umol-py 0.6.0__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 (572) hide show
  1. umol_py-0.6.0/Cargo.lock +2637 -0
  2. umol_py-0.6.0/Cargo.toml +23 -0
  3. umol_py-0.6.0/LICENSE-APACHE +201 -0
  4. umol_py-0.6.0/LICENSE-MIT +21 -0
  5. umol_py-0.6.0/PKG-INFO +66 -0
  6. umol_py-0.6.0/README.md +46 -0
  7. umol_py-0.6.0/pyproject.toml +35 -0
  8. umol_py-0.6.0/python/umol/__init__.py +463 -0
  9. umol_py-0.6.0/python/umol/elements.py +31 -0
  10. umol_py-0.6.0/umol-chem/Cargo.toml +44 -0
  11. umol_py-0.6.0/umol-chem/LICENSE-APACHE +201 -0
  12. umol_py-0.6.0/umol-chem/LICENSE-MIT +21 -0
  13. umol_py-0.6.0/umol-chem/README.md +46 -0
  14. umol_py-0.6.0/umol-chem/benches/elements.rs +105 -0
  15. umol_py-0.6.0/umol-chem/src/configuration.rs +388 -0
  16. umol_py-0.6.0/umol-chem/src/element.rs +1478 -0
  17. umol_py-0.6.0/umol-chem/src/error.rs +91 -0
  18. umol_py-0.6.0/umol-chem/src/isotope.rs +564 -0
  19. umol_py-0.6.0/umol-chem/src/isotope_data.rs +3486 -0
  20. umol_py-0.6.0/umol-chem/src/lib.rs +11 -0
  21. umol_py-0.6.0/umol-chem/src/occupation.rs +206 -0
  22. umol_py-0.6.0/umol-chem/src/spin.rs +667 -0
  23. umol_py-0.6.0/umol-chem/src/units/angle.rs +139 -0
  24. umol_py-0.6.0/umol-chem/src/units/length.rs +142 -0
  25. umol_py-0.6.0/umol-chem/src/units/time.rs +173 -0
  26. umol_py-0.6.0/umol-chem/src/units.rs +8 -0
  27. umol_py-0.6.0/umol-edn/Cargo.toml +60 -0
  28. umol_py-0.6.0/umol-edn/LICENSE-APACHE +201 -0
  29. umol_py-0.6.0/umol-edn/LICENSE-MIT +21 -0
  30. umol_py-0.6.0/umol-edn/README.md +86 -0
  31. umol_py-0.6.0/umol-edn/benches/memory.rs +138 -0
  32. umol_py-0.6.0/umol-edn/benches/parsing.rs +508 -0
  33. umol_py-0.6.0/umol-edn/spec/edn-spec.md +256 -0
  34. umol_py-0.6.0/umol-edn/src/bigdecimal.rs +204 -0
  35. umol_py-0.6.0/umol-edn/src/bigint.rs +224 -0
  36. umol_py-0.6.0/umol-edn/src/collections.rs +1039 -0
  37. umol_py-0.6.0/umol-edn/src/config.rs +102 -0
  38. umol_py-0.6.0/umol-edn/src/de.rs +1390 -0
  39. umol_py-0.6.0/umol-edn/src/display.rs +260 -0
  40. umol_py-0.6.0/umol-edn/src/dyn_edn.rs +935 -0
  41. umol_py-0.6.0/umol-edn/src/edn.rs +1079 -0
  42. umol_py-0.6.0/umol-edn/src/error.rs +202 -0
  43. umol_py-0.6.0/umol-edn/src/formatter.rs +782 -0
  44. umol_py-0.6.0/umol-edn/src/lib.rs +189 -0
  45. umol_py-0.6.0/umol-edn/src/list.rs +289 -0
  46. umol_py-0.6.0/umol-edn/src/parser.rs +1188 -0
  47. umol_py-0.6.0/umol-edn/src/reader.rs +81 -0
  48. umol_py-0.6.0/umol-edn/src/ser.rs +1690 -0
  49. umol_py-0.6.0/umol-edn/src/serde.rs +44 -0
  50. umol_py-0.6.0/umol-edn/src/set.rs +320 -0
  51. umol_py-0.6.0/umol-edn/src/streaming.rs +785 -0
  52. umol_py-0.6.0/umol-edn/src/tagged.rs +246 -0
  53. umol_py-0.6.0/umol-edn/src/tags.rs +69 -0
  54. umol_py-0.6.0/umol-edn/src/traits.rs +1198 -0
  55. umol_py-0.6.0/umol-edn/tests/conformance.rs +1092 -0
  56. umol_py-0.6.0/umol-edn/tests/derives.rs +684 -0
  57. umol_py-0.6.0/umol-edn/tests/import_paths.rs +37 -0
