chemicalml 0.2.1 → 0.3.0

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 (347) hide show
  1. checksums.yaml +4 -4
  2. data/.rubocop.yml +23 -0
  3. data/CLAUDE.md +49 -1
  4. data/README.adoc +154 -26
  5. data/TODO.align/61-parallel-array-attrs.md +54 -0
  6. data/TODO.align/62-per-element-attribute-gaps.md +49 -0
  7. data/TODO.align/63-universal-children-mixin.md +42 -0
  8. data/TODO.align/64-per-element-child-gaps.md +81 -0
  9. data/TODO.align/65-simple-unit-convention.md +40 -0
  10. data/TODO.align/66-schema24-legacy-children.md +32 -0
  11. data/TODO.align/67-final-verification.md +32 -0
  12. data/TODO.align/68-detection-coverage.md +33 -0
  13. data/TODO.align/69-json-yaml-roundtrip.md +27 -0
  14. data/TODO.align/70-iterative-walker.md +40 -0
  15. data/TODO.align/71-violation-value.md +25 -0
  16. data/TODO.align/72-close-child-gaps.md +66 -0
  17. data/TODO.align/73-schema24-parse-limitation.md +64 -0
  18. data/TODO.align/74-final-verification-round18.md +15 -0
  19. data/TODO.align/75-key-value-mappings.md +43 -0
  20. data/TODO.align/76-schema24-workaround.md +57 -0
  21. data/TODO.align/77-convention-coverage-matrix.md +31 -0
  22. data/TODO.align/78-fixture-audit.md +23 -0
  23. data/TODO.align/79-final-verification-round19.md +15 -0
  24. data/TODO.align/80-xsd-enum-constants.md +35 -0
  25. data/TODO.align/81-enum-validation-constraints.md +29 -0
  26. data/TODO.align/82-reference-resolver.md +33 -0
  27. data/TODO.align/83-toml-roundtrip.md +20 -0
  28. data/TODO.align/84-final-verification-round21.md +16 -0
  29. data/TODO.align/85-bond-distinct-atoms.md +25 -0
  30. data/TODO.align/86-references-should-resolve.md +20 -0
  31. data/TODO.align/87-cli-utility.md +26 -0
  32. data/TODO.align/88-diverse-fixtures.md +26 -0
  33. data/TODO.align/89-final-verification-round22.md +15 -0
  34. data/TODO.align/90-bond-stereo-completeness.md +31 -0
  35. data/TODO.align/91-atomparity-distinct.md +21 -0
  36. data/TODO.align/92-unit-dictionary-completeness.md +28 -0
  37. data/TODO.align/93-yard-docs.md +23 -0
  38. data/TODO.align/94-final-verification-round23.md +15 -0
  39. data/TODO.align/README.round17.md +28 -0
  40. data/TODO.align/README.round18.md +37 -0
  41. data/TODO.align/README.round19.md +40 -0
  42. data/TODO.align/README.round20.md +49 -0
  43. data/TODO.align/README.round21.md +35 -0
  44. data/TODO.align/README.round22.md +48 -0
  45. data/TODO.align/README.round23.md +46 -0
  46. data/TODO.align/README.round24.md +53 -0
  47. data/TODO.align/README.round25.md +66 -0
  48. data/TODO.align/README.round26.md +55 -0
  49. data/TODO.align/README.round27.md +51 -0
  50. data/TODO.align/README.round28.md +61 -0
  51. data/TODO.align/README.round29.md +64 -0
  52. data/TODO.align/README.round30.md +50 -0
  53. data/TODO.align/README.round31.md +54 -0
  54. data/TODO.align/README.round32.md +67 -0
  55. data/TODO.align/README.round33.md +62 -0
  56. data/TODO.align/README.round34.md +70 -0
  57. data/docs/constraints.md +161 -0
  58. data/docs/generate_constraint_docs.rb +44 -0
  59. data/exe/chemicalml +6 -0
  60. data/lib/chemicalml/cli/base.rb +68 -0
  61. data/lib/chemicalml/cli/command.rb +43 -0
  62. data/lib/chemicalml/cli/constraints_command.rb +27 -0
  63. data/lib/chemicalml/cli/conventions_command.rb +14 -0
  64. data/lib/chemicalml/cli/dictionaries_command.rb +14 -0
  65. data/lib/chemicalml/cli/elements_command.rb +17 -0
  66. data/lib/chemicalml/cli/enums_command.rb +17 -0
  67. data/lib/chemicalml/cli/info_command.rb +77 -0
  68. data/lib/chemicalml/cli/inspect_command.rb +39 -0
  69. data/lib/chemicalml/cli/validate_command.rb +54 -0
  70. data/lib/chemicalml/cli.rb +43 -0
  71. data/lib/chemicalml/cml/base/abundance.rb +18 -8
  72. data/lib/chemicalml/cml/base/action.rb +34 -16
  73. data/lib/chemicalml/cml/base/action_list.rb +35 -17
  74. data/lib/chemicalml/cml/base/alternative.rb +13 -4
  75. data/lib/chemicalml/cml/base/amount.rb +14 -6
  76. data/lib/chemicalml/cml/base/angle.rb +28 -13
  77. data/lib/chemicalml/cml/base/annotation.rb +14 -6
  78. data/lib/chemicalml/cml/base/any_cml.rb +12 -5
  79. data/lib/chemicalml/cml/base/appinfo.rb +14 -6
  80. data/lib/chemicalml/cml/base/arg.rb +47 -13
  81. data/lib/chemicalml/cml/base/array.rb +40 -19
  82. data/lib/chemicalml/cml/base/array_list.rb +14 -6
  83. data/lib/chemicalml/cml/base/atom.rb +84 -28
  84. data/lib/chemicalml/cml/base/atom_array.rb +60 -23
  85. data/lib/chemicalml/cml/base/atom_parity.rb +14 -6
  86. data/lib/chemicalml/cml/base/atom_set.rb +14 -6
  87. data/lib/chemicalml/cml/base/atom_type.rb +25 -9
  88. data/lib/chemicalml/cml/base/atom_type_list.rb +22 -8
  89. data/lib/chemicalml/cml/base/atomic_basis_function.rb +33 -13
  90. data/lib/chemicalml/cml/base/band.rb +21 -8
  91. data/lib/chemicalml/cml/base/band_list.rb +15 -7
  92. data/lib/chemicalml/cml/base/basis_set.rb +24 -9
  93. data/lib/chemicalml/cml/base/bond.rb +36 -10
  94. data/lib/chemicalml/cml/base/bond_array.rb +34 -11
  95. data/lib/chemicalml/cml/base/bond_set.rb +14 -6
  96. data/lib/chemicalml/cml/base/bond_stereo.rb +20 -9
  97. data/lib/chemicalml/cml/base/bond_type.rb +23 -8
  98. data/lib/chemicalml/cml/base/bond_type_list.rb +22 -8
  99. data/lib/chemicalml/cml/base/cell_parameter.rb +28 -10
  100. data/lib/chemicalml/cml/base/cml_module.rb +36 -11
  101. data/lib/chemicalml/cml/base/common_children.rb +35 -0
  102. data/lib/chemicalml/cml/base/complex_object.rb +12 -5
  103. data/lib/chemicalml/cml/base/condition_list.rb +26 -10
  104. data/lib/chemicalml/cml/base/crystal.rb +26 -10
  105. data/lib/chemicalml/cml/base/definition.rb +12 -5
  106. data/lib/chemicalml/cml/base/description.rb +14 -6
  107. data/lib/chemicalml/cml/base/dictionary.rb +27 -10
  108. data/lib/chemicalml/cml/base/dictionary_entry.rb +67 -8
  109. data/lib/chemicalml/cml/base/dimension.rb +26 -12
  110. data/lib/chemicalml/cml/base/document.rb +18 -8
