0
  675. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/__init__.py +0 -0
  676. {synkit-1.6.3 → synkit-1.6.5}/synkit/Synthesis/reactor_utils.py +0 -0
  677. {synkit-1.6.3 → synkit-1.6.5}/synkit/Utils/__init__.py +0 -0
  678. {synkit-1.6.3 → synkit-1.6.5}/synkit/Utils/utils.py +0 -0
  679. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/__init__.py +0 -0
  680. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/crn/__init__.py +0 -0
  681. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/__init__.py +0 -0
  682. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/arrows.py +0 -0
  683. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/chem.py +0 -0
  684. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/constants.py +0 -0
  685. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/layout.py +0 -0
  686. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/mapping.py +0 -0
  687. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/models.py +0 -0
  688. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/render.py +0 -0
  689. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/utils.py +0 -0
  690. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/epd/visualizer.py +0 -0
  691. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/graph_visualizer.py +0 -0
  692. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/its/__init__.py +0 -0
  693. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/its/drawer.py +0 -0
  694. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/its_drawer.py +0 -0
  695. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/molecule/__init__.py +0 -0
  696. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/molecule/drawer.py +0 -0
  697. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/molecule/reaction.py +0 -0
  698. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/molecule_drawer.py +0 -0
  699. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/mtg/__init__.py +0 -0
  700. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/mtg/drawer.py +0 -0
  701. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/mtg_drawer.py +0 -0
  702. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/pdf_writer.py +0 -0
  703. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/reaction/__init__.py +0 -0
  704. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/reaction/rule.py +0 -0
  705. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/reaction/rxn.py +0 -0
  706. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/reaction_drawer.py +0 -0
  707. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/space/__init__.py +0 -0
  708. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/space/chemical.py +0 -0
  709. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/space/embedding.py +0 -0
  710. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/vis_synedu/Vis/__init__.py +0 -0
  711. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/vis_synedu/Vis/dpo.py +0 -0
  712. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/vis_synedu/rxn_vis.py +0 -0
  713. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/vis_synedu/vis.py +0 -0
  714. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/visual_drawer.py +0 -0
  715. {synkit-1.6.3 → synkit-1.6.5}/synkit/Vis/visual_model.py +0 -0
  716. {synkit-1.6.3 → synkit-1.6.5}/synkit/__init__.py +0 -0
  717. {synkit-1.6.3 → synkit-1.6.5}/synkit/examples.py +0 -0
{synkit-1.6.3 → synkit-1.6.5}/.gitignore RENAMED
@@ -19,6 +19,10 @@ venv/
19
19
  # Optional Mapper kernel artifacts are rebuilt from the shipped C++ source.
20
20
  libsynkit_distance_*.so
21
21
  libsynkit_distance_*.json
22
+ libsynkit_mapper_*.so
23
+ libsynkit_mapper_*.dylib
24
+ libsynkit_mapper_*.dll
25
+ libsynkit_mapper_*.json
22
26
 
23
27
  # Generated logs, reports, notebooks, and data files
24
28
  *.log
@@ -31,8 +35,14 @@ libsynkit_distance_*.json
31
35
  *.json.gz
32
36
  *.pkl.gz
33
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  *.txt
38
+ !synkit/Chem/Mapper/solvers/native/cpp/CMakeLists.txt
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+ !synkit/Graph/Canon/cpp/CMakeLists.txt
40
+ !synkit/CRN/cpp/CMakeLists.txt
41
+ !synkit/Chem/Mapper/solvers/native/cpp/**/CMakeLists.txt
42
+ !synkit/Chem/Mapper/solvers/native/cpp/src/symmetry/vendor/nauty/LICENSE-2.0.txt
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43
 
35
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  # Package resources and repository evidence retained despite the broad rules
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+ !/CMakeLists.txt
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  !Experiment/CRN/LICENSES/*.txt
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  !synkit/CRN/Benchmark/data/kegg_modules.json
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48
  !Data/Conformance/stereomolgraph_graph_conformance.json
@@ -103,6 +113,7 @@ libsynkit_distance_*.json
103
113
  /Experiment/RBL/*checkpoint*.jsonl
104
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  # Development and scratch paths
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+ /Experiment/atom_map/
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  /Test/Conformance/
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  /crn/
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  /debug/
@@ -126,3 +137,12 @@ test_syn_reactor.py
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137
 
