omgkit 0.0.1__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 (164) hide show
  1. omgkit-0.0.1/Cargo.lock +730 -0
  2. omgkit-0.0.1/Cargo.toml +68 -0
  3. omgkit-0.0.1/LICENSE +28 -0
  4. omgkit-0.0.1/PKG-INFO +129 -0
  5. omgkit-0.0.1/README.md +111 -0
  6. omgkit-0.0.1/crates/omgkit-chem/Cargo.toml +24 -0
  7. omgkit-0.0.1/crates/omgkit-chem/README.md +111 -0
  8. omgkit-0.0.1/crates/omgkit-chem/examples/bench_kekulize.rs +74 -0
  9. omgkit-0.0.1/crates/omgkit-chem/examples/bench_pipeline.rs +66 -0
  10. omgkit-0.0.1/crates/omgkit-chem/examples/dump_canonical.rs +28 -0
  11. omgkit-0.0.1/crates/omgkit-chem/examples/dump_sanitized.rs +27 -0
  12. omgkit-0.0.1/crates/omgkit-chem/src/adjust_hs.rs +160 -0
  13. omgkit-0.0.1/crates/omgkit-chem/src/aromaticity.rs +790 -0
  14. omgkit-0.0.1/crates/omgkit-chem/src/cleanup.rs +307 -0
  15. omgkit-0.0.1/crates/omgkit-chem/src/cleanup_chirality.rs +221 -0
  16. omgkit-0.0.1/crates/omgkit-chem/src/conjugation.rs +397 -0
  17. omgkit-0.0.1/crates/omgkit-chem/src/explicit_hs.rs +218 -0
  18. omgkit-0.0.1/crates/omgkit-chem/src/kekulize.rs +1114 -0
  19. omgkit-0.0.1/crates/omgkit-chem/src/lib.rs +64 -0
  20. omgkit-0.0.1/crates/omgkit-chem/src/organometallics.rs +279 -0
  21. omgkit-0.0.1/crates/omgkit-chem/src/pipeline.rs +206 -0
  22. omgkit-0.0.1/crates/omgkit-chem/src/radicals.rs +214 -0
  23. omgkit-0.0.1/crates/omgkit-chem/src/remove_hs.rs +205 -0
  24. omgkit-0.0.1/crates/omgkit-chem/src/rings.rs +693 -0
  25. omgkit-0.0.1/crates/omgkit-chem/src/sssr.rs +797 -0
  26. omgkit-0.0.1/crates/omgkit-chem/src/valence.rs +154 -0
  27. omgkit-0.0.1/crates/omgkit-chem/tests/canonical_write_survives_resanitize.rs +293 -0
  28. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_aromaticity.rs +291 -0
  29. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_cleanup.rs +302 -0
  30. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_full.rs +302 -0
  31. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_hybrid.rs +313 -0
  32. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_kekulize.rs +324 -0
  33. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_radicals.rs +258 -0
  34. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_rings.rs +306 -0
  35. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_ringset.rs +361 -0
  36. omgkit-0.0.1/crates/omgkit-chem/tests/differential_l2_valence.rs +260 -0
  37. omgkit-0.0.1/crates/omgkit-chem/tests/documented_measurements.rs +154 -0
  38. omgkit-0.0.1/crates/omgkit-chem/tests/remove_hs.rs +199 -0
  39. omgkit-0.0.1/crates/omgkit-chem/tests/scaling.rs +393 -0
  40. omgkit-0.0.1/crates/omgkit-conf/Cargo.toml +27 -0