  111. data/lib/chemicalml/cml/base/documentation.rb +12 -5
  112. data/lib/chemicalml/cml/base/eigen.rb +32 -8
  113. data/lib/chemicalml/cml/base/electron.rb +26 -12
  114. data/lib/chemicalml/cml/base/enumeration.rb +16 -7
  115. data/lib/chemicalml/cml/base/expression.rb +21 -6
  116. data/lib/chemicalml/cml/base/float.rb +22 -10
  117. data/lib/chemicalml/cml/base/float_array.rb +24 -11
  118. data/lib/chemicalml/cml/base/formula.rb +31 -10
  119. data/lib/chemicalml/cml/base/fragment.rb +30 -12
  120. data/lib/chemicalml/cml/base/fragment_list.rb +24 -9
  121. data/lib/chemicalml/cml/base/gradient.rb +19 -6
  122. data/lib/chemicalml/cml/base/identifier.rb +18 -8
  123. data/lib/chemicalml/cml/base/integer.rb +22 -10
  124. data/lib/chemicalml/cml/base/integer_array.rb +24 -11
  125. data/lib/chemicalml/cml/base/isotope.rb +28 -9
  126. data/lib/chemicalml/cml/base/isotope_list.rb +17 -8
  127. data/lib/chemicalml/cml/base/join.rb +25 -9
  128. data/lib/chemicalml/cml/base/kpoint.rb +16 -7
  129. data/lib/chemicalml/cml/base/kpoint_list.rb +15 -7
  130. data/lib/chemicalml/cml/base/label.rb +14 -6
  131. data/lib/chemicalml/cml/base/lattice.rb +35 -10
  132. data/lib/chemicalml/cml/base/lattice_vector.rb +16 -7
  133. data/lib/chemicalml/cml/base/length.rb +26 -12
  134. data/lib/chemicalml/cml/base/line3.rb +18 -8
  135. data/lib/chemicalml/cml/base/link.rb +41 -20
  136. data/lib/chemicalml/cml/base/list.rb +22 -10
  137. data/lib/chemicalml/cml/base/map.rb +32 -11
  138. data/lib/chemicalml/cml/base/matrix.rb +32 -15
  139. data/lib/chemicalml/cml/base/mechanism.rb +20 -7
  140. data/lib/chemicalml/cml/base/mechanism_component.rb +14 -6
  141. data/lib/chemicalml/cml/base/metadata.rb +18 -8
  142. data/lib/chemicalml/cml/base/metadata_list.rb +27 -8
  143. data/lib/chemicalml/cml/base/molecule.rb +90 -26
  144. data/lib/chemicalml/cml/base/molecule_list.rb +26 -8
  145. data/lib/chemicalml/cml/base/name.rb +10 -4
  146. data/lib/chemicalml/cml/base/object.rb +18 -8
  147. data/lib/chemicalml/cml/base/observation.rb +16 -7
  148. data/lib/chemicalml/cml/base/operator.rb +14 -6
  149. data/lib/chemicalml/cml/base/parameter.rb +33 -13
  150. data/lib/chemicalml/cml/base/parameter_list.rb +27 -8
  151. data/lib/chemicalml/cml/base/particle.rb +20 -9
  152. data/lib/chemicalml/cml/base/peak.rb +71 -26
  153. data/lib/chemicalml/cml/base/peak_group.rb +62 -26
  154. data/lib/chemicalml/cml/base/peak_list.rb +24 -9
  155. data/lib/chemicalml/cml/base/peak_structure.rb +40 -13
  156. data/lib/chemicalml/cml/base/plane3.rb +14 -6
  157. data/lib/chemicalml/cml/base/point3.rb +14 -6
  158. data/lib/chemicalml/cml/base/potential.rb +17 -6
  159. data/lib/chemicalml/cml/base/potential_form.rb +30 -7
  160. data/lib/chemicalml/cml/base/potential_list.rb +15 -7
  161. data/lib/chemicalml/cml/base/product.rb +45 -10
  162. data/lib/chemicalml/cml/base/product_list.rb +29 -9
  163. data/lib/chemicalml/cml/base/property.rb +29 -11
  164. data/lib/chemicalml/cml/base/property_list.rb +23 -8
  165. data/lib/chemicalml/cml/base/reactant.rb +45 -10
  166. data/lib/chemicalml/cml/base/reactant_list.rb +29 -9
  167. data/lib/chemicalml/cml/base/reaction.rb +74 -20
  168. data/lib/chemicalml/cml/base/reaction_list.rb +23 -8
  169. data/lib/chemicalml/cml/base/reaction_scheme.rb +43 -13
  170. data/lib/chemicalml/cml/base/reaction_step.rb +30 -12
  171. data/lib/chemicalml/cml/base/reaction_step_list.rb +30 -11
  172. data/lib/chemicalml/cml/base/reactive_centre.rb +31 -6
  173. data/lib/chemicalml/cml/base/region.rb +20 -9
  174. data/lib/chemicalml/cml/base/related_entry.rb +11 -3
  175. data/lib/chemicalml/cml/base/sample.rb +30 -7
  176. data/lib/chemicalml/cml/base/scalar.rb +32 -15
  177. data/lib/chemicalml/cml/base/spectator.rb +25 -6
  178. data/lib/chemicalml/cml/base/spectator_list.rb +20 -7
  179. data/lib/chemicalml/cml/base/spectrum.rb +57 -18
  180. data/lib/chemicalml/cml/base/spectrum_data.rb +19 -9
  181. data/lib/chemicalml/cml/base/spectrum_list.rb +28 -9
  182. data/lib/chemicalml/cml/base/sphere3.rb +14 -6
  183. data/lib/chemicalml/cml/base/stmml.rb +12 -5
  184. data/lib/chemicalml/cml/base/string.rb +14 -6
  185. data/lib/chemicalml/cml/base/string_array.rb +22 -10
  186. data/lib/chemicalml/cml/base/substance.rb +36 -14
  187. data/lib/chemicalml/cml/base/substance_list.rb +29 -10
  188. data/lib/chemicalml/cml/base/symmetry.rb +31 -9
  189. data/lib/chemicalml/cml/base/system.rb +21 -10
  190. data/lib/chemicalml/cml/base/table.rb +38 -13
  191. data/lib/chemicalml/cml/base/table_cell.rb +12 -5
  192. data/lib/chemicalml/cml/base/table_content.rb +19 -9
  193. data/lib/chemicalml/cml/base/table_header.rb +15 -7
  194. data/lib/chemicalml/cml/base/table_header_cell.rb +22 -10
  195. data/lib/chemicalml/cml/base/table_row.rb +15 -7
  196. data/lib/chemicalml/cml/base/table_row_list.rb +15 -7
  197. data/lib/chemicalml/cml/base/tcell.rb +16 -7
  198. data/lib/chemicalml/cml/base/torsion.rb +28 -13
  199. data/lib/chemicalml/cml/base/transform3.rb +12 -5
  200. data/lib/chemicalml/cml/base/transition_state.rb +23 -5
  201. data/lib/chemicalml/cml/base/trow.rb +22 -6
  202. data/lib/chemicalml/cml/base/unit.rb +39 -16
  203. data/lib/chemicalml/cml/base/unit_list.rb +34 -12
  204. data/lib/chemicalml/cml/base/unit_type.rb +27 -10
  205. data/lib/chemicalml/cml/base/unit_type_list.rb +29 -11
  206. data/lib/chemicalml/cml/base/vector3.rb +14 -6
  207. data/lib/chemicalml/cml/base/xaxis.rb +30 -10
  208. data/lib/chemicalml/cml/base/yaxis.rb +30 -10
  209. data/lib/chemicalml/cml/base/z_matrix.rb +26 -5
  210. data/lib/chemicalml/cml/base.rb +139 -138
  211. data/lib/chemicalml/cml/canonical_comparison.rb +54 -0
  212. data/lib/chemicalml/cml/elements.rb +145 -136
  213. data/lib/chemicalml/cml/enums.rb +55 -0
  214. data/lib/chemicalml/cml/namespace.rb +2 -3
  215. data/lib/chemicalml/cml/patterns.rb +33 -0