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  # Local benchmark outputs and frozen source copies stay local.
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  /benchmark_results/
140
+
141
+ # Keep unreleased experiments local; publish only CRN and Lewis until release.
142
+ /Experiment/*
143
+ !/Experiment/CRN/
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+ !/Experiment/Lewis/
145
+ !/Experiment/__init__.py
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+
147
+ # Experiment READMEs are local documentation, including nested directories.
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+ /Experiment/**/[Rr][Ee][Aa][Dd][Mm][Ee]*
synkit-1.6.5/CMakeLists.txt ADDED
@@ -0,0 +1,23 @@
1
+ cmake_minimum_required(VERSION 3.20)
2
+ project(synkit_native VERSION 1.6.5 LANGUAGES C CXX)
3
+
4
+ option(SYNKIT_BUILD_MAPPER "Build the atom mapper and its solver backends" ON)
5
+ option(SYNKIT_BUILD_CRN "Build exact chemical reaction network analysis" ON)
6
+ option(SYNKIT_BUILD_CANON "Build graph and stereograph canonicalization" ON)
7
+ option(SYNKIT_NATIVE_WHEEL "Install native libraries into their Python packages" OFF)
8
+
9
+ if(SYNKIT_NATIVE_WHEEL)
10
+ set(SYNKIT_MAPPER_WHEEL ON CACHE BOOL "Install mapper into the wheel" FORCE)
11
+ set(SYNKIT_CANON_WHEEL ON CACHE BOOL "Install canonicalization into the wheel" FORCE)
12
+ endif()
13
+
14
+ enable_testing()
15
+ if(SYNKIT_BUILD_MAPPER)
16
+ add_subdirectory(synkit/Chem/Mapper/solvers/native/cpp mapper)
17
+ endif()
18
+ if(SYNKIT_BUILD_CRN)
19
+ add_subdirectory(synkit/CRN/cpp crn)
20
+ endif()
21
+ if(SYNKIT_BUILD_CANON)
22
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23
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+ </g>
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+ <text x="929.65" y="126.25" text-anchor="middle" font-size="16.5" font-weight="700" fill="#ffffff">1</text>
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+ <text x="1057.24" y="157.84" text-anchor="start" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">IO</text>
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+ <text x="1057.24" y="187.84" text-anchor="start" font-size="21" fill="#5A5F63">Parsing &amp; conversion</text>
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+ </g>
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+ <circle cx="1138.78" cy="288.00" r="62" fill="#DCF0E8" stroke="#009E73" stroke-opacity="0.55" stroke-width="2"/>
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+ <g transform="translate(1138.78,288.00) scale(0.86)">
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+ <circle cx="21" cy="-24" r="11" stroke="#009E73" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <path d="M 16 -24 L 19.6 -20 L 26 -28.5" stroke="#009E73" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ </g>
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+ <circle cx="1099.19" cy="248.41" r="15" fill="#009E73"/>
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+ <text x="1099.19" y="254.41" text-anchor="middle" font-size="16.5" font-weight="700" fill="#ffffff">2</text>
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+ <text x="1226.78" y="286.00" text-anchor="start" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">Chem</text>
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+ <g id="mod-graph">
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+ <g transform="translate(1179.76,490.09) scale(0.86)">
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+ <path d="M 0 -27 L 26 -8" stroke="#E69F00" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <circle cx="26" cy="-8" r="6.5" fill="#FBFAF7" stroke="#E69F00" stroke-width="2.6"/>
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+ <circle cx="16" cy="25" r="6.5" fill="#FBFAF7" stroke="#E69F00" stroke-width="2.6"/>
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+ <circle cx="-16" cy="25" r="6.5" fill="#FBFAF7" stroke="#E69F00" stroke-width="2.6"/>
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+ <circle cx="-26" cy="-8" r="6.5" fill="#FBFAF7" stroke="#E69F00" stroke-width="2.6"/>
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+ <circle cx="0" cy="0" r="9" fill="#E69F00" stroke="none"/>
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+ </g>
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+ <circle cx="1140.17" cy="450.50" r="15" fill="#E69F00"/>
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+ <text x="1140.17" y="456.50" text-anchor="middle" font-size="16.5" font-weight="700" fill="#ffffff">3</text>
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+ <text x="1267.76" y="488.09" text-anchor="start" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">Graph</text>
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+ <text x="1267.76" y="518.09" text-anchor="start" font-size="21" fill="#5A5F63">ITS / MTG &amp; canonicalization</text>
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+ </g>
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+ <g id="mod-rule">
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+ <circle cx="1070.85" cy="660.94" r="67" fill="#B0559A" fill-opacity="0.10"/>
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+ <circle cx="1070.85" cy="660.94" r="62" fill="#F1E5EE" stroke="#B0559A" stroke-opacity="0.55" stroke-width="2"/>
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+ <g transform="translate(1070.85,660.94) scale(0.86)">
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+ <rect x="-42" y="-12" width="26" height="26" rx="5" stroke="#B0559A" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <circle cx="4.5" cy="-1" r="3.2" fill="#B0559A" stroke="none"/>
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+ <path d="M 6 -24 L 18 -24" stroke="#B0559A" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <path d="M 15 -27.8 L 20 -24 L 15 -20.2 Z" fill="#B0559A" stroke="none"/>
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+ <path d="M -29 22 L -6 22 M 6 22 L 29 22" stroke="#B0559A" stroke-opacity="0.4" stroke-width="2" fill="none"/>
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+ </g>
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+ <circle cx="1031.26" cy="621.35" r="15" fill="#B0559A"/>
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+ <text x="1031.26" y="627.35" text-anchor="middle" font-size="16.5" font-weight="700" fill="#ffffff">4</text>
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+ <text x="1158.85" y="658.94" text-anchor="start" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">Rule</text>
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+ <text x="1158.85" y="688.94" text-anchor="start" font-size="21" fill="#5A5F63">Compose reaction rules</text>
