chemicalml 0.2.0 → 0.2.1

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 (304) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/release.yml +7 -1
  3. data/CLAUDE.md +48 -41
  4. data/TODO.align/36-molecular-convention-coverage.md +46 -0
  5. data/TODO.align/37-compchem-convention-coverage.md +55 -0
  6. data/TODO.align/38-dictionary-convention-coverage.md +34 -0
  7. data/TODO.align/39-unit-dictionary-convention-coverage.md +33 -0
  8. data/TODO.align/40-unit-type-dictionary-convention-coverage.md +28 -0
  9. data/TODO.align/41-expand-canonical-model-layer.md +43 -0
  10. data/TODO.align/42-translator-wire-new-models.md +31 -0
  11. data/TODO.align/43-dictionary-model-no-to-h.md +39 -0
  12. data/TODO.align/44-schema3-only-and-schema24-module.md +44 -0
  13. data/TODO.align/45-documentation-and-final-verification.md +23 -0
  14. data/TODO.align/46-lattice-vector-content.md +24 -0
  15. data/TODO.align/47-molecule-crystal-spectra-property-lists.md +23 -0
  16. data/TODO.align/48-model-list-and-module-lists.md +21 -0
  17. data/TODO.align/49-more-chemistry-models.md +34 -0
  18. data/TODO.align/50-validation-report.md +29 -0
  19. data/TODO.align/51-convention-auto-detection.md +30 -0
  20. data/TODO.align/52-schema24-legacy-elements.md +28 -0
  21. data/TODO.align/53-round-trip-integration-specs.md +30 -0
  22. data/TODO.align/54-document-versioned-parser-shim.md +38 -0
  23. data/TODO.align/55-molecule-missing-attributes.md +20 -0
  24. data/TODO.align/56-geometry-models.md +24 -0
  25. data/TODO.align/57-compchem-models.md +26 -0
  26. data/TODO.align/58-remaining-models.md +24 -0
  27. data/TODO.align/59-wire-new-models-translator.md +18 -0
  28. data/TODO.align/60-docs-and-final-verification.md +19 -0
  29. data/lib/chemicalml/cml/base/abundance.rb +6 -0
  30. data/lib/chemicalml/cml/base/action.rb +20 -0
  31. data/lib/chemicalml/cml/base/action_list.rb +18 -0
  32. data/lib/chemicalml/cml/base/alternative.rb +28 -0
  33. data/lib/chemicalml/cml/base/amount.rb +2 -0
  34. data/lib/chemicalml/cml/base/angle.rb +12 -0
  35. data/lib/chemicalml/cml/base/annotation.rb +30 -0
  36. data/lib/chemicalml/cml/base/appinfo.rb +32 -0
  37. data/lib/chemicalml/cml/base/arg.rb +46 -0
  38. data/lib/chemicalml/cml/base/array.rb +22 -0
  39. data/lib/chemicalml/cml/base/array_list.rb +2 -0
  40. data/lib/chemicalml/cml/base/atom.rb +18 -0
  41. data/lib/chemicalml/cml/base/atom_array.rb +38 -0
  42. data/lib/chemicalml/cml/base/atom_parity.rb +8 -0
  43. data/lib/chemicalml/cml/base/atom_set.rb +2 -0
  44. data/lib/chemicalml/cml/base/atom_type.rb +4 -0
  45. data/lib/chemicalml/cml/base/atom_type_list.rb +2 -0
  46. data/lib/chemicalml/cml/base/atomic_basis_function.rb +4 -0
  47. data/lib/chemicalml/cml/base/band.rb +2 -0
  48. data/lib/chemicalml/cml/base/basis_set.rb +4 -0
  49. data/lib/chemicalml/cml/base/bond.rb +6 -0
  50. data/lib/chemicalml/cml/base/bond_array.rb +16 -0
  51. data/lib/chemicalml/cml/base/bond_set.rb +2 -0
  52. data/lib/chemicalml/cml/base/bond_stereo.rb +10 -0
  53. data/lib/chemicalml/cml/base/bond_type.rb +2 -0
  54. data/lib/chemicalml/cml/base/bond_type_list.rb +2 -0
  55. data/lib/chemicalml/cml/base/cell_parameter.rb +4 -0
  56. data/lib/chemicalml/cml/base/complex_object.rb +30 -0
  57. data/lib/chemicalml/cml/base/condition_list.rb +4 -0
  58. data/lib/chemicalml/cml/base/crystal.rb +2 -0
  59. data/lib/chemicalml/cml/base/description.rb +2 -0
  60. data/lib/chemicalml/cml/base/dictionary.rb +6 -0
  61. data/lib/chemicalml/cml/base/dimension.rb +10 -0
  62. data/lib/chemicalml/cml/base/eigen.rb +2 -0
  63. data/lib/chemicalml/cml/base/electron.rb +6 -0
  64. data/lib/chemicalml/cml/base/enumeration.rb +32 -0
  65. data/lib/chemicalml/cml/base/expression.rb +32 -0
  66. data/lib/chemicalml/cml/base/float.rb +40 -0
  67. data/lib/chemicalml/cml/base/float_array.rb +42 -0