  216. data/lib/chemicalml/cml/reference_resolver.rb +137 -0
  217. data/lib/chemicalml/cml/role.rb +138 -138
  218. data/lib/chemicalml/cml/schema24/configuration.rb +11 -1
  219. data/lib/chemicalml/cml/schema24.rb +139 -139
  220. data/lib/chemicalml/cml/schema3.rb +123 -123
  221. data/lib/chemicalml/cml/visitable.rb +77 -3
  222. data/lib/chemicalml/cml/wire_class_registry.rb +3 -3
  223. data/lib/chemicalml/cml.rb +163 -129
  224. data/lib/chemicalml/context_configuration.rb +4 -2
  225. data/lib/chemicalml/convention/cascade/constraints/reaction_scheme_must_have_content.rb +33 -0
  226. data/lib/chemicalml/convention/cascade/constraints/reaction_step_list_must_contain_steps.rb +31 -0
  227. data/lib/chemicalml/convention/cascade/constraints/reaction_step_must_have_reaction_or_lists.rb +33 -0
  228. data/lib/chemicalml/convention/cascade/constraints/reactive_centre_atom_refs_should_be_present.rb +34 -0
  229. data/lib/chemicalml/convention/cascade/constraints.rb +18 -0
  230. data/lib/chemicalml/convention/cascade.rb +43 -0
  231. data/lib/chemicalml/convention/compchem/constraints/array_rules.rb +1 -1
  232. data/lib/chemicalml/convention/compchem/constraints/calculation_requires_finalization.rb +1 -1
  233. data/lib/chemicalml/convention/compchem/constraints/compchem_module_must_contain_job_list.rb +2 -1
  234. data/lib/chemicalml/convention/compchem/constraints/environment_at_most_one_property_list.rb +1 -1
  235. data/lib/chemicalml/convention/compchem/constraints/environment_must_not_contain_parameter.rb +1 -1
  236. data/lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_molecule.rb +1 -1
  237. data/lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_property_list.rb +1 -1
  238. data/lib/chemicalml/convention/compchem/constraints/finalization_must_have_content.rb +44 -0
  239. data/lib/chemicalml/convention/compchem/constraints/finalization_must_not_contain_parameter.rb +1 -1
  240. data/lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_molecule.rb +1 -1
  241. data/lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_parameter_list.rb +1 -1
  242. data/lib/chemicalml/convention/compchem/constraints/initialization_must_have_content.rb +54 -0
  243. data/lib/chemicalml/convention/compchem/constraints/initialization_must_not_contain_property.rb +1 -1
  244. data/lib/chemicalml/convention/compchem/constraints/job_list_module_must_have_id.rb +1 -0
  245. data/lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_environment.rb +1 -1
  246. data/lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_finalization.rb +1 -1
  247. data/lib/chemicalml/convention/compchem/constraints/job_module_must_have_id.rb +1 -0
  248. data/lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb +1 -0
  249. data/lib/chemicalml/convention/compchem/constraints/matrix_rules.rb +1 -1
  250. data/lib/chemicalml/convention/compchem/constraints/scalar_units.rb +1 -1
  251. data/lib/chemicalml/convention/compchem/constraints.rb +4 -0
  252. data/lib/chemicalml/convention/compchem.rb +4 -2
  253. data/lib/chemicalml/convention/constraint.rb +40 -9
  254. data/lib/chemicalml/convention/coordinator.rb +4 -3
  255. data/lib/chemicalml/convention/detection.rb +10 -4
  256. data/lib/chemicalml/convention/dictionary/constraints/dictionary_must_have_namespace.rb +1 -0
  257. data/lib/chemicalml/convention/dictionary/constraints/dictionary_namespace_should_end_with_slash_or_hash.rb +1 -1
  258. data/lib/chemicalml/convention/dictionary/constraints/entry_id_must_match_pattern.rb +1 -1
  259. data/lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb +1 -1
  260. data/lib/chemicalml/convention/dictionary/constraints/entry_must_contain_definition.rb +1 -0
  261. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb +1 -1
  262. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_unit_type.rb +1 -0
  263. data/lib/chemicalml/convention/dictionary/constraints/entry_units_co_constraints.rb +1 -1
  264. data/lib/chemicalml/convention/dictionary/constraints.rb +8 -8
  265. data/lib/chemicalml/convention/dictionary.rb +2 -2
  266. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_be_child_of_molecule_or_formula.rb +1 -0
  267. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb +15 -6
  268. data/lib/chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired.rb +1 -1
  269. data/lib/chemicalml/convention/molecular/constraints/atom_element_type_should_be_in_periodic_table.rb +39 -0
  270. data/lib/chemicalml/convention/molecular/constraints/atom_id_must_match_pattern.rb +3 -2
  271. data/lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb +1 -0
  272. data/lib/chemicalml/convention/molecular/constraints/atom_must_have_element_type.rb +1 -1
  273. data/lib/chemicalml/convention/molecular/constraints/atom_must_have_id.rb +2 -1
  274. data/lib/chemicalml/convention/molecular/constraints/atom_parity_atom_refs4_should_be_distinct.rb +44 -0
  275. data/lib/chemicalml/convention/molecular/constraints/atom_parity_should_include_parent_atom.rb +65 -0
  276. data/lib/chemicalml/convention/molecular/constraints/bond_array_must_be_child_of_molecule.rb +1 -0
  277. data/lib/chemicalml/convention/molecular/constraints/bond_atom_refs2_should_be_distinct.rb +44 -0
  278. data/lib/chemicalml/convention/molecular/constraints/bond_id_should_match_pattern.rb +38 -0
  279. data/lib/chemicalml/convention/molecular/constraints/bond_ids_unique_within_molecule.rb +1 -0
  280. data/lib/chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2.rb +1 -1
  281. data/lib/chemicalml/convention/molecular/constraints/bond_must_have_order.rb +2 -1
  282. data/lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb +1 -0
  283. data/lib/chemicalml/convention/molecular/constraints/bond_order_other_must_have_dict_ref.rb +1 -0
  284. data/lib/chemicalml/convention/molecular/constraints/bond_order_should_be_in_enum.rb +39 -0
  285. data/lib/chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric.rb +1 -1
