molframe 0.1.1__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 (1418) hide show
  1. molframe-0.1.1/Cargo.lock +4747 -0
  2. molframe-0.1.1/Cargo.toml +120 -0
  3. molframe-0.1.1/LICENSE +21 -0
  4. molframe-0.1.1/PKG-INFO +7 -0
  5. molframe-0.1.1/crates/molframe/Cargo.toml +107 -0
  6. molframe-0.1.1/crates/molframe/LICENSE +21 -0
  7. molframe-0.1.1/crates/molframe/README.md +36 -0
  8. molframe-0.1.1/crates/molframe/benches/facade.rs +90 -0
  9. molframe-0.1.1/crates/molframe/benches/golden/native.rs +354 -0
  10. molframe-0.1.1/crates/molframe/benches/golden/native_pending/analysis.rs +341 -0
  11. molframe-0.1.1/crates/molframe/benches/golden/native_pending/compare_interop.rs +275 -0
  12. molframe-0.1.1/crates/molframe/benches/golden/native_pending/trajectory.rs +151 -0
  13. molframe-0.1.1/crates/molframe/benches/golden/native_pending/xtal.rs +226 -0
  14. molframe-0.1.1/crates/molframe/benches/golden/native_pending.rs +17 -0
  15. molframe-0.1.1/crates/molframe/benches/golden.rs +256 -0
  16. molframe-0.1.1/crates/molframe/src/engine/core.rs +23 -0
  17. molframe-0.1.1/crates/molframe/src/extensions/analysis.rs +365 -0
  18. molframe-0.1.1/crates/molframe/src/extensions/analysis_impl.rs +302 -0
  19. molframe-0.1.1/crates/molframe/src/extensions/compare.rs +447 -0
  20. molframe-0.1.1/crates/molframe/src/extensions/extension_tests.rs +178 -0
  21. molframe-0.1.1/crates/molframe/src/extensions/mod.rs +56 -0
  22. molframe-0.1.1/crates/molframe/src/extensions/validation.rs +423 -0
  23. molframe-0.1.1/crates/molframe/src/facade/cif_family.rs +63 -0
  24. molframe-0.1.1/crates/molframe/src/facade/extensions.rs +142 -0
  25. molframe-0.1.1/crates/molframe/src/facade/facade_tests.rs +478 -0
  26. molframe-0.1.1/crates/molframe/src/facade/formats/bcif.rs +26 -0
  27. molframe-0.1.1/crates/molframe/src/facade/formats/chem.rs +23 -0
  28. molframe-0.1.1/crates/molframe/src/facade/formats/mmcif.rs +101 -0
  29. molframe-0.1.1/crates/molframe/src/facade/formats/mod.rs +31 -0
  30. molframe-0.1.1/crates/molframe/src/facade/formats/pdb.rs +18 -0
  31. molframe-0.1.1/crates/molframe/src/facade/formats/transform.rs +39 -0
  32. molframe-0.1.1/crates/molframe/src/facade/namespace_tests.rs +73 -0
  33. molframe-0.1.1/crates/molframe/src/facade/plddt_tests.rs +53 -0
  34. molframe-0.1.1/crates/molframe/src/facade/structure_batches.rs +152 -0
  35. molframe-0.1.1/crates/molframe/src/facade/structure_batches_tests.rs +98 -0
  36. molframe-0.1.1/crates/molframe/src/facade.rs +364 -0
  37. molframe-0.1.1/crates/molframe/src/formats.rs +19 -0
  38. molframe-0.1.1/crates/molframe/src/lib.rs +268 -0
  39. molframe-0.1.1/crates/molframe/src/policy_config.rs +410 -0
  40. molframe-0.1.1/crates/molframe/src/policy_config_tests.rs +68 -0
  41. molframe-0.1.1/crates/molframe/src/prelude.rs +75 -0
  42. molframe-0.1.1/crates/molframe/src/structure/backbone.rs +167 -0
  43. molframe-0.1.1/crates/molframe/src/structure/backbone_tests.rs +55 -0
  44. molframe-0.1.1/crates/molframe/src/structure/bonds.rs +198 -0
  45. molframe-0.1.1/crates/molframe/src/structure/bonds_tests.rs +26 -0
  46. molframe-0.1.1/crates/molframe/src/structure/collections.rs +224 -0
  47. molframe-0.1.1/crates/molframe/src/structure/difference.rs +26 -0
  48. molframe-0.1.1/crates/molframe/src/structure/editor.rs +98 -0
  49. molframe-0.1.1/crates/molframe/src/structure/extensions.rs +77 -0
  50. molframe-0.1.1/crates/molframe/src/structure/handle.rs +228 -0