  41. omgkit-0.0.1/crates/omgkit-conf/README.md +111 -0
  42. omgkit-0.0.1/crates/omgkit-conf/data/mmff.angles.tsv +174 -0
  43. omgkit-0.0.1/crates/omgkit-conf/data/mmff.bonds.tsv +135 -0
  44. omgkit-0.0.1/crates/omgkit-conf/data/mmff.ringtorsion.tsv +22 -0
  45. omgkit-0.0.1/crates/omgkit-conf/examples/bench_conformers.rs +86 -0
  46. omgkit-0.0.1/crates/omgkit-conf/examples/bounds_oracle.rs +766 -0
  47. omgkit-0.0.1/crates/omgkit-conf/examples/chiral_oracle.rs +346 -0
  48. omgkit-0.0.1/crates/omgkit-conf/examples/conformer_oracle.rs +495 -0
  49. omgkit-0.0.1/crates/omgkit-conf/examples/dump_conformers.rs +113 -0
  50. omgkit-0.0.1/crates/omgkit-conf/examples/dump_molblock3d.rs +73 -0
  51. omgkit-0.0.1/crates/omgkit-conf/examples/eigen_oracle.rs +300 -0
  52. omgkit-0.0.1/crates/omgkit-conf/examples/feasibility.rs +689 -0
  53. omgkit-0.0.1/crates/omgkit-conf/examples/shared/baseline_mol.rs +162 -0
  54. omgkit-0.0.1/crates/omgkit-conf/examples/smooth_oracle.rs +156 -0
  55. omgkit-0.0.1/crates/omgkit-conf/examples/threading_oracle.rs +324 -0
  56. omgkit-0.0.1/crates/omgkit-conf/src/bounds.rs +1302 -0
  57. omgkit-0.0.1/crates/omgkit-conf/src/chiral.rs +590 -0
  58. omgkit-0.0.1/crates/omgkit-conf/src/embed.rs +528 -0
  59. omgkit-0.0.1/crates/omgkit-conf/src/field.rs +892 -0
  60. omgkit-0.0.1/crates/omgkit-conf/src/lib.rs +110 -0
  61. omgkit-0.0.1/crates/omgkit-conf/src/linalg.rs +720 -0
  62. omgkit-0.0.1/crates/omgkit-conf/src/optimize.rs +903 -0
  63. omgkit-0.0.1/crates/omgkit-conf/src/params.rs +407 -0
  64. omgkit-0.0.1/crates/omgkit-conf/src/pipeline.rs +629 -0
  65. omgkit-0.0.1/crates/omgkit-conf/src/smooth.rs +308 -0
  66. omgkit-0.0.1/crates/omgkit-conf/src/spread.rs +202 -0
  67. omgkit-0.0.1/crates/omgkit-conf/src/threading.rs +609 -0
  68. omgkit-0.0.1/crates/omgkit-conf/tests/baseline_sizes.rs +208 -0
  69. omgkit-0.0.1/crates/omgkit-conf/tests/chirality_truth.rs +227 -0
  70. omgkit-0.0.1/crates/omgkit-conf/tests/small_molecule_geometry.rs +86 -0
  71. omgkit-0.0.1/crates/omgkit-core/Cargo.toml +20 -0
  72. omgkit-0.0.1/crates/omgkit-core/README.md +111 -0
  73. omgkit-0.0.1/crates/omgkit-core/src/batch.rs +456 -0
  74. omgkit-0.0.1/crates/omgkit-core/src/builder.rs +785 -0
  75. omgkit-0.0.1/crates/omgkit-core/src/element.rs +248 -0
  76. omgkit-0.0.1/crates/omgkit-core/src/element_data.rs +1694 -0
  77. omgkit-0.0.1/crates/omgkit-core/src/error.rs +72 -0
  78. omgkit-0.0.1/crates/omgkit-core/src/lib.rs +64 -0
  79. omgkit-0.0.1/crates/omgkit-core/src/polyhedron.rs +420 -0
  80. omgkit-0.0.1/crates/omgkit-core/src/types.rs +377 -0
  81. omgkit-0.0.1/crates/omgkit-core/src/valence.rs +431 -0