  68. data/lib/chemicalml/cml/base/fragment.rb +6 -0
  69. data/lib/chemicalml/cml/base/fragment_list.rb +4 -0
  70. data/lib/chemicalml/cml/base/identifier.rb +8 -0
  71. data/lib/chemicalml/cml/base/integer.rb +40 -0
  72. data/lib/chemicalml/cml/base/integer_array.rb +42 -0
  73. data/lib/chemicalml/cml/base/isotope.rb +2 -0
  74. data/lib/chemicalml/cml/base/isotope_list.rb +2 -0
  75. data/lib/chemicalml/cml/base/join.rb +6 -0
  76. data/lib/chemicalml/cml/base/kpoint.rb +2 -0
  77. data/lib/chemicalml/cml/base/label.rb +2 -0
  78. data/lib/chemicalml/cml/base/lattice.rb +2 -0
  79. data/lib/chemicalml/cml/base/lattice_vector.rb +2 -0
  80. data/lib/chemicalml/cml/base/length.rb +10 -0
  81. data/lib/chemicalml/cml/base/line3.rb +6 -0
  82. data/lib/chemicalml/cml/base/link.rb +20 -0
  83. data/lib/chemicalml/cml/base/list.rb +2 -0
  84. data/lib/chemicalml/cml/base/map.rb +12 -0
  85. data/lib/chemicalml/cml/base/matrix.rb +12 -0
  86. data/lib/chemicalml/cml/base/metadata.rb +4 -0
  87. data/lib/chemicalml/cml/base/metadata_list.rb +6 -0
  88. data/lib/chemicalml/cml/base/molecule.rb +10 -0
  89. data/lib/chemicalml/cml/base/molecule_list.rb +2 -0
  90. data/lib/chemicalml/cml/base/name.rb +2 -0
  91. data/lib/chemicalml/cml/base/object.rb +4 -0
  92. data/lib/chemicalml/cml/base/observation.rb +4 -0
  93. data/lib/chemicalml/cml/base/operator.rb +32 -0
  94. data/lib/chemicalml/cml/base/parameter.rb +10 -0
  95. data/lib/chemicalml/cml/base/parameter_list.rb +6 -0
  96. data/lib/chemicalml/cml/base/particle.rb +6 -0
  97. data/lib/chemicalml/cml/base/peak.rb +30 -0
  98. data/lib/chemicalml/cml/base/peak_group.rb +38 -0
  99. data/lib/chemicalml/cml/base/peak_list.rb +2 -0
  100. data/lib/chemicalml/cml/base/peak_structure.rb +14 -0
  101. data/lib/chemicalml/cml/base/plane3.rb +2 -0
  102. data/lib/chemicalml/cml/base/point3.rb +2 -0
  103. data/lib/chemicalml/cml/base/potential_form.rb +2 -0
  104. data/lib/chemicalml/cml/base/product.rb +16 -0
  105. data/lib/chemicalml/cml/base/product_list.rb +14 -0
  106. data/lib/chemicalml/cml/base/property.rb +6 -0
  107. data/lib/chemicalml/cml/base/property_list.rb +6 -0
  108. data/lib/chemicalml/cml/base/reactant.rb +16 -0
  109. data/lib/chemicalml/cml/base/reactant_list.rb +14 -0
  110. data/lib/chemicalml/cml/base/reaction.rb +16 -0
  111. data/lib/chemicalml/cml/base/reaction_list.rb +12 -0
  112. data/lib/chemicalml/cml/base/reaction_scheme.rb +10 -0
  113. data/lib/chemicalml/cml/base/reaction_step.rb +6 -0
  114. data/lib/chemicalml/cml/base/reaction_step_list.rb +8 -0
  115. data/lib/chemicalml/cml/base/region.rb +8 -0
  116. data/lib/chemicalml/cml/base/related_entry.rb +26 -0
  117. data/lib/chemicalml/cml/base/sample.rb +4 -0
  118. data/lib/chemicalml/cml/base/scalar.rb +18 -0
  119. data/lib/chemicalml/cml/base/spectator.rb +2 -0
  120. data/lib/chemicalml/cml/base/spectrum.rb +12 -0
  121. data/lib/chemicalml/cml/base/spectrum_data.rb +2 -0
  122. data/lib/chemicalml/cml/base/spectrum_list.rb +4 -0
  123. data/lib/chemicalml/cml/base/sphere3.rb +2 -0
  124. data/lib/chemicalml/cml/base/string.rb +32 -0
  125. data/lib/chemicalml/cml/base/string_array.rb +40 -0
  126. data/lib/chemicalml/cml/base/substance.rb +12 -0
  127. data/lib/chemicalml/cml/base/substance_list.rb +6 -0
  128. data/lib/chemicalml/cml/base/symmetry.rb +4 -0
  129. data/lib/chemicalml/cml/base/system.rb +4 -0
  130. data/lib/chemicalml/cml/base/table.rb +10 -0
  131. data/lib/chemicalml/cml/base/table_content.rb +2 -0
  132. data/lib/chemicalml/cml/base/table_header_cell.rb +10 -0
  133. data/lib/chemicalml/cml/base/tcell.rb +34 -0
  134. data/lib/chemicalml/cml/base/torsion.rb +12 -0
  135. data/lib/chemicalml/cml/base/trow.rb +32 -0
  136. data/lib/chemicalml/cml/base/unit.rb +12 -0
  137. data/lib/chemicalml/cml/base/unit_list.rb +12 -0