  286. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_atom_refs4_should_be_distinct.rb +43 -0
  287. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_cis_trans_must_have_atom_refs4.rb +1 -1
  288. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_other_must_have_dict_ref.rb +1 -0
  289. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_should_be_in_enum.rb +38 -0
  290. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_wedge_hash_must_have_atom_refs2.rb +1 -1
  291. data/lib/chemicalml/convention/molecular/constraints/dict_ref_should_resolve.rb +59 -0
  292. data/lib/chemicalml/convention/molecular/constraints/molecule_atom_array_mutually_exclusive_with_children.rb +1 -0
  293. data/lib/chemicalml/convention/molecular/constraints/molecule_bond_array_mutually_exclusive_with_children.rb +1 -0
  294. data/lib/chemicalml/convention/molecular/constraints/molecule_chirality_should_be_in_enum.rb +38 -0
  295. data/lib/chemicalml/convention/molecular/constraints/molecule_count_must_not_appear_on_top_level.rb +1 -0
  296. data/lib/chemicalml/convention/molecular/constraints/molecule_id_should_match_pattern.rb +38 -0
  297. data/lib/chemicalml/convention/molecular/constraints/molecule_must_have_id.rb +1 -1
  298. data/lib/chemicalml/convention/molecular/constraints/property_must_have_dict_ref.rb +1 -1
  299. data/lib/chemicalml/convention/molecular/constraints/property_scalar_data_type_matches_dictionary.rb +58 -0
  300. data/lib/chemicalml/convention/molecular/constraints/references_should_resolve.rb +37 -0
  301. data/lib/chemicalml/convention/molecular/constraints/scalar_must_have_data_type.rb +1 -1
  302. data/lib/chemicalml/convention/molecular/constraints.rb +49 -23
  303. data/lib/chemicalml/convention/molecular.rb +15 -2
  304. data/lib/chemicalml/convention/registry.rb +79 -11
  305. data/lib/chemicalml/convention/simple_unit/constraints/root_must_be_unit_list.rb +24 -0
  306. data/lib/chemicalml/convention/simple_unit/constraints/unit_must_have_power.rb +32 -0
  307. data/lib/chemicalml/convention/simple_unit/constraints/unit_must_have_symbol.rb +31 -0
  308. data/lib/chemicalml/convention/simple_unit/constraints.rb +16 -0
  309. data/lib/chemicalml/convention/simple_unit.rb +37 -0
  310. data/lib/chemicalml/convention/spectroscopy/constraints/peak_list_must_contain_peaks.rb +31 -0
  311. data/lib/chemicalml/convention/spectroscopy/constraints/peak_should_have_values.rb +34 -0
  312. data/lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_content.rb +31 -0
  313. data/lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_convention.rb +32 -0
  314. data/lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_format.rb +31 -0
  315. data/lib/chemicalml/convention/spectroscopy/constraints.rb +20 -0
  316. data/lib/chemicalml/convention/spectroscopy.rb +41 -0
  317. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_contain_at_least_one_unit.rb +1 -0
  318. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_have_namespace.rb +1 -1
  319. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_contain_definition.rb +1 -0
  320. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_id.rb +1 -0
  321. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_multiplier_or_constant_to_si.rb +34 -0
  322. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_parent_si.rb +32 -0
  323. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_symbol_and_unit_type.rb +1 -1
  324. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_title.rb +32 -0
  325. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_parent_si_should_resolve.rb +45 -0
  326. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_unit_type_should_resolve.rb +46 -0
  327. data/lib/chemicalml/convention/unit_dictionary/constraints.rb +10 -0
  328. data/lib/chemicalml/convention/unit_dictionary.rb +7 -2
  329. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_id_must_match_pattern.rb +1 -1
  330. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_contain_at_least_one_unit_type.rb +1 -0
  331. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_have_namespace.rb +1 -1
  332. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_contain_definition.rb +1 -0
  333. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb +1 -1
  334. data/lib/chemicalml/convention/unit_type_dictionary.rb +2 -2
  335. data/lib/chemicalml/convention/validation_report.rb +30 -3
  336. data/lib/chemicalml/convention/violation.rb +9 -3
  337. data/lib/chemicalml/convention.rb +41 -14
  338. data/lib/chemicalml/dictionary.rb +13 -9
  339. data/lib/chemicalml/logger.rb +47 -0
  340. data/lib/chemicalml/schema/definition.rb +2 -2
  341. data/lib/chemicalml/schema.rb +7 -7
  342. data/lib/chemicalml/version.rb +1 -1
  343. data/lib/chemicalml/versioned_parser.rb +10 -10
  344. data/lib/chemicalml.rb +78 -15
  345. data/lib/tasks/reference_fetch.rake +30 -31
  346. data/lib/tasks/scrape_fixtures.rake +23 -24
  347. metadata +114 -3
data/lib/chemicalml/cml/schema24.rb CHANGED
@@ -25,148 +25,148 @@ module Chemicalml
25
25
  module Schema24
26
26
  extend Chemicalml::VersionedParser
27
27
 
28
- autoload :Abundance, "chemicalml/cml/schema24/abundance"
29
- autoload :Action, "chemicalml/cml/schema24/action"
30
- autoload :ActionList, "chemicalml/cml/schema24/action_list"
31
- autoload :Amount, "chemicalml/cml/schema24/amount"
32
- autoload :Angle, "chemicalml/cml/schema24/angle"
33
- autoload :ArrayList, "chemicalml/cml/schema24/array_list"
34
- autoload :AtomSet, "chemicalml/cml/schema24/atom_set"
35
- autoload :AtomType, "chemicalml/cml/schema24/atom_type"
36
- autoload :AtomTypeList, "chemicalml/cml/schema24/atom_type_list"
37
- autoload :AtomicBasisFunction, "chemicalml/cml/schema24/atomic_basis_function"
38
- autoload :Band, "chemicalml/cml/schema24/band"
39
- autoload :BandList, "chemicalml/cml/schema24/band_list"
40
- autoload :BasisSet, "chemicalml/cml/schema24/basis_set"