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+ </g>
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+ <g id="mod-synth">
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+ <circle cx="609.15" cy="660.94" r="67" fill="#D55E00" fill-opacity="0.10"/>
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+ <circle cx="609.15" cy="660.94" r="62" fill="#FADFD1" stroke="#D55E00" stroke-opacity="0.55" stroke-width="2"/>
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+ <g transform="translate(609.15,660.94) scale(0.86)">
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+ <path d="M -28 0 L -10 0" stroke="#D55E00" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <path d="M -10 0 C 0 0 0 -22 10 -22" stroke="#D55E00" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <path d="M 8 18.4 L 14 22 L 8 25.6 Z" fill="#D55E00" stroke="none"/>
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+ <circle cx="-28" cy="0" r="5.5" fill="#D55E00" stroke="none"/>
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+ <circle cx="22" cy="22" r="5.5" fill="#FBFAF7" stroke="#D55E00" stroke-width="2.6"/>
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+ <text x="648.74" y="627.35" text-anchor="middle" font-size="16.5" font-weight="700" fill="#ffffff">5</text>
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+ <text x="521.15" y="658.94" text-anchor="end" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">Synthesis</text>
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+ <text x="521.15" y="688.94" text-anchor="end" font-size="21" fill="#5A5F63">Predict &amp; explore</text>
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+ </g>
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+ <g id="mod-crn">
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+ <circle cx="495.00" cy="438.00" r="67" fill="#B8860B" fill-opacity="0.10"/>
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+ <circle cx="495.00" cy="438.00" r="62" fill="#F7EDCF" stroke="#B8860B" stroke-opacity="0.55" stroke-width="2"/>
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+ <g transform="translate(495.00,438.00) scale(0.86)">
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+ <rect x="-3" y="-17" width="10" height="10" rx="1.5" fill="#B8860B" stroke="none"/>
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+ <path d="M -26 0 L 2 -12" stroke="#B8860B" stroke-width="2.1" fill="none"/>
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+ <path d="M -26 0 L 2 14" stroke="#B8860B" stroke-width="2.1" fill="none"/>
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+ <path d="M -26 22 L 2 14" stroke="#B8860B" stroke-width="2.1" fill="none"/>
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+ <path d="M 2 -12 L 28 -22" stroke="#B8860B" stroke-width="2.1" fill="none"/>
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+ <path d="M 2 14 L 28 12" stroke="#B8860B" stroke-width="2.1" fill="none"/>
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+ <path d="M 2 -12 L 28 12" stroke="#B8860B" stroke-width="2.1" fill="none"/>
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+ <circle cx="-26" cy="-22" r="6" fill="#FBFAF7" stroke="#B8860B" stroke-width="2.6"/>
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+ <circle cx="-26" cy="0" r="6" fill="#FBFAF7" stroke="#B8860B" stroke-width="2.6"/>
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+ <circle cx="-26" cy="22" r="6" fill="#FBFAF7" stroke="#B8860B" stroke-width="2.6"/>
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+ <circle cx="28" cy="-22" r="6" fill="#FBFAF7" stroke="#B8860B" stroke-width="2.6"/>
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+ <circle cx="28" cy="12" r="6" fill="#FBFAF7" stroke="#B8860B" stroke-width="2.6"/>
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+ <path d="M -18 29 L -23 29 L -23 41 L -18 41 M 18 29 L 23 29 L 23 41 L 18 41" stroke="#B8860B" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <path d="M -13 33 L -6 33 M 4 33 L 11 33 M -13 39 L -6 39 M 4 39 L 11 39" stroke="#B8860B" stroke-width="2.4" stroke-linecap="round" fill="none"/>
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+ <circle cx="534.59" cy="398.41" r="15" fill="#B8860B"/>
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+ <text x="407.00" y="436.00" text-anchor="end" font-size="38" font-weight="800" fill="#1A1A1A" letter-spacing="-0.5">CRN</text>
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+ <text x="407.00" y="466.00" text-anchor="end" font-size="21" fill="#5A5F63">Networks &amp; properties</text>
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+ <g id="mod-vis">
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+ <rect x="-30" y="-26" width="60" height="52" rx="5" stroke="#3D8FC4" fill="none" stroke-width="2.6" stroke-linecap="round" stroke-linejoin="round"/>
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+ <g font-size="21" text-anchor="middle">
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+ <text x="840" y="896" fill="#5A5F63"><tspan fill="#0E5C63" font-weight="700">Open source · MIT</tspan><tspan fill="#D9DBD6"> · </tspan><tspan>pip install synkit</tspan><tspan fill="#D9DBD6"> · </tspan><tspan>github.com/TieuLongPhan/SynKit</tspan></text>
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synkit-1.6.5/Experiment/CRN/AGENTS.md ADDED
@@ -0,0 +1,13 @@
1
+ # CRN experiment scope
2
+
3
+ - Keep experiment drivers, benchmark inputs, timing harnesses, and result/report
4
+ tools here. Put regression test cases and assertions in `Test/CRN/`; do not
5
+ create a second test runner inside `Experiment/CRN`.
6
+ - Reuse the public `synkit.CRN` APIs and shared benchmark inputs. Extend existing
7
+ studies and helpers before adding overlapping scripts or copied fixtures.
8
+ - Keep inputs self-contained. Do not depend on manuscript directories, LaTeX
9
+ sources, or paper-specific helpers and filenames. Document rendering belongs
10
+ with the document that consumes the experiment reports.
11
+ - Scientific outcome checks and report-completeness checks belong in study
12
+ reports. Keep generated outputs, native build artifacts, and downloaded XML
13
+ caches out of version control and package distributions.
synkit-1.6.5/Experiment/CRN/__init__.py ADDED
@@ -0,0 +1,6 @@
1
+ """Reproducible chemical reaction network studies and benchmarks.
2
+
3
+ Study drivers live in :mod:`Experiment.CRN.studies`, fixtures and timing code
4
+ in :mod:`Experiment.CRN.benchmarks`, and verification helpers in
5
+ :mod:`Experiment.CRN.tools`. Run the studies with ``run_all.py``.
6
+ """
{synkit-1.6.3/synkit/CRN/Benchmark → synkit-1.6.5/Experiment/CRN/benchmarks}/__init__.py RENAMED
@@ -2,14 +2,14 @@
2
2
 