  51. molframe-0.1.1/crates/molframe/src/structure/mod.rs +52 -0
  52. molframe-0.1.1/crates/molframe/src/structure/query.rs +99 -0
  53. molframe-0.1.1/crates/molframe/src/structure/query_tests.rs +33 -0
  54. molframe-0.1.1/crates/molframe/src/structure/roles.rs +63 -0
  55. molframe-0.1.1/crates/molframe/src/structure/selection.rs +112 -0
  56. molframe-0.1.1/crates/molframe/src/structure/side_chains.rs +169 -0
  57. molframe-0.1.1/crates/molframe/src/structure/side_chains_tests.rs +116 -0
  58. molframe-0.1.1/crates/molframe/tests/golden/native_pending/analysis.rs +229 -0
  59. molframe-0.1.1/crates/molframe/tests/golden/native_pending/compare_interop.rs +281 -0
  60. molframe-0.1.1/crates/molframe/tests/golden/native_pending/trajectory.rs +115 -0
  61. molframe-0.1.1/crates/molframe/tests/golden/native_pending/xtal.rs +214 -0
  62. molframe-0.1.1/crates/molframe/tests/golden/native_pending.rs +10 -0
  63. molframe-0.1.1/crates/molframe/tests/golden_tests.rs +228 -0
  64. molframe-0.1.1/crates/molframe/tests/golden_workflows.rs +448 -0
  65. molframe-0.1.1/crates/molframe-adapters/Cargo.toml +28 -0
  66. molframe-0.1.1/crates/molframe-adapters/LICENSE +21 -0
  67. molframe-0.1.1/crates/molframe-adapters/README.md +28 -0
  68. molframe-0.1.1/crates/molframe-adapters/benches/adapters.rs +27 -0
  69. molframe-0.1.1/crates/molframe-adapters/src/download.rs +134 -0
  70. molframe-0.1.1/crates/molframe-adapters/src/download_tests.rs +37 -0
  71. molframe-0.1.1/crates/molframe-adapters/src/lib.rs +12 -0
  72. molframe-0.1.1/crates/molframe-adapters/src/topology.rs +432 -0
  73. molframe-0.1.1/crates/molframe-adapters/src/topology_import.rs +465 -0
  74. molframe-0.1.1/crates/molframe-adapters/src/topology_tests.rs +99 -0
  75. molframe-0.1.1/crates/molframe-analysis/Cargo.toml +33 -0
  76. molframe-0.1.1/crates/molframe-analysis/LICENSE +21 -0
  77. molframe-0.1.1/crates/molframe-analysis/README.md +33 -0
  78. molframe-0.1.1/crates/molframe-analysis/benches/analysis/extended.rs +380 -0
  79. molframe-0.1.1/crates/molframe-analysis/benches/analysis/gnm.rs +61 -0
  80. molframe-0.1.1/crates/molframe-analysis/benches/analysis/pore.rs +180 -0
  81. molframe-0.1.1/crates/molframe-analysis/benches/analysis.rs +307 -0
  82. molframe-0.1.1/crates/molframe-analysis/src/anm/hessian.rs +131 -0
  83. molframe-0.1.1/crates/molframe-analysis/src/anm/hessian_tests.rs +125 -0
  84. molframe-0.1.1/crates/molframe-analysis/src/anm/solver.rs +133 -0
  85. molframe-0.1.1/crates/molframe-analysis/src/anm.rs +282 -0
  86. molframe-0.1.1/crates/molframe-analysis/src/anm_tests.rs +262 -0
  87. molframe-0.1.1/crates/molframe-analysis/src/base_pair.rs +203 -0
  88. molframe-0.1.1/crates/molframe-analysis/src/base_pair_tests.rs +144 -0
  89. molframe-0.1.1/crates/molframe-analysis/src/cation_pi.rs +147 -0
  90. molframe-0.1.1/crates/molframe-analysis/src/cation_pi_tests.rs +83 -0
  91. molframe-0.1.1/crates/molframe-analysis/src/chemistry.rs +69 -0
  92. molframe-0.1.1/crates/molframe-analysis/src/chemistry_test_support.rs +49 -0
  93. molframe-0.1.1/crates/molframe-analysis/src/contact_map.rs +185 -0
  94. molframe-0.1.1/crates/molframe-analysis/src/contact_map_tests.rs +109 -0
  95. molframe-0.1.1/crates/molframe-analysis/src/contacts.rs +302 -0
  96. molframe-0.1.1/crates/molframe-analysis/src/contacts_tests.rs +169 -0
  97. molframe-0.1.1/crates/molframe-analysis/src/density.rs +229 -0
  98. molframe-0.1.1/crates/molframe-analysis/src/density_tests.rs +62 -0