41
- autoload :BondSet, "chemicalml/cml/schema24/bond_set"
42
- autoload :BondType, "chemicalml/cml/schema24/bond_type"
43
- autoload :BondTypeList, "chemicalml/cml/schema24/bond_type_list"
44
- autoload :CellParameter, "chemicalml/cml/schema24/cell_parameter"
45
- autoload :ConditionList, "chemicalml/cml/schema24/condition_list"
46
- autoload :Crystal, "chemicalml/cml/schema24/crystal"
47
- autoload :Definition, "chemicalml/cml/schema24/definition"
48
- autoload :Description, "chemicalml/cml/schema24/description"
49
- autoload :Dimension, "chemicalml/cml/schema24/dimension"
50
- autoload :Documentation, "chemicalml/cml/schema24/documentation"
51
- autoload :Eigen, "chemicalml/cml/schema24/eigen"
52
- autoload :Electron, "chemicalml/cml/schema24/electron"
53
- autoload :Fragment, "chemicalml/cml/schema24/fragment"
54
- autoload :FragmentList, "chemicalml/cml/schema24/fragment_list"
55
- autoload :Gradient, "chemicalml/cml/schema24/gradient"
56
- autoload :Isotope, "chemicalml/cml/schema24/isotope"
57
- autoload :IsotopeList, "chemicalml/cml/schema24/isotope_list"
58
- autoload :Join, "chemicalml/cml/schema24/join"
59
- autoload :Kpoint, "chemicalml/cml/schema24/kpoint"
60
- autoload :KpointList, "chemicalml/cml/schema24/kpoint_list"
61
- autoload :Lattice, "chemicalml/cml/schema24/lattice"
62
- autoload :LatticeVector, "chemicalml/cml/schema24/lattice_vector"
63
- autoload :Length, "chemicalml/cml/schema24/length"
64
- autoload :Line3, "chemicalml/cml/schema24/line3"
65
- autoload :Link, "chemicalml/cml/schema24/link"
66
- autoload :Map, "chemicalml/cml/schema24/map"
67
- autoload :Mechanism, "chemicalml/cml/schema24/mechanism"
68
- autoload :MechanismComponent, "chemicalml/cml/schema24/mechanism_component"
69
- autoload :MoleculeList, "chemicalml/cml/schema24/molecule_list"
70
- autoload :Object, "chemicalml/cml/schema24/object"
71
- autoload :Observation, "chemicalml/cml/schema24/observation"
72
- autoload :Particle, "chemicalml/cml/schema24/particle"
73
- autoload :Peak, "chemicalml/cml/schema24/peak"
74
- autoload :PeakGroup, "chemicalml/cml/schema24/peak_group"
75
- autoload :PeakList, "chemicalml/cml/schema24/peak_list"
76
- autoload :PeakStructure, "chemicalml/cml/schema24/peak_structure"
77
- autoload :Plane3, "chemicalml/cml/schema24/plane3"
78
- autoload :Point3, "chemicalml/cml/schema24/point3"
79
- autoload :Potential, "chemicalml/cml/schema24/potential"
80
- autoload :PotentialForm, "chemicalml/cml/schema24/potential_form"
81
- autoload :PotentialList, "chemicalml/cml/schema24/potential_list"
82
- autoload :ReactionScheme, "chemicalml/cml/schema24/reaction_scheme"
83
- autoload :ReactionStep, "chemicalml/cml/schema24/reaction_step"
84
- autoload :ReactionStepList, "chemicalml/cml/schema24/reaction_step_list"
85
- autoload :ReactiveCentre, "chemicalml/cml/schema24/reactive_centre"
86
- autoload :Region, "chemicalml/cml/schema24/region"
87
- autoload :Sample, "chemicalml/cml/schema24/sample"
88
- autoload :Spectator, "chemicalml/cml/schema24/spectator"
89
- autoload :SpectatorList, "chemicalml/cml/schema24/spectator_list"
90
- autoload :Spectrum, "chemicalml/cml/schema24/spectrum"
91
- autoload :SpectrumData, "chemicalml/cml/schema24/spectrum_data"
92
- autoload :SpectrumList, "chemicalml/cml/schema24/spectrum_list"
93
- autoload :Sphere3, "chemicalml/cml/schema24/sphere3"
94
- autoload :Stmml, "chemicalml/cml/schema24/stmml"
95
- autoload :SubstanceList, "chemicalml/cml/schema24/substance_list"
96
- autoload :Symmetry, "chemicalml/cml/schema24/symmetry"
97
- autoload :System, "chemicalml/cml/schema24/system"
98
- autoload :Table, "chemicalml/cml/schema24/table"
99
- autoload :TableCell, "chemicalml/cml/schema24/table_cell"
100
- autoload :TableContent, "chemicalml/cml/schema24/table_content"
101
- autoload :TableHeader, "chemicalml/cml/schema24/table_header"
102
- autoload :TableHeaderCell, "chemicalml/cml/schema24/table_header_cell"
103
- autoload :TableRow, "chemicalml/cml/schema24/table_row"
104
- autoload :TableRowList, "chemicalml/cml/schema24/table_row_list"
105
- autoload :Torsion, "chemicalml/cml/schema24/torsion"
106
- autoload :Transform3, "chemicalml/cml/schema24/transform3"
107
- autoload :TransitionState, "chemicalml/cml/schema24/transition_state"
108
- autoload :Vector3, "chemicalml/cml/schema24/vector3"
109
- autoload :Xaxis, "chemicalml/cml/schema24/xaxis"
110
- autoload :Yaxis, "chemicalml/cml/schema24/yaxis"
111
- autoload :ZMatrix, "chemicalml/cml/schema24/z_matrix"
28
+ autoload :Abundance, 'chemicalml/cml/schema24/abundance'
29
+ autoload :Action, 'chemicalml/cml/schema24/action'
30
+ autoload :ActionList, 'chemicalml/cml/schema24/action_list'
31
+ autoload :Amount, 'chemicalml/cml/schema24/amount'
32
+ autoload :Angle, 'chemicalml/cml/schema24/angle'
33
+ autoload :ArrayList, 'chemicalml/cml/schema24/array_list'
34
+ autoload :AtomSet, 'chemicalml/cml/schema24/atom_set'
35
+ autoload :AtomType, 'chemicalml/cml/schema24/atom_type'
36
+ autoload :AtomTypeList, 'chemicalml/cml/schema24/atom_type_list'
37
+ autoload :AtomicBasisFunction, 'chemicalml/cml/schema24/atomic_basis_function'
38
+ autoload :Band, 'chemicalml/cml/schema24/band'
39
+ autoload :BandList, 'chemicalml/cml/schema24/band_list'
40
+ autoload :BasisSet, 'chemicalml/cml/schema24/basis_set'
41
+ autoload :BondSet, 'chemicalml/cml/schema24/bond_set'
42
+ autoload :BondType, 'chemicalml/cml/schema24/bond_type'
43
+ autoload :BondTypeList, 'chemicalml/cml/schema24/bond_type_list'
44
+ autoload :CellParameter, 'chemicalml/cml/schema24/cell_parameter'
45
+ autoload :ConditionList, 'chemicalml/cml/schema24/condition_list'
46
+ autoload :Crystal, 'chemicalml/cml/schema24/crystal'
47
+ autoload :Definition, 'chemicalml/cml/schema24/definition'
48
+ autoload :Description, 'chemicalml/cml/schema24/description'
49
+ autoload :Dimension, 'chemicalml/cml/schema24/dimension'
50
+ autoload :Documentation, 'chemicalml/cml/schema24/documentation'