3
3
  The package includes:
4
4
 
5
- - **A validation set** (:mod:`~synkit.CRN.Benchmark.networks`,
6
- :mod:`~synkit.CRN.Benchmark.validate`) — literature and regression networks
5
+ - **A validation set** (:mod:`~Experiment.CRN.benchmarks.networks`,
6
+ :mod:`~Experiment.CRN.benchmarks.validate`) — literature and regression networks
7
7
  with the structural verdicts they must reproduce, each quantity additionally
8
8
  recomputed by an independent route from
9
- :mod:`~synkit.CRN.Benchmark.crosschecks`.
10
- - **A scaling benchmark** (:mod:`~synkit.CRN.Benchmark.scaling`) — wall-clock
9
+ :mod:`~Experiment.CRN.benchmarks.crosschecks`.
10
+ - **A scaling benchmark** (:mod:`~Experiment.CRN.benchmarks.scaling`) — wall-clock
11
11
  timings of the analysis stack against network size.
12
- - **A metabolic case study** (:mod:`~synkit.CRN.Benchmark.kegg`) — cached KEGG
12
+ - **A metabolic case study** (:mod:`~Experiment.CRN.benchmarks.kegg`) — cached KEGG
13
13
  modules processed from pathway retrieval through
14
14
  conservation laws, persistence and flux realizability.
15
15
 
@@ -17,7 +17,7 @@ The package includes:
17
17
 
18
18
  .. code-block:: python
19
19
 
20
- from synkit.CRN.Benchmark import run_validation, validation_table
20
+ from Experiment.CRN.benchmarks import run_validation, validation_table
21
21
 
22
22
  print(validation_table(run_validation()))
23
23
  """