  82. omgkit-0.0.1/crates/omgkit-core/src/view.rs +412 -0
  83. omgkit-0.0.1/crates/omgkit-depict/Cargo.toml +56 -0
  84. omgkit-0.0.1/crates/omgkit-depict/README.md +111 -0
  85. omgkit-0.0.1/crates/omgkit-depict/examples/audit.rs +1352 -0
  86. omgkit-0.0.1/crates/omgkit-depict/examples/draw.rs +136 -0
  87. omgkit-0.0.1/crates/omgkit-depict/examples/dump_molblock.rs +98 -0
  88. omgkit-0.0.1/crates/omgkit-depict/examples/label_dirs.rs +122 -0
  89. omgkit-0.0.1/crates/omgkit-depict/src/arcs.rs +978 -0
  90. omgkit-0.0.1/crates/omgkit-depict/src/chains.rs +1523 -0
  91. omgkit-0.0.1/crates/omgkit-depict/src/geom.rs +332 -0
  92. omgkit-0.0.1/crates/omgkit-depict/src/hydrogens.rs +324 -0
  93. omgkit-0.0.1/crates/omgkit-depict/src/label.rs +811 -0
  94. omgkit-0.0.1/crates/omgkit-depict/src/layout.rs +880 -0
  95. omgkit-0.0.1/crates/omgkit-depict/src/lib.rs +1072 -0
  96. omgkit-0.0.1/crates/omgkit-depict/src/orient.rs +278 -0
  97. omgkit-0.0.1/crates/omgkit-depict/src/raster.rs +281 -0
  98. omgkit-0.0.1/crates/omgkit-depict/src/refine.rs +2101 -0
  99. omgkit-0.0.1/crates/omgkit-depict/src/render.rs +3591 -0
  100. omgkit-0.0.1/crates/omgkit-depict/src/rings.rs +1962 -0
  101. omgkit-0.0.1/crates/omgkit-depict/src/stereo.rs +926 -0
  102. omgkit-0.0.1/crates/omgkit-depict/src/style.rs +452 -0
  103. omgkit-0.0.1/crates/omgkit-depict/src/svg.rs +326 -0
  104. omgkit-0.0.1/crates/omgkit-depict/src/templates.rs +418 -0
  105. omgkit-0.0.1/crates/omgkit-depict/src/templates_data.rs +58 -0
  106. omgkit-0.0.1/crates/omgkit-io/Cargo.toml +24 -0
  107. omgkit-0.0.1/crates/omgkit-io/README.md +111 -0
  108. omgkit-0.0.1/crates/omgkit-io/examples/dump_bond_stereo.rs +39 -0
  109. omgkit-0.0.1/crates/omgkit-io/examples/dump_smarts.rs +39 -0
  110. omgkit-0.0.1/crates/omgkit-io/examples/dump_smarts_written.rs +22 -0
  111. omgkit-0.0.1/crates/omgkit-io/examples/dump_written.rs +16 -0
  112. omgkit-0.0.1/crates/omgkit-io/examples/rank_cost.rs +65 -0
  113. omgkit-0.0.1/crates/omgkit-io/examples/read_molblock.rs +65 -0
  114. omgkit-0.0.1/crates/omgkit-io/examples/read_sdf.rs +59 -0
  115. omgkit-0.0.1/crates/omgkit-io/examples/write_smiles.rs +51 -0
  116. omgkit-0.0.1/crates/omgkit-io/src/canon.rs +748 -0
  117. omgkit-0.0.1/crates/omgkit-io/src/error.rs +119 -0
  118. omgkit-0.0.1/crates/omgkit-io/src/lib.rs +34 -0
  119. omgkit-0.0.1/crates/omgkit-io/src/molblock.rs +1072 -0
  120. omgkit-0.0.1/crates/omgkit-io/src/smarts/bond.rs +237 -0
  121. omgkit-0.0.1/crates/omgkit-io/src/smarts/eval.rs +496 -0
  122. omgkit-0.0.1/crates/omgkit-io/src/smarts/expr.rs +184 -0
  123. omgkit-0.0.1/crates/omgkit-io/src/smarts/mol.rs +696 -0