  138. data/lib/chemicalml/cml/base/unit_type.rb +10 -0
  139. data/lib/chemicalml/cml/base/unit_type_list.rb +10 -0
  140. data/lib/chemicalml/cml/base/vector3.rb +2 -0
  141. data/lib/chemicalml/cml/base/xaxis.rb +6 -0
  142. data/lib/chemicalml/cml/base/yaxis.rb +6 -0
  143. data/lib/chemicalml/cml/base.rb +17 -0
  144. data/lib/chemicalml/cml/elements.rb +39 -4
  145. data/lib/chemicalml/cml/role/alternative.rb +10 -0
  146. data/lib/chemicalml/cml/role/annotation.rb +10 -0
  147. data/lib/chemicalml/cml/role/appinfo.rb +10 -0
  148. data/lib/chemicalml/cml/role/arg.rb +10 -0
  149. data/lib/chemicalml/cml/role/cml_module.rb +2 -3
  150. data/lib/chemicalml/cml/role/complex_object.rb +10 -0
  151. data/lib/chemicalml/cml/role/enumeration.rb +10 -0
  152. data/lib/chemicalml/cml/role/expression.rb +10 -0
  153. data/lib/chemicalml/cml/role/float.rb +10 -0
  154. data/lib/chemicalml/cml/role/float_array.rb +10 -0
  155. data/lib/chemicalml/cml/role/integer.rb +10 -0
  156. data/lib/chemicalml/cml/role/integer_array.rb +10 -0
  157. data/lib/chemicalml/cml/role/operator.rb +10 -0
  158. data/lib/chemicalml/cml/role/related_entry.rb +10 -0
  159. data/lib/chemicalml/cml/role/string.rb +10 -0
  160. data/lib/chemicalml/cml/role/string_array.rb +10 -0
  161. data/lib/chemicalml/cml/role/tcell.rb +10 -0
  162. data/lib/chemicalml/cml/role/trow.rb +10 -0
  163. data/lib/chemicalml/cml/role.rb +17 -0
  164. data/lib/chemicalml/cml/schema24/alternative.rb +14 -0
  165. data/lib/chemicalml/cml/schema24/annotation.rb +15 -0
  166. data/lib/chemicalml/cml/schema24/appinfo.rb +15 -0
  167. data/lib/chemicalml/cml/schema24/arg.rb +14 -0
  168. data/lib/chemicalml/cml/schema24/cml_module.rb +18 -0
  169. data/lib/chemicalml/cml/schema24/complex_object.rb +14 -0
  170. data/lib/chemicalml/cml/schema24/configuration.rb +5 -2
  171. data/lib/chemicalml/cml/schema24/enumeration.rb +16 -0
  172. data/lib/chemicalml/cml/schema24/expression.rb +14 -0
  173. data/lib/chemicalml/cml/schema24/float.rb +14 -0
  174. data/lib/chemicalml/cml/schema24/float_array.rb +14 -0
  175. data/lib/chemicalml/cml/schema24/integer.rb +14 -0
  176. data/lib/chemicalml/cml/schema24/integer_array.rb +14 -0
  177. data/lib/chemicalml/cml/schema24/operator.rb +14 -0
  178. data/lib/chemicalml/cml/schema24/related_entry.rb +14 -0
  179. data/lib/chemicalml/cml/schema24/string.rb +14 -0
  180. data/lib/chemicalml/cml/schema24/string_array.rb +14 -0
  181. data/lib/chemicalml/cml/schema24/tcell.rb +14 -0
  182. data/lib/chemicalml/cml/schema24/trow.rb +14 -0
  183. data/lib/chemicalml/cml/schema24.rb +33 -5
  184. data/lib/chemicalml/cml.rb +1 -3
  185. data/lib/chemicalml/context_configuration.rb +8 -2
  186. data/lib/chemicalml/convention/base.rb +17 -3
  187. data/lib/chemicalml/convention/compchem/constraints/array_rules.rb +44 -0
  188. data/lib/chemicalml/convention/compchem/constraints/calculation_requires_finalization.rb +28 -0
  189. data/lib/chemicalml/convention/compchem/constraints/compchem_module_must_contain_job_list.rb +4 -4
  190. data/lib/chemicalml/convention/compchem/constraints/environment_at_most_one_property_list.rb +26 -0
  191. data/lib/chemicalml/convention/compchem/constraints/environment_must_not_contain_parameter.rb +28 -0
  192. data/lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_molecule.rb +26 -0
  193. data/lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_property_list.rb +26 -0
  194. data/lib/chemicalml/convention/compchem/constraints/finalization_must_not_contain_parameter.rb +27 -0
  195. data/lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_molecule.rb +26 -0
  196. data/lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_parameter_list.rb +26 -0
  197. data/lib/chemicalml/convention/compchem/constraints/initialization_must_not_contain_property.rb +28 -0
  198. data/lib/chemicalml/convention/compchem/constraints/job_list_module_must_have_id.rb +24 -0