51
+ autoload :Eigen, 'chemicalml/cml/schema24/eigen'
52
+ autoload :Electron, 'chemicalml/cml/schema24/electron'
53
+ autoload :Fragment, 'chemicalml/cml/schema24/fragment'
54
+ autoload :FragmentList, 'chemicalml/cml/schema24/fragment_list'
55
+ autoload :Gradient, 'chemicalml/cml/schema24/gradient'
56
+ autoload :Isotope, 'chemicalml/cml/schema24/isotope'
57
+ autoload :IsotopeList, 'chemicalml/cml/schema24/isotope_list'
58
+ autoload :Join, 'chemicalml/cml/schema24/join'
59
+ autoload :Kpoint, 'chemicalml/cml/schema24/kpoint'
60
+ autoload :KpointList, 'chemicalml/cml/schema24/kpoint_list'
61
+ autoload :Lattice, 'chemicalml/cml/schema24/lattice'
62
+ autoload :LatticeVector, 'chemicalml/cml/schema24/lattice_vector'
63
+ autoload :Length, 'chemicalml/cml/schema24/length'
64
+ autoload :Line3, 'chemicalml/cml/schema24/line3'
65
+ autoload :Link, 'chemicalml/cml/schema24/link'
66
+ autoload :Map, 'chemicalml/cml/schema24/map'
67
+ autoload :Mechanism, 'chemicalml/cml/schema24/mechanism'
68
+ autoload :MechanismComponent, 'chemicalml/cml/schema24/mechanism_component'
69
+ autoload :MoleculeList, 'chemicalml/cml/schema24/molecule_list'
70
+ autoload :Object, 'chemicalml/cml/schema24/object'
71
+ autoload :Observation, 'chemicalml/cml/schema24/observation'
72
+ autoload :Particle, 'chemicalml/cml/schema24/particle'
73
+ autoload :Peak, 'chemicalml/cml/schema24/peak'
74
+ autoload :PeakGroup, 'chemicalml/cml/schema24/peak_group'
75
+ autoload :PeakList, 'chemicalml/cml/schema24/peak_list'
76
+ autoload :PeakStructure, 'chemicalml/cml/schema24/peak_structure'
77
+ autoload :Plane3, 'chemicalml/cml/schema24/plane3'
78
+ autoload :Point3, 'chemicalml/cml/schema24/point3'
79
+ autoload :Potential, 'chemicalml/cml/schema24/potential'
80
+ autoload :PotentialForm, 'chemicalml/cml/schema24/potential_form'
81
+ autoload :PotentialList, 'chemicalml/cml/schema24/potential_list'
82
+ autoload :ReactionScheme, 'chemicalml/cml/schema24/reaction_scheme'
83
+ autoload :ReactionStep, 'chemicalml/cml/schema24/reaction_step'
84
+ autoload :ReactionStepList, 'chemicalml/cml/schema24/reaction_step_list'
85
+ autoload :ReactiveCentre, 'chemicalml/cml/schema24/reactive_centre'
86
+ autoload :Region, 'chemicalml/cml/schema24/region'
87
+ autoload :Sample, 'chemicalml/cml/schema24/sample'
88
+ autoload :Spectator, 'chemicalml/cml/schema24/spectator'
89
+ autoload :SpectatorList, 'chemicalml/cml/schema24/spectator_list'
90
+ autoload :Spectrum, 'chemicalml/cml/schema24/spectrum'
91
+ autoload :SpectrumData, 'chemicalml/cml/schema24/spectrum_data'
92
+ autoload :SpectrumList, 'chemicalml/cml/schema24/spectrum_list'
93
+ autoload :Sphere3, 'chemicalml/cml/schema24/sphere3'
94
+ autoload :Stmml, 'chemicalml/cml/schema24/stmml'
95
+ autoload :SubstanceList, 'chemicalml/cml/schema24/substance_list'
96
+ autoload :Symmetry, 'chemicalml/cml/schema24/symmetry'
97
+ autoload :System, 'chemicalml/cml/schema24/system'
98
+ autoload :Table, 'chemicalml/cml/schema24/table'
99
+ autoload :TableCell, 'chemicalml/cml/schema24/table_cell'
100
+ autoload :TableContent, 'chemicalml/cml/schema24/table_content'
101
+ autoload :TableHeader, 'chemicalml/cml/schema24/table_header'
102
+ autoload :TableHeaderCell, 'chemicalml/cml/schema24/table_header_cell'
103
+ autoload :TableRow, 'chemicalml/cml/schema24/table_row'
104
+ autoload :TableRowList, 'chemicalml/cml/schema24/table_row_list'
105
+ autoload :Torsion, 'chemicalml/cml/schema24/torsion'
106
+ autoload :Transform3, 'chemicalml/cml/schema24/transform3'
107
+ autoload :TransitionState, 'chemicalml/cml/schema24/transition_state'
108
+ autoload :Vector3, 'chemicalml/cml/schema24/vector3'
109
+ autoload :Xaxis, 'chemicalml/cml/schema24/xaxis'
110
+ autoload :Yaxis, 'chemicalml/cml/schema24/yaxis'
111
+ autoload :ZMatrix, 'chemicalml/cml/schema24/z_matrix'
112
112
 
113
113
  SCHEMA = Chemicalml::Schema::Registry.lookup(:schema24)
114
114
 
115
- autoload :Configuration, "chemicalml/cml/schema24/configuration"
116
- autoload :Context, "chemicalml/cml/schema24/context"
117
- autoload :Array, "chemicalml/cml/schema24/array"
118
- autoload :Atom, "chemicalml/cml/schema24/atom"
119
- autoload :AtomArray, "chemicalml/cml/schema24/atom_array"
120
- autoload :AtomParity, "chemicalml/cml/schema24/atom_parity"
121
- autoload :Bond, "chemicalml/cml/schema24/bond"
122
- autoload :BondArray, "chemicalml/cml/schema24/bond_array"
123
- autoload :BondStereo, "chemicalml/cml/schema24/bond_stereo"
124
- autoload :Dictionary, "chemicalml/cml/schema24/dictionary"
125
- autoload :DictionaryEntry, "chemicalml/cml/schema24/dictionary_entry"
126
- autoload :Document, "chemicalml/cml/schema24/document"
127
- autoload :Formula, "chemicalml/cml/schema24/formula"
128
- autoload :Identifier, "chemicalml/cml/schema24/identifier"
129
- autoload :Label, "chemicalml/cml/schema24/label"
130
- autoload :List, "chemicalml/cml/schema24/list"
131
- autoload :Matrix, "chemicalml/cml/schema24/matrix"
132
- autoload :Metadata, "chemicalml/cml/schema24/metadata"
133
- autoload :MetadataList, "chemicalml/cml/schema24/metadata_list"
134
- autoload :Module, "chemicalml/cml/schema24/cml_module"
135
- autoload :Molecule, "chemicalml/cml/schema24/molecule"
136
- autoload :Name, "chemicalml/cml/schema24/name"
137
- autoload :Parameter, "chemicalml/cml/schema24/parameter"
138
- autoload :ParameterList, "chemicalml/cml/schema24/parameter_list"
139
- autoload :Product, "chemicalml/cml/schema24/product"
140
- autoload :ProductList, "chemicalml/cml/schema24/product_list"
141
- autoload :Property, "chemicalml/cml/schema24/property"
142
- autoload :PropertyList, "chemicalml/cml/schema24/property_list"
143
- autoload :Reaction, "chemicalml/cml/schema24/reaction"
144
- autoload :ReactionList, "chemicalml/cml/schema24/reaction_list"
145
- autoload :Reactant, "chemicalml/cml/schema24/reactant"
146
- autoload :ReactantList, "chemicalml/cml/schema24/reactant_list"