  124. omgkit-0.0.1/crates/omgkit-io/src/smarts/parse.rs +570 -0
  125. omgkit-0.0.1/crates/omgkit-io/src/smarts/reaction.rs +286 -0
  126. omgkit-0.0.1/crates/omgkit-io/src/smarts/write.rs +378 -0
  127. omgkit-0.0.1/crates/omgkit-io/src/smarts.rs +121 -0
  128. omgkit-0.0.1/crates/omgkit-io/src/smiles/write.rs +918 -0
  129. omgkit-0.0.1/crates/omgkit-io/src/smiles.rs +1759 -0
  130. omgkit-0.0.1/crates/omgkit-io/src/stereo.rs +1947 -0
  131. omgkit-0.0.1/crates/omgkit-io/src/wedge.rs +323 -0
  132. omgkit-0.0.1/crates/omgkit-io/tests/adjacency_index.rs +146 -0
  133. omgkit-0.0.1/crates/omgkit-io/tests/canon_scaling.rs +203 -0
  134. omgkit-0.0.1/crates/omgkit-io/tests/canonical_invariance.rs +804 -0
  135. omgkit-0.0.1/crates/omgkit-io/tests/differential_l1.rs +322 -0
  136. omgkit-0.0.1/crates/omgkit-io/tests/differential_l3.rs +405 -0
  137. omgkit-0.0.1/crates/omgkit-io/tests/differential_smarts.rs +141 -0
  138. omgkit-0.0.1/crates/omgkit-io/tests/roundtrip_smarts.rs +329 -0
  139. omgkit-0.0.1/crates/omgkit-io/tests/roundtrip_smiles.rs +1105 -0
  140. omgkit-0.0.1/crates/omgkit-io/tests/smarts_parse.rs +246 -0
  141. omgkit-0.0.1/crates/omgkit-match/Cargo.toml +24 -0
  142. omgkit-0.0.1/crates/omgkit-match/README.md +111 -0
  143. omgkit-0.0.1/crates/omgkit-match/examples/demo_extreme.rs +104 -0
  144. omgkit-0.0.1/crates/omgkit-match/examples/demo_hard.rs +116 -0
  145. omgkit-0.0.1/crates/omgkit-match/examples/demo_reactions.rs +155 -0
  146. omgkit-0.0.1/crates/omgkit-match/examples/dump_matches.rs +98 -0
  147. omgkit-0.0.1/crates/omgkit-match/examples/dump_reactions.rs +114 -0
  148. omgkit-0.0.1/crates/omgkit-match/src/byproduct.rs +948 -0
  149. omgkit-0.0.1/crates/omgkit-match/src/lib.rs +32 -0
  150. omgkit-0.0.1/crates/omgkit-match/src/matcher.rs +616 -0
  151. omgkit-0.0.1/crates/omgkit-match/src/props.rs +144 -0
  152. omgkit-0.0.1/crates/omgkit-match/src/react.rs +1817 -0
  153. omgkit-0.0.1/crates/omgkit-match/tests/basic.rs +317 -0
  154. omgkit-0.0.1/crates/omgkit-match/tests/byproduct.rs +555 -0
  155. omgkit-0.0.1/crates/omgkit-match/tests/differential.rs +364 -0
  156. omgkit-0.0.1/crates/omgkit-match/tests/reaction.rs +1368 -0
  157. omgkit-0.0.1/crates/omgkit-match/tests/scaling.rs +578 -0
  158. omgkit-0.0.1/crates/omgkit-match/tests/smarts_write_semantics.rs +255 -0
  159. omgkit-0.0.1/crates/omgkit-py/Cargo.toml +55 -0
  160. omgkit-0.0.1/crates/omgkit-py/LICENSE +28 -0
  161. omgkit-0.0.1/crates/omgkit-py/README.md +111 -0
  162. omgkit-0.0.1/crates/omgkit-py/build.rs +21 -0
  163. omgkit-0.0.1/crates/omgkit-py/src/lib.rs +855 -0
  164. omgkit-0.0.1/pyproject.toml +35 -0
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