  99. molframe-0.1.1/crates/molframe-analysis/src/dssp.rs +373 -0
  100. molframe-0.1.1/crates/molframe-analysis/src/dssp_binary.rs +108 -0
  101. molframe-0.1.1/crates/molframe-analysis/src/dssp_binary_tests.rs +23 -0
  102. molframe-0.1.1/crates/molframe-analysis/src/dssp_tests.rs +138 -0
  103. molframe-0.1.1/crates/molframe-analysis/src/dynamics.rs +158 -0
  104. molframe-0.1.1/crates/molframe-analysis/src/dynamics_tests.rs +31 -0
  105. molframe-0.1.1/crates/molframe-analysis/src/ensemble.rs +16 -0
  106. molframe-0.1.1/crates/molframe-analysis/src/fragment.rs +128 -0
  107. molframe-0.1.1/crates/molframe-analysis/src/fragment_tests.rs +60 -0
  108. molframe-0.1.1/crates/molframe-analysis/src/gnm/solver.rs +487 -0
  109. molframe-0.1.1/crates/molframe-analysis/src/gnm.rs +187 -0
  110. molframe-0.1.1/crates/molframe-analysis/src/gnm_tests.rs +309 -0
  111. molframe-0.1.1/crates/molframe-analysis/src/governed/adapters_tests.rs +96 -0
  112. molframe-0.1.1/crates/molframe-analysis/src/governed/common.rs +29 -0
  113. molframe-0.1.1/crates/molframe-analysis/src/governed/descriptor.rs +47 -0
  114. molframe-0.1.1/crates/molframe-analysis/src/governed/dynamics.rs +77 -0
  115. molframe-0.1.1/crates/molframe-analysis/src/governed/error.rs +86 -0
  116. molframe-0.1.1/crates/molframe-analysis/src/governed/execute.rs +325 -0
  117. molframe-0.1.1/crates/molframe-analysis/src/governed/execute_tests.rs +215 -0
  118. molframe-0.1.1/crates/molframe-analysis/src/governed/helical.rs +66 -0
  119. molframe-0.1.1/crates/molframe-analysis/src/governed/interactions.rs +215 -0
  120. molframe-0.1.1/crates/molframe-analysis/src/governed/kernel.rs +226 -0
  121. molframe-0.1.1/crates/molframe-analysis/src/governed/mod.rs +47 -0
  122. molframe-0.1.1/crates/molframe-analysis/src/governed/native.rs +128 -0
  123. molframe-0.1.1/crates/molframe-analysis/src/governed/physical.rs +315 -0
  124. molframe-0.1.1/crates/molframe-analysis/src/governed/standalone.rs +127 -0
  125. molframe-0.1.1/crates/molframe-analysis/src/governed/structure.rs +127 -0
  126. molframe-0.1.1/crates/molframe-analysis/src/hbond.rs +262 -0
  127. molframe-0.1.1/crates/molframe-analysis/src/hbond_tests.rs +205 -0
  128. molframe-0.1.1/crates/molframe-analysis/src/helical.rs +206 -0
  129. molframe-0.1.1/crates/molframe-analysis/src/helical_tests.rs +48 -0
  130. molframe-0.1.1/crates/molframe-analysis/src/hse.rs +210 -0
  131. molframe-0.1.1/crates/molframe-analysis/src/hse_tests.rs +89 -0
  132. molframe-0.1.1/crates/molframe-analysis/src/interface.rs +161 -0
  133. molframe-0.1.1/crates/molframe-analysis/src/interface_tests.rs +141 -0
  134. molframe-0.1.1/crates/molframe-analysis/src/leaflet.rs +134 -0
  135. molframe-0.1.1/crates/molframe-analysis/src/leaflet_tests.rs +48 -0
  136. molframe-0.1.1/crates/molframe-analysis/src/lib.rs +162 -0
  137. molframe-0.1.1/crates/molframe-analysis/src/native.rs +132 -0
  138. molframe-0.1.1/crates/molframe-analysis/src/native_tests.rs +120 -0
  139. molframe-0.1.1/crates/molframe-analysis/src/network/graph.rs +321 -0
  140. molframe-0.1.1/crates/molframe-analysis/src/network.rs +91 -0
  141. molframe-0.1.1/crates/molframe-analysis/src/nmd.rs +315 -0
  142. molframe-0.1.1/crates/molframe-analysis/src/nmd_tests.rs +112 -0
  143. molframe-0.1.1/crates/molframe-analysis/src/nucleic.rs +287 -0
  144. molframe-0.1.1/crates/molframe-analysis/src/nucleic_tests.rs +83 -0
  145. molframe-0.1.1/crates/molframe-analysis/src/numeric.rs +44 -0