  58. umol_py-0.6.0/umol-edn/tests/macros.rs +144 -0
  59. umol_py-0.6.0/umol-edn/tests/parity.rs +468 -0
  60. umol_py-0.6.0/umol-edn/tests/property.rs +223 -0
  61. umol_py-0.6.0/umol-edn-macros/Cargo.toml +20 -0
  62. umol_py-0.6.0/umol-edn-macros/LICENSE-APACHE +201 -0
  63. umol_py-0.6.0/umol-edn-macros/LICENSE-MIT +21 -0
  64. umol_py-0.6.0/umol-edn-macros/README.md +46 -0
  65. umol_py-0.6.0/umol-edn-macros/src/derive_from_edn.rs +983 -0
  66. umol_py-0.6.0/umol-edn-macros/src/derive_to_edn.rs +412 -0
  67. umol_py-0.6.0/umol-edn-macros/src/lib.rs +329 -0
  68. umol_py-0.6.0/umol-geometric-core/Cargo.toml +24 -0
  69. umol_py-0.6.0/umol-geometric-core/LICENSE-APACHE +201 -0
  70. umol_py-0.6.0/umol-geometric-core/LICENSE-MIT +21 -0
  71. umol_py-0.6.0/umol-geometric-core/README.md +46 -0
  72. umol_py-0.6.0/umol-geometric-core/src/lib.rs +9 -0
  73. umol_py-0.6.0/umol-geometric-core/src/orientation.rs +50 -0
  74. umol_py-0.6.0/umol-geometric-core/src/plane.rs +43 -0
  75. umol_py-0.6.0/umol-geometric-core/src/point.rs +29 -0
  76. umol_py-0.6.0/umol-graph/.cargo/config.toml +8 -0
  77. umol_py-0.6.0/umol-graph/Cargo.toml +102 -0
  78. umol_py-0.6.0/umol-graph/LICENSE-APACHE +201 -0
  79. umol_py-0.6.0/umol-graph/LICENSE-MIT +21 -0
  80. umol_py-0.6.0/umol-graph/README.md +46 -0
  81. umol_py-0.6.0/umol-graph/benches/fingerprint.rs +203 -0
  82. umol_py-0.6.0/umol-graph/benches/morgan_rdkit.py +60 -0
  83. umol_py-0.6.0/umol-graph/benches/resolve.rs +34 -0
  84. umol_py-0.6.0/umol-graph/benches/substructure.rs +209 -0
  85. umol_py-0.6.0/umol-graph/benches/substructure_rdkit.py +38 -0
  86. umol_py-0.6.0/umol-graph/config/default-registry.toml +1221 -0
  87. umol_py-0.6.0/umol-graph/config/default-valence-table.toml +156 -0
  88. umol_py-0.6.0/umol-graph/config/mdl-valence-table.toml +165 -0
  89. umol_py-0.6.0/umol-graph/config/smiles-valence-table.toml +194 -0
  90. umol_py-0.6.0/umol-graph/insta.yaml +28 -0
  91. umol_py-0.6.0/umol-graph/src/bin/classify_mol_files.rs +443 -0
  92. umol_py-0.6.0/umol-graph/src/bin/classify_sdf_files.rs +443 -0
  93. umol_py-0.6.0/umol-graph/src/bin/classify_smiles_strings.rs +832 -0
  94. umol_py-0.6.0/umol-graph/src/bin/test_mol_file.rs +119 -0
  95. umol_py-0.6.0/umol-graph/src/bin/test_smiles.rs +92 -0
  96. umol_py-0.6.0/umol-graph/src/bin/verify_stereo.rs +241 -0
  97. umol_py-0.6.0/umol-graph/src/fingerprint/bit_fp.rs +293 -0
  98. umol_py-0.6.0/umol-graph/src/fingerprint/ecfp.rs +204 -0
  99. umol_py-0.6.0/umol-graph/src/fingerprint/feature_set.rs +301 -0
  100. umol_py-0.6.0/umol-graph/src/fingerprint/featurizer.rs +57 -0
  101. umol_py-0.6.0/umol-graph/src/fingerprint/morgan.rs +175 -0
  102. umol_py-0.6.0/umol-graph/src/fingerprint/pattern.rs +280 -0
  103. umol_py-0.6.0/umol-graph/src/fingerprint/reaction.rs +145 -0
  104. umol_py-0.6.0/umol-graph/src/fingerprint/substructure.rs +186 -0
  105. umol_py-0.6.0/umol-graph/src/fingerprint/wl.rs +152 -0
  106. umol_py-0.6.0/umol-graph/src/fingerprint.rs +21 -0