  199. data/lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_environment.rb +25 -0
  200. data/lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_finalization.rb +25 -0
  201. data/lib/chemicalml/convention/compchem/constraints/job_module_must_have_id.rb +24 -0
  202. data/lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb +6 -9
  203. data/lib/chemicalml/convention/compchem/constraints/matrix_rules.rb +48 -0
  204. data/lib/chemicalml/convention/compchem/constraints/module_predicates.rb +50 -0
  205. data/lib/chemicalml/convention/compchem/constraints/scalar_units.rb +42 -0
  206. data/lib/chemicalml/convention/compchem/constraints.rb +36 -2
  207. data/lib/chemicalml/convention/compchem.rb +16 -0
  208. data/lib/chemicalml/convention/constraint.rb +31 -18
  209. data/lib/chemicalml/convention/coordinator.rb +89 -0
  210. data/lib/chemicalml/convention/detection.rb +33 -0
  211. data/lib/chemicalml/convention/dictionary/constraints/dictionary_must_have_namespace.rb +28 -0
  212. data/lib/chemicalml/convention/dictionary/constraints/dictionary_namespace_should_end_with_slash_or_hash.rb +32 -0
  213. data/lib/chemicalml/convention/dictionary/constraints/entry_id_must_match_pattern.rb +33 -0
  214. data/lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb +3 -3
  215. data/lib/chemicalml/convention/dictionary/constraints/entry_must_contain_definition.rb +28 -0
  216. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb +5 -5
  217. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_unit_type.rb +30 -0
  218. data/lib/chemicalml/convention/dictionary/constraints/entry_units_co_constraints.rb +44 -0
  219. data/lib/chemicalml/convention/dictionary/constraints.rb +12 -0
  220. data/lib/chemicalml/convention/dictionary.rb +6 -0
  221. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_be_child_of_molecule_or_formula.rb +40 -0
  222. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb +3 -3
  223. data/lib/chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired.rb +5 -5
  224. data/lib/chemicalml/convention/molecular/constraints/atom_id_must_match_pattern.rb +4 -4
  225. data/lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb +2 -2
  226. data/lib/chemicalml/convention/molecular/constraints/atom_must_have_element_type.rb +3 -3
  227. data/lib/chemicalml/convention/molecular/constraints/atom_must_have_id.rb +3 -3
  228. data/lib/chemicalml/convention/molecular/constraints/bond_array_must_be_child_of_molecule.rb +36 -0
  229. data/lib/chemicalml/convention/molecular/constraints/bond_ids_unique_within_molecule.rb +43 -0
  230. data/lib/chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2.rb +3 -3
  231. data/lib/chemicalml/convention/molecular/constraints/bond_must_have_order.rb +3 -3
  232. data/lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb +3 -3
  233. data/lib/chemicalml/convention/molecular/constraints/bond_order_other_must_have_dict_ref.rb +33 -0
  234. data/lib/chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric.rb +2 -2
  235. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_cis_trans_must_have_atom_refs4.rb +45 -0
  236. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_other_must_have_dict_ref.rb +32 -0
  237. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_wedge_hash_must_have_atom_refs2.rb +45 -0
  238. data/lib/chemicalml/convention/molecular/constraints/molecule_atom_array_mutually_exclusive_with_children.rb +32 -0
  239. data/lib/chemicalml/convention/molecular/constraints/molecule_bond_array_mutually_exclusive_with_children.rb +31 -0
  240. data/lib/chemicalml/convention/molecular/constraints/molecule_count_must_not_appear_on_top_level.rb +34 -0
  241. data/lib/chemicalml/convention/molecular/constraints/molecule_must_have_id.rb +3 -3
  242. data/lib/chemicalml/convention/molecular/constraints/property_must_have_dict_ref.rb +3 -3