147
- autoload :Scalar, "chemicalml/cml/schema24/scalar"
148
- autoload :Substance, "chemicalml/cml/schema24/substance"
149
- autoload :Unit, "chemicalml/cml/schema24/unit"
150
- autoload :UnitList, "chemicalml/cml/schema24/unit_list"
151
- autoload :UnitType, "chemicalml/cml/schema24/unit_type"
152
- autoload :UnitTypeList, "chemicalml/cml/schema24/unit_type_list"
153
- autoload :Alternative, "chemicalml/cml/schema24/alternative"
154
- autoload :Arg, "chemicalml/cml/schema24/arg"
155
- autoload :ComplexObject, "chemicalml/cml/schema24/complex_object"
156
- autoload :Expression, "chemicalml/cml/schema24/expression"
157
- autoload :Float, "chemicalml/cml/schema24/float"
158
- autoload :FloatArray, "chemicalml/cml/schema24/float_array"
159
- autoload :Integer, "chemicalml/cml/schema24/integer"
160
- autoload :IntegerArray, "chemicalml/cml/schema24/integer_array"
161
- autoload :Operator, "chemicalml/cml/schema24/operator"
162
- autoload :RelatedEntry, "chemicalml/cml/schema24/related_entry"
163
- autoload :String, "chemicalml/cml/schema24/string"
164
- autoload :StringArray, "chemicalml/cml/schema24/string_array"
165
- autoload :Tcell, "chemicalml/cml/schema24/tcell"
166
- autoload :Trow, "chemicalml/cml/schema24/trow"
167
- autoload :Annotation, "chemicalml/cml/schema24/annotation"
168
- autoload :Appinfo, "chemicalml/cml/schema24/appinfo"
169
- autoload :Enumeration, "chemicalml/cml/schema24/enumeration"
115
+ autoload :Configuration, 'chemicalml/cml/schema24/configuration'
116
+ autoload :Context, 'chemicalml/cml/schema24/context'
117
+ autoload :Array, 'chemicalml/cml/schema24/array'
118
+ autoload :Atom, 'chemicalml/cml/schema24/atom'
119
+ autoload :AtomArray, 'chemicalml/cml/schema24/atom_array'
120
+ autoload :AtomParity, 'chemicalml/cml/schema24/atom_parity'
121
+ autoload :Bond, 'chemicalml/cml/schema24/bond'
122
+ autoload :BondArray, 'chemicalml/cml/schema24/bond_array'
123
+ autoload :BondStereo, 'chemicalml/cml/schema24/bond_stereo'
124
+ autoload :Dictionary, 'chemicalml/cml/schema24/dictionary'
125
+ autoload :DictionaryEntry, 'chemicalml/cml/schema24/dictionary_entry'
126
+ autoload :Document, 'chemicalml/cml/schema24/document'
127
+ autoload :Formula, 'chemicalml/cml/schema24/formula'
128
+ autoload :Identifier, 'chemicalml/cml/schema24/identifier'
129
+ autoload :Label, 'chemicalml/cml/schema24/label'
130
+ autoload :List, 'chemicalml/cml/schema24/list'
131
+ autoload :Matrix, 'chemicalml/cml/schema24/matrix'
132
+ autoload :Metadata, 'chemicalml/cml/schema24/metadata'
133
+ autoload :MetadataList, 'chemicalml/cml/schema24/metadata_list'
134
+ autoload :Module, 'chemicalml/cml/schema24/cml_module'
135
+ autoload :Molecule, 'chemicalml/cml/schema24/molecule'
136
+ autoload :Name, 'chemicalml/cml/schema24/name'
137
+ autoload :Parameter, 'chemicalml/cml/schema24/parameter'
138
+ autoload :ParameterList, 'chemicalml/cml/schema24/parameter_list'
139
+ autoload :Product, 'chemicalml/cml/schema24/product'
140
+ autoload :ProductList, 'chemicalml/cml/schema24/product_list'
141
+ autoload :Property, 'chemicalml/cml/schema24/property'
142
+ autoload :PropertyList, 'chemicalml/cml/schema24/property_list'
143
+ autoload :Reaction, 'chemicalml/cml/schema24/reaction'
144
+ autoload :ReactionList, 'chemicalml/cml/schema24/reaction_list'
145
+ autoload :Reactant, 'chemicalml/cml/schema24/reactant'
146
+ autoload :ReactantList, 'chemicalml/cml/schema24/reactant_list'
147
+ autoload :Scalar, 'chemicalml/cml/schema24/scalar'
148
+ autoload :Substance, 'chemicalml/cml/schema24/substance'
149
+ autoload :Unit, 'chemicalml/cml/schema24/unit'
150
+ autoload :UnitList, 'chemicalml/cml/schema24/unit_list'
151
+ autoload :UnitType, 'chemicalml/cml/schema24/unit_type'
152
+ autoload :UnitTypeList, 'chemicalml/cml/schema24/unit_type_list'
153
+ autoload :Alternative, 'chemicalml/cml/schema24/alternative'
154
+ autoload :Arg, 'chemicalml/cml/schema24/arg'
155
+ autoload :ComplexObject, 'chemicalml/cml/schema24/complex_object'
156
+ autoload :Expression, 'chemicalml/cml/schema24/expression'
157
+ autoload :Float, 'chemicalml/cml/schema24/float'
158
+ autoload :FloatArray, 'chemicalml/cml/schema24/float_array'
159
+ autoload :Integer, 'chemicalml/cml/schema24/integer'
160
+ autoload :IntegerArray, 'chemicalml/cml/schema24/integer_array'
161
+ autoload :Operator, 'chemicalml/cml/schema24/operator'
162
+ autoload :RelatedEntry, 'chemicalml/cml/schema24/related_entry'
163
+ autoload :String, 'chemicalml/cml/schema24/string'
164
+ autoload :StringArray, 'chemicalml/cml/schema24/string_array'
165
+ autoload :Tcell, 'chemicalml/cml/schema24/tcell'
166
+ autoload :Trow, 'chemicalml/cml/schema24/trow'
167
+ autoload :Annotation, 'chemicalml/cml/schema24/annotation'
168
+ autoload :Appinfo, 'chemicalml/cml/schema24/appinfo'
169
+ autoload :Enumeration, 'chemicalml/cml/schema24/enumeration'
170
170
 
171
171
  def self.schema
172
172
  SCHEMA
data/lib/chemicalml/cml/schema3.rb CHANGED
@@ -16,132 +16,132 @@ module Chemicalml
16
16
  module Schema3
17
17
  extend Chemicalml::VersionedParser
18
18
 
19
- autoload :Abundance, "chemicalml/cml/schema3/abundance"
20
- autoload :Action, "chemicalml/cml/schema3/action"
21
- autoload :ActionList, "chemicalml/cml/schema3/action_list"
22
- autoload :Amount, "chemicalml/cml/schema3/amount"
23
- autoload :Angle, "chemicalml/cml/schema3/angle"
24
- autoload :AnyCml, "chemicalml/cml/schema3/any_cml"
25
- autoload :ArrayList, "chemicalml/cml/schema3/array_list"
26
- autoload :AtomSet, "chemicalml/cml/schema3/atom_set"
27
- autoload :AtomType, "chemicalml/cml/schema3/atom_type"
28
- autoload :AtomTypeList, "chemicalml/cml/schema3/atom_type_list"
29
- autoload :AtomicBasisFunction, "chemicalml/cml/schema3/atomic_basis_function"
30
- autoload :Band, "chemicalml/cml/schema3/band"
31
- autoload :BandList, "chemicalml/cml/schema3/band_list"
32
- autoload :BasisSet, "chemicalml/cml/schema3/basis_set"
33