  107. umol_py-0.6.0/umol-graph/src/hash.rs +497 -0
  108. umol_py-0.6.0/umol-graph/src/ingest.rs +1660 -0
  109. umol_py-0.6.0/umol-graph/src/lib.rs +8 -0
  110. umol_py-0.6.0/umol-graph/src/ops/aromaticity/clar.rs +411 -0
  111. umol_py-0.6.0/umol-graph/src/ops/aromaticity/hmo.rs +593 -0
  112. umol_py-0.6.0/umol-graph/src/ops/aromaticity/hueckel.rs +765 -0
  113. umol_py-0.6.0/umol-graph/src/ops/aromaticity.rs +1094 -0
  114. umol_py-0.6.0/umol-graph/src/ops/canonicalize.rs +66 -0
  115. umol_py-0.6.0/umol-graph/src/ops/invariant.rs +854 -0
  116. umol_py-0.6.0/umol-graph/src/ops/model.rs +654 -0
  117. umol_py-0.6.0/umol-graph/src/ops/resolve/aromaticity.rs +2012 -0
  118. umol_py-0.6.0/umol-graph/src/ops/resolve/bonds.rs +142 -0
  119. umol_py-0.6.0/umol-graph/src/ops/resolve/multicenter.rs +232 -0
  120. umol_py-0.6.0/umol-graph/src/ops/resolve/stereo.rs +1044 -0
  121. umol_py-0.6.0/umol-graph/src/ops/resolve/valence.rs +264 -0
  122. umol_py-0.6.0/umol-graph/src/ops/resolve.rs +1569 -0
  123. umol_py-0.6.0/umol-graph/src/ops/stereo.rs +679 -0
  124. umol_py-0.6.0/umol-graph/src/ops/transform/aromatizer.rs +228 -0
  125. umol_py-0.6.0/umol-graph/src/ops/transform/delocalize_charge.rs +231 -0
  126. umol_py-0.6.0/umol-graph/src/ops/transform/kekulizer.rs +917 -0
  127. umol_py-0.6.0/umol-graph/src/ops/transform.rs +35 -0
  128. umol_py-0.6.0/umol-graph/src/ops/valence/atom_typing.rs +382 -0
  129. umol_py-0.6.0/umol-graph/src/ops/valence/compare.rs +157 -0
  130. umol_py-0.6.0/umol-graph/src/ops/valence/completion.rs +345 -0
  131. umol_py-0.6.0/umol-graph/src/ops/valence/counts.rs +797 -0
  132. umol_py-0.6.0/umol-graph/src/ops/valence/registry.rs +346 -0
  133. umol_py-0.6.0/umol-graph/src/ops/valence/table.rs +392 -0
  134. umol_py-0.6.0/umol-graph/src/ops/valence.rs +16 -0
  135. umol_py-0.6.0/umol-graph/src/ops/validate/aromaticity.rs +291 -0
  136. umol_py-0.6.0/umol-graph/src/ops/validate/connectivity.rs +331 -0
  137. umol_py-0.6.0/umol-graph/src/ops/validate/constraint/incidence.rs +874 -0
  138. umol_py-0.6.0/umol-graph/src/ops/validate/constraint/molecule.rs +384 -0
  139. umol_py-0.6.0/umol-graph/src/ops/validate/constraint/relational.rs +859 -0
  140. umol_py-0.6.0/umol-graph/src/ops/validate/constraint/ring.rs +408 -0
  141. umol_py-0.6.0/umol-graph/src/ops/validate/constraint.rs +889 -0
  142. umol_py-0.6.0/umol-graph/src/ops/validate/spin.rs +614 -0
  143. umol_py-0.6.0/umol-graph/src/ops/validate/stereo.rs +548 -0
  144. umol_py-0.6.0/umol-graph/src/ops/validate/valence.rs +115 -0
  145. umol_py-0.6.0/umol-graph/src/ops/validate.rs +629 -0
  146. umol_py-0.6.0/umol-graph/src/ops.rs +15 -0
  147. umol_py-0.6.0/umol-graph/src/parse.rs +202 -0
  148. umol_py-0.6.0/umol-graph/src/utils.rs +9 -0
  149. umol_py-0.6.0/umol-graph-core/Cargo.toml +40 -0
  150. umol_py-0.6.0/umol-graph-core/LICENSE-APACHE +201 -0
  151. umol_py-0.6.0/umol-graph-core/LICENSE-MIT +21 -0