  146. molframe-0.1.1/crates/molframe-analysis/src/pi_stacking.rs +192 -0
  147. molframe-0.1.1/crates/molframe-analysis/src/pi_stacking_tests.rs +97 -0
  148. molframe-0.1.1/crates/molframe-analysis/src/polymer.rs +102 -0
  149. molframe-0.1.1/crates/molframe-analysis/src/polymer_tests.rs +29 -0
  150. molframe-0.1.1/crates/molframe-analysis/src/pore/index.rs +304 -0
  151. molframe-0.1.1/crates/molframe-analysis/src/pore.rs +396 -0
  152. molframe-0.1.1/crates/molframe-analysis/src/pore_tests.rs +277 -0
  153. molframe-0.1.1/crates/molframe-analysis/src/pucker.rs +55 -0
  154. molframe-0.1.1/crates/molframe-analysis/src/pucker_tests.rs +34 -0
  155. molframe-0.1.1/crates/molframe-analysis/src/radial.rs +323 -0
  156. molframe-0.1.1/crates/molframe-analysis/src/radial_tests.rs +120 -0
  157. molframe-0.1.1/crates/molframe-analysis/src/salt_bridge.rs +116 -0
  158. molframe-0.1.1/crates/molframe-analysis/src/salt_bridge_tests.rs +153 -0
  159. molframe-0.1.1/crates/molframe-analysis/src/stream_surface.rs +62 -0
  160. molframe-0.1.1/crates/molframe-analysis/src/stream_surface_tests.rs +84 -0
  161. molframe-0.1.1/crates/molframe-analysis/src/surface_contacts.rs +197 -0
  162. molframe-0.1.1/crates/molframe-analysis/src/surface_contacts_tests.rs +62 -0
  163. molframe-0.1.1/crates/molframe-analysis/src/tables.rs +83 -0
  164. molframe-0.1.1/crates/molframe-analysis/src/vector_field.rs +307 -0
  165. molframe-0.1.1/crates/molframe-analysis/src/vector_field_tests.rs +63 -0
  166. molframe-0.1.1/crates/molframe-analysis/src/water_bridge.rs +92 -0
  167. molframe-0.1.1/crates/molframe-analysis/src/water_bridge_tests.rs +91 -0
  168. molframe-0.1.1/crates/molframe-audit/Cargo.toml +24 -0
  169. molframe-0.1.1/crates/molframe-audit/LICENSE +21 -0
  170. molframe-0.1.1/crates/molframe-audit/README.md +28 -0
  171. molframe-0.1.1/crates/molframe-audit/benches/audit.rs +56 -0
  172. molframe-0.1.1/crates/molframe-audit/src/batch.rs +119 -0
  173. molframe-0.1.1/crates/molframe-audit/src/batch_tests.rs +67 -0
  174. molframe-0.1.1/crates/molframe-audit/src/engine.rs +134 -0
  175. molframe-0.1.1/crates/molframe-audit/src/engine_tests.rs +54 -0
  176. molframe-0.1.1/crates/molframe-audit/src/lib.rs +22 -0
  177. molframe-0.1.1/crates/molframe-audit/src/numeric.rs +10 -0
  178. molframe-0.1.1/crates/molframe-audit/src/plan.rs +276 -0
  179. molframe-0.1.1/crates/molframe-audit/src/plan_tests.rs +62 -0
  180. molframe-0.1.1/crates/molframe-audit/src/report.rs +43 -0
  181. molframe-0.1.1/crates/molframe-audit/src/value.rs +39 -0
  182. molframe-0.1.1/crates/molframe-bcif/Cargo.toml +32 -0
  183. molframe-0.1.1/crates/molframe-bcif/LICENSE +21 -0
  184. molframe-0.1.1/crates/molframe-bcif/README.md +27 -0
  185. molframe-0.1.1/crates/molframe-bcif/benches/bcif.rs +128 -0
  186. molframe-0.1.1/crates/molframe-bcif/proptest-regressions/encode/float_tests.txt +7 -0
  187. molframe-0.1.1/crates/molframe-bcif/src/codec/decode.rs +472 -0
  188. molframe-0.1.1/crates/molframe-bcif/src/codec/decode_tests.rs +158 -0
  189. molframe-0.1.1/crates/molframe-bcif/src/codec/mod.rs +11 -0
  190. molframe-0.1.1/crates/molframe-bcif/src/codec/numeric_into.rs +408 -0
  191. molframe-0.1.1/crates/molframe-bcif/src/codec/numeric_into_tests.rs +43 -0
  192. molframe-0.1.1/crates/molframe-bcif/src/codec/string_column.rs +171 -0
  193. molframe-0.1.1/crates/molframe-bcif/src/container/document.rs +244 -0
  194. molframe-0.1.1/crates/molframe-bcif/src/container/mod.rs +5 -0