  243. data/lib/chemicalml/convention/molecular/constraints/scalar_must_have_data_type.rb +3 -3
  244. data/lib/chemicalml/convention/molecular/constraints.rb +20 -0
  245. data/lib/chemicalml/convention/molecular.rb +10 -0
  246. data/lib/chemicalml/convention/registry.rb +17 -0
  247. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_contain_at_least_one_unit.rb +28 -0
  248. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_have_namespace.rb +36 -0
  249. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_contain_definition.rb +27 -0
  250. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_id.rb +27 -0
  251. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_symbol_and_unit_type.rb +3 -3
  252. data/lib/chemicalml/convention/unit_dictionary/constraints.rb +9 -1
  253. data/lib/chemicalml/convention/unit_dictionary.rb +4 -0
  254. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_id_must_match_pattern.rb +31 -0
  255. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_contain_at_least_one_unit_type.rb +27 -0
  256. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_have_namespace.rb +35 -0
  257. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_contain_definition.rb +27 -0
  258. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb +5 -5
  259. data/lib/chemicalml/convention/unit_type_dictionary/constraints.rb +9 -1
  260. data/lib/chemicalml/convention/unit_type_dictionary.rb +4 -0
  261. data/lib/chemicalml/convention/validation_report.rb +63 -0
  262. data/lib/chemicalml/convention.rb +11 -0
  263. data/lib/chemicalml/dictionary/entry.rb +6 -6
  264. data/lib/chemicalml/dictionary/enum.rb +1 -1
  265. data/lib/chemicalml/dictionary/link.rb +3 -3
  266. data/lib/chemicalml/dictionary/loader.rb +19 -19
  267. data/lib/chemicalml/dictionary/model.rb +5 -5
  268. data/lib/chemicalml/dictionary/registry.rb +9 -9
  269. data/lib/chemicalml/version.rb +1 -1
  270. data/lib/chemicalml/versioned_parser.rb +18 -0
  271. data/lib/chemicalml.rb +1 -2
  272. metadata +123 -34
  273. data/lib/chemicalml/cml/child_mappings.rb +0 -168
  274. data/lib/chemicalml/cml/translator/value_translations.rb +0 -270
  275. data/lib/chemicalml/cml/translator.rb +0 -484
  276. data/lib/chemicalml/model/atom.rb +0 -64
  277. data/lib/chemicalml/model/atom_parity.rb +0 -21
  278. data/lib/chemicalml/model/bond.rb +0 -39
  279. data/lib/chemicalml/model/bond_stereo.rb +0 -29
  280. data/lib/chemicalml/model/cml_array.rb +0 -27
  281. data/lib/chemicalml/model/cml_module.rb +0 -45
  282. data/lib/chemicalml/model/document.rb +0 -29
  283. data/lib/chemicalml/model/formula.rb +0 -34
  284. data/lib/chemicalml/model/identifier.rb +0 -21
  285. data/lib/chemicalml/model/label.rb +0 -21
  286. data/lib/chemicalml/model/matrix.rb +0 -29
  287. data/lib/chemicalml/model/metadata.rb +0 -23
  288. data/lib/chemicalml/model/metadata_list.rb +0 -25
  289. data/lib/chemicalml/model/molecule.rb +0 -45
  290. data/lib/chemicalml/model/name.rb +0 -21
  291. data/lib/chemicalml/model/node.rb +0 -45
  292. data/lib/chemicalml/model/parameter.rb +0 -27
  293. data/lib/chemicalml/model/parameter_list.rb +0 -25
  294. data/lib/chemicalml/model/product.rb +0 -21
  295. data/lib/chemicalml/model/product_list.rb +0 -21
  296. data/lib/chemicalml/model/property.rb +0 -28
  297. data/lib/chemicalml/model/property_list.rb +0 -25
  298. data/lib/chemicalml/model/reactant.rb +0 -21
  299. data/lib/chemicalml/model/reactant_list.rb +0 -21
  300. data/lib/chemicalml/model/reaction.rb +0 -41
  301. data/lib/chemicalml/model/reaction_list.rb +0 -23
  302. data/lib/chemicalml/model/scalar.rb +0 -25
  303. data/lib/chemicalml/model/substance.rb +0 -25
  304. data/lib/chemicalml/model.rb +0 -40
data/lib/chemicalml/model.rb DELETED
@@ -1,40 +0,0 @@
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- # frozen_string_literal: true