  152. umol_py-0.6.0/umol-graph-core/README.md +84 -0
  153. umol_py-0.6.0/umol-graph-core/benches/algorithms.rs +1367 -0
  154. umol_py-0.6.0/umol-graph-core/benches/matching/data/azulene_planar.toml +22 -0
  155. umol_py-0.6.0/umol-graph-core/benches/matching/data/benzene_planar.toml +16 -0
  156. umol_py-0.6.0/umol-graph-core/benches/matching/data/coronene_planar.toml +46 -0
  157. umol_py-0.6.0/umol-graph-core/benches/matching/data/four_disconnected_hexagons.toml +33 -0
  158. umol_py-0.6.0/umol-graph-core/benches/matching/data/fullerene_c60_planar.toml +130 -0
  159. umol_py-0.6.0/umol-graph-core/benches/matching/data/grid_3x3_planar.toml +25 -0
  160. umol_py-0.6.0/umol-graph-core/benches/matching/data/ladder_2x4_planar.toml +22 -0
  161. umol_py-0.6.0/umol-graph-core/benches/matching/data/naphthalene_planar.toml +22 -0
  162. umol_py-0.6.0/umol-graph-core/src/algorithms/automorphism.rs +643 -0
  163. umol_py-0.6.0/umol-graph-core/src/algorithms/bipartite.rs +152 -0
  164. umol_py-0.6.0/umol-graph-core/src/algorithms/common_subgraph/enumeration.rs +692 -0
  165. umol_py-0.6.0/umol-graph-core/src/algorithms/common_subgraph/maximum.rs +1010 -0
  166. umol_py-0.6.0/umol-graph-core/src/algorithms/common_subgraph.rs +15 -0
  167. umol_py-0.6.0/umol-graph-core/src/algorithms/connected_subgraphs.rs +242 -0
  168. umol_py-0.6.0/umol-graph-core/src/algorithms/connectivity/biconnected.rs +158 -0
  169. umol_py-0.6.0/umol-graph-core/src/algorithms/connectivity/components.rs +80 -0
  170. umol_py-0.6.0/umol-graph-core/src/algorithms/connectivity.rs +14 -0
  171. umol_py-0.6.0/umol-graph-core/src/algorithms/cycles/basis.rs +400 -0
  172. umol_py-0.6.0/umol-graph-core/src/algorithms/cycles/relevant.rs +1065 -0
  173. umol_py-0.6.0/umol-graph-core/src/algorithms/cycles/simple.rs +249 -0
  174. umol_py-0.6.0/umol-graph-core/src/algorithms/cycles/urf.rs +314 -0
  175. umol_py-0.6.0/umol-graph-core/src/algorithms/cycles.rs +1960 -0
  176. umol_py-0.6.0/umol-graph-core/src/algorithms/independent_set.rs +113 -0
  177. umol_py-0.6.0/umol-graph-core/src/algorithms/matching/count.rs +695 -0
  178. umol_py-0.6.0/umol-graph-core/src/algorithms/matching/enumeration.rs +336 -0
  179. umol_py-0.6.0/umol-graph-core/src/algorithms/matching/maximum.rs +1734 -0
  180. umol_py-0.6.0/umol-graph-core/src/algorithms/matching.rs +22 -0
  181. umol_py-0.6.0/umol-graph-core/src/algorithms/paths.rs +217 -0
  182. umol_py-0.6.0/umol-graph-core/src/algorithms/refinement.rs +369 -0
  183. umol_py-0.6.0/umol-graph-core/src/algorithms/subgraph_isomorphism.rs +2503 -0
  184. umol_py-0.6.0/umol-graph-core/src/algorithms/topological_sort.rs +87 -0
  185. umol_py-0.6.0/umol-graph-core/src/algorithms/traversal.rs +89 -0
  186. umol_py-0.6.0/umol-graph-core/src/algorithms.rs +21 -0
  187. umol_py-0.6.0/umol-graph-core/src/correspondence.rs +1024 -0
  188. umol_py-0.6.0/umol-graph-core/src/digraph.rs +102 -0
  189. umol_py-0.6.0/umol-graph-core/src/graph.rs +1263 -0