  195. molframe-0.1.1/crates/molframe-bcif/src/encode/float.rs +156 -0
  196. molframe-0.1.1/crates/molframe-bcif/src/encode/float_tests.rs +31 -0
  197. molframe-0.1.1/crates/molframe-bcif/src/encode/integer.rs +415 -0
  198. molframe-0.1.1/crates/molframe-bcif/src/encode/integer_tests.rs +74 -0
  199. molframe-0.1.1/crates/molframe-bcif/src/encode/mod.rs +11 -0
  200. molframe-0.1.1/crates/molframe-bcif/src/encode/strategy.rs +66 -0
  201. molframe-0.1.1/crates/molframe-bcif/src/encode/strategy_tests.rs +48 -0
  202. molframe-0.1.1/crates/molframe-bcif/src/encode/string.rs +119 -0
  203. molframe-0.1.1/crates/molframe-bcif/src/encode/string_tests.rs +25 -0
  204. molframe-0.1.1/crates/molframe-bcif/src/lib.rs +24 -0
  205. molframe-0.1.1/crates/molframe-bcif/src/messagepack.rs +175 -0
  206. molframe-0.1.1/crates/molframe-bcif/src/messagepack_tests.rs +41 -0
  207. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/append.rs +29 -0
  208. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/budget.rs +20 -0
  209. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/decoded.rs +89 -0
  210. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/pull.rs +151 -0
  211. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/stream/checkpoint.rs +162 -0
  212. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/stream/metrics.rs +27 -0
  213. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/stream.rs +491 -0
  214. molframe-0.1.1/crates/molframe-bcif/src/reader/batch/stream_primitive.rs +197 -0
  215. molframe-0.1.1/crates/molframe-bcif/src/reader/batch.rs +460 -0
  216. molframe-0.1.1/crates/molframe-bcif/src/reader/batch_tests.rs +301 -0
  217. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/column.rs +284 -0
  218. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/container.rs +159 -0
  219. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/container_tests.rs +22 -0
  220. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/ensemble.rs +108 -0
  221. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/external.rs +144 -0
  222. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/mod.rs +15 -0
  223. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/projection.rs +132 -0
  224. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/reader.rs +94 -0
  225. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/values.rs +204 -0
  226. molframe-0.1.1/crates/molframe-bcif/src/reader/direct/values_tests.rs +34 -0
  227. molframe-0.1.1/crates/molframe-bcif/src/reader/index/cursor.rs +116 -0
  228. molframe-0.1.1/crates/molframe-bcif/src/reader/index/marker.rs +124 -0
  229. molframe-0.1.1/crates/molframe-bcif/src/reader/index.rs +244 -0
  230. molframe-0.1.1/crates/molframe-bcif/src/reader/index_tests.rs +154 -0
  231. molframe-0.1.1/crates/molframe-bcif/src/reader/mod.rs +9 -0
  232. molframe-0.1.1/crates/molframe-bcif/src/reader/structure.rs +109 -0
  233. molframe-0.1.1/crates/molframe-bcif/src/reader/structure_tests.rs +239 -0
  234. molframe-0.1.1/crates/molframe-bcif/src/writer/atoms.rs +175 -0
  235. molframe-0.1.1/crates/molframe-bcif/src/writer/column.rs +195 -0
  236. molframe-0.1.1/crates/molframe-bcif/src/writer/connections.rs +184 -0
  237. molframe-0.1.1/crates/molframe-bcif/src/writer/document.rs +191 -0
  238. molframe-0.1.1/crates/molframe-bcif/src/writer/document_tests.rs +71 -0
  239. molframe-0.1.1/crates/molframe-bcif/src/writer/metadata.rs +282 -0
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