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-
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- module Chemicalml
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- # Canonical chemistry representation model. Format-agnostic plain
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- # Ruby classes; not tied to any wire format.
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- #
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- # Every adapter (CML XML, AsciiChem text, future SMILES/InChI/MOL)
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- # speaks the canonical model. Adapters never talk to each other
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- # directly — only through these classes.
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- module Model
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- autoload :Array, "chemicalml/model/cml_array"
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- autoload :Atom, "chemicalml/model/atom"
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- autoload :AtomParity, "chemicalml/model/atom_parity"
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- autoload :Bond, "chemicalml/model/bond"
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- autoload :BondStereo, "chemicalml/model/bond_stereo"
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- autoload :Document, "chemicalml/model/document"
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- autoload :Formula, "chemicalml/model/formula"
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- autoload :Identifier, "chemicalml/model/identifier"
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- autoload :Label, "chemicalml/model/label"
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- autoload :Matrix, "chemicalml/model/matrix"
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- autoload :Metadata, "chemicalml/model/metadata"
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- autoload :MetadataList, "chemicalml/model/metadata_list"
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- autoload :Module, "chemicalml/model/cml_module"
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- autoload :Molecule, "chemicalml/model/molecule"
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- autoload :Name, "chemicalml/model/name"
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- autoload :Node, "chemicalml/model/node"
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- autoload :Parameter, "chemicalml/model/parameter"
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- autoload :ParameterList, "chemicalml/model/parameter_list"
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- autoload :Product, "chemicalml/model/product"
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- autoload :ProductList, "chemicalml/model/product_list"
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- autoload :Property, "chemicalml/model/property"
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- autoload :PropertyList, "chemicalml/model/property_list"
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- autoload :Reaction, "chemicalml/model/reaction"
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- autoload :ReactionList, "chemicalml/model/reaction_list"
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- autoload :Reactant, "chemicalml/model/reactant"
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- autoload :ReactantList, "chemicalml/model/reactant_list"
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- autoload :Scalar, "chemicalml/model/scalar"
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- autoload :Substance, "chemicalml/model/substance"
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- end
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- end