  190. umol_py-0.6.0/umol-graph-core/src/lib.rs +60 -0
  191. umol_py-0.6.0/umol-graph-core/src/relation.rs +3276 -0
  192. umol_py-0.6.0/umol-graph-core/src/rewriting.rs +410 -0
  193. umol_py-0.6.0/umol-graph-core/src/union_find.rs +114 -0
  194. umol_py-0.6.0/umol-graph-ir/Cargo.toml +90 -0
  195. umol_py-0.6.0/umol-graph-ir/LICENSE-APACHE +201 -0
  196. umol_py-0.6.0/umol-graph-ir/LICENSE-MIT +21 -0
  197. umol_py-0.6.0/umol-graph-ir/README.md +46 -0
  198. umol_py-0.6.0/umol-graph-ir/benches/canonicalize.rs +505 -0
  199. umol_py-0.6.0/umol-graph-ir/benches/concrete.rs +130 -0
  200. umol_py-0.6.0/umol-graph-ir/benches/conversion.rs +65 -0
  201. umol_py-0.6.0/umol-graph-ir/benches/fixtures.rs +60 -0
  202. umol_py-0.6.0/umol-graph-ir/benches/parsing.rs +159 -0
  203. umol_py-0.6.0/umol-graph-ir/benches/rendering.rs +41 -0
  204. umol_py-0.6.0/umol-graph-ir/examples/profile_indole.rs +26 -0
  205. umol_py-0.6.0/umol-graph-ir/spec/umol-dsl-spec.md +1395 -0
  206. umol_py-0.6.0/umol-graph-ir/src/dsl/aromatic.rs +871 -0
  207. umol_py-0.6.0/umol-graph-ir/src/dsl/atom.rs +1933 -0
  208. umol_py-0.6.0/umol-graph-ir/src/dsl/bond.rs +979 -0
  209. umol_py-0.6.0/umol-graph-ir/src/dsl/boolean.rs +182 -0
  210. umol_py-0.6.0/umol-graph-ir/src/dsl/config.rs +903 -0
  211. umol_py-0.6.0/umol-graph-ir/src/dsl/constraint.rs +2157 -0
  212. umol_py-0.6.0/umol-graph-ir/src/dsl/dative.rs +786 -0
  213. umol_py-0.6.0/umol-graph-ir/src/dsl/edit.rs +5302 -0
  214. umol_py-0.6.0/umol-graph-ir/src/dsl/edn_utils.rs +234 -0
  215. umol_py-0.6.0/umol-graph-ir/src/dsl/electrons.rs +101 -0
  216. umol_py-0.6.0/umol-graph-ir/src/dsl/error.rs +137 -0
  217. umol_py-0.6.0/umol-graph-ir/src/dsl/metadata.rs +1594 -0
  218. umol_py-0.6.0/umol-graph-ir/src/dsl/molecule/tests.rs +1176 -0
  219. umol_py-0.6.0/umol-graph-ir/src/dsl/molecule.rs +1553 -0
  220. umol_py-0.6.0/umol-graph-ir/src/dsl/multicenter.rs +870 -0
  221. umol_py-0.6.0/umol-graph-ir/src/dsl/namespace.rs +1117 -0
  222. umol_py-0.6.0/umol-graph-ir/src/dsl/noncovalent.rs +762 -0
  223. umol_py-0.6.0/umol-graph-ir/src/dsl/num.rs +709 -0
  224. umol_py-0.6.0/umol-graph-ir/src/dsl/operators.rs +43 -0
  225. umol_py-0.6.0/umol-graph-ir/src/dsl/predicate.rs +594 -0
  226. umol_py-0.6.0/umol-graph-ir/src/dsl/reaction.rs +4172 -0
  227. umol_py-0.6.0/umol-graph-ir/src/dsl/reaction_span.rs +2725 -0
  228. umol_py-0.6.0/umol-graph-ir/src/dsl/refs.rs +1015 -0
  229. umol_py-0.6.0/umol-graph-ir/src/dsl/relational.rs +1237 -0
  230. umol_py-0.6.0/umol-graph-ir/src/dsl/stereo.rs +2581 -0
  231. umol_py-0.6.0/umol-graph-ir/src/dsl.rs +86 -0
  232. umol_py-0.6.0/umol-graph-ir/src/ir/aromatic.rs +430 -0
  233. umol_py-0.6.0/umol-graph-ir/src/ir/atom.rs +1381 -0
  234. umol_py-0.6.0/umol-graph-ir/src/ir/bond.rs +424 -0
  235. umol_py-0.6.0/umol-graph-ir/src/ir/boolean.rs +157 -0
  236. umol_py-0.6.0/umol-graph-ir/src/ir/canonicalize/tests.rs +4525 -0
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