- autoload :BondSet, "chemicalml/cml/schema3/bond_set"
34
- autoload :BondType, "chemicalml/cml/schema3/bond_type"
35
- autoload :BondTypeList, "chemicalml/cml/schema3/bond_type_list"
36
- autoload :CellParameter, "chemicalml/cml/schema3/cell_parameter"
37
- autoload :ConditionList, "chemicalml/cml/schema3/condition_list"
38
- autoload :Crystal, "chemicalml/cml/schema3/crystal"
39
- autoload :Definition, "chemicalml/cml/schema3/definition"
40
- autoload :Description, "chemicalml/cml/schema3/description"
41
- autoload :Dimension, "chemicalml/cml/schema3/dimension"
42
- autoload :Documentation, "chemicalml/cml/schema3/documentation"
43
- autoload :Eigen, "chemicalml/cml/schema3/eigen"
44
- autoload :Electron, "chemicalml/cml/schema3/electron"
45
- autoload :Fragment, "chemicalml/cml/schema3/fragment"
46
- autoload :FragmentList, "chemicalml/cml/schema3/fragment_list"
47
- autoload :Gradient, "chemicalml/cml/schema3/gradient"
48
- autoload :Isotope, "chemicalml/cml/schema3/isotope"
49
- autoload :IsotopeList, "chemicalml/cml/schema3/isotope_list"
50
- autoload :Join, "chemicalml/cml/schema3/join"
51
- autoload :Kpoint, "chemicalml/cml/schema3/kpoint"
52
- autoload :KpointList, "chemicalml/cml/schema3/kpoint_list"
53
- autoload :Lattice, "chemicalml/cml/schema3/lattice"
54
- autoload :LatticeVector, "chemicalml/cml/schema3/lattice_vector"
55
- autoload :Length, "chemicalml/cml/schema3/length"
56
- autoload :Line3, "chemicalml/cml/schema3/line3"
57
- autoload :Link, "chemicalml/cml/schema3/link"
58
- autoload :Map, "chemicalml/cml/schema3/map"
59
- autoload :Mechanism, "chemicalml/cml/schema3/mechanism"
60
- autoload :MechanismComponent, "chemicalml/cml/schema3/mechanism_component"
61
- autoload :MoleculeList, "chemicalml/cml/schema3/molecule_list"
62
- autoload :Object, "chemicalml/cml/schema3/object"
63
- autoload :Observation, "chemicalml/cml/schema3/observation"
64
- autoload :Particle, "chemicalml/cml/schema3/particle"
65
- autoload :Peak, "chemicalml/cml/schema3/peak"
66
- autoload :PeakGroup, "chemicalml/cml/schema3/peak_group"
67
- autoload :PeakList, "chemicalml/cml/schema3/peak_list"
68
- autoload :PeakStructure, "chemicalml/cml/schema3/peak_structure"
69
- autoload :Plane3, "chemicalml/cml/schema3/plane3"
70
- autoload :Point3, "chemicalml/cml/schema3/point3"
71
- autoload :Potential, "chemicalml/cml/schema3/potential"
72
- autoload :PotentialForm, "chemicalml/cml/schema3/potential_form"
73
- autoload :PotentialList, "chemicalml/cml/schema3/potential_list"
74
- autoload :ReactionScheme, "chemicalml/cml/schema3/reaction_scheme"
75
- autoload :ReactionStep, "chemicalml/cml/schema3/reaction_step"
76
- autoload :ReactionStepList, "chemicalml/cml/schema3/reaction_step_list"
77
- autoload :ReactiveCentre, "chemicalml/cml/schema3/reactive_centre"
78
- autoload :Region, "chemicalml/cml/schema3/region"
79
- autoload :Sample, "chemicalml/cml/schema3/sample"
80
- autoload :Spectator, "chemicalml/cml/schema3/spectator"
81
- autoload :SpectatorList, "chemicalml/cml/schema3/spectator_list"
82
- autoload :Spectrum, "chemicalml/cml/schema3/spectrum"
83
- autoload :SpectrumData, "chemicalml/cml/schema3/spectrum_data"
84
- autoload :SpectrumList, "chemicalml/cml/schema3/spectrum_list"
85
- autoload :Sphere3, "chemicalml/cml/schema3/sphere3"
86
- autoload :Stmml, "chemicalml/cml/schema3/stmml"
87
- autoload :SubstanceList, "chemicalml/cml/schema3/substance_list"
88
- autoload :Symmetry, "chemicalml/cml/schema3/symmetry"
89
- autoload :System, "chemicalml/cml/schema3/system"
90
- autoload :Table, "chemicalml/cml/schema3/table"
91
- autoload :TableCell, "chemicalml/cml/schema3/table_cell"
92
- autoload :TableContent, "chemicalml/cml/schema3/table_content"
93
- autoload :TableHeader, "chemicalml/cml/schema3/table_header"
94
- autoload :TableHeaderCell, "chemicalml/cml/schema3/table_header_cell"
95
- autoload :TableRow, "chemicalml/cml/schema3/table_row"
96
- autoload :TableRowList, "chemicalml/cml/schema3/table_row_list"
97
- autoload :Torsion, "chemicalml/cml/schema3/torsion"
98
- autoload :Transform3, "chemicalml/cml/schema3/transform3"
99
- autoload :TransitionState, "chemicalml/cml/schema3/transition_state"
100
- autoload :Vector3, "chemicalml/cml/schema3/vector3"
101
- autoload :Xaxis, "chemicalml/cml/schema3/xaxis"
102
- autoload :Yaxis, "chemicalml/cml/schema3/yaxis"
103
- autoload :ZMatrix, "chemicalml/cml/schema3/z_matrix"
19
+ autoload :Abundance, 'chemicalml/cml/schema3/abundance'
20
+ autoload :Action, 'chemicalml/cml/schema3/action'
21
+ autoload :ActionList, 'chemicalml/cml/schema3/action_list'
22
+ autoload :Amount, 'chemicalml/cml/schema3/amount'
23
+ autoload :Angle, 'chemicalml/cml/schema3/angle'
24
+ autoload :AnyCml, 'chemicalml/cml/schema3/any_cml'
25
+ autoload :ArrayList, 'chemicalml/cml/schema3/array_list'
26
+ autoload :AtomSet, 'chemicalml/cml/schema3/atom_set'
27
+ autoload :AtomType, 'chemicalml/cml/schema3/atom_type'
28
+ autoload :AtomTypeList, 'chemicalml/cml/schema3/atom_type_list'
29
+ autoload :AtomicBasisFunction, 'chemicalml/cml/schema3/atomic_basis_function'
30
+ autoload :Band, 'chemicalml/cml/schema3/band'
31
+ autoload :BandList, 'chemicalml/cml/schema3/band_list'
32
+ autoload :BasisSet, 'chemicalml/cml/schema3/basis_set'
33
+ autoload :BondSet, 'chemicalml/cml/schema3/bond_set'
34
+ autoload :BondType, 'chemicalml/cml/schema3/bond_type'
35
+ autoload :BondTypeList, 'chemicalml/cml/schema3/bond_type_list'
36
+ autoload :CellParameter, 'chemicalml/cml/schema3/cell_parameter'
37
+ autoload :ConditionList, 'chemicalml/cml/schema3/condition_list'
38
+ autoload :Crystal, 'chemicalml/cml/schema3/crystal'
39
+ autoload :Definition, 'chemicalml/cml/schema3/definition'
40
+ autoload :Description, 'chemicalml/cml/schema3/description'
41
+ autoload :Dimension, 'chemicalml/cml/schema3/dimension'
42
+ autoload :Documentation, 'chemicalml/cml/schema3/documentation'
43
+ autoload :Eigen, 'chemicalml/cml/schema3/eigen'
44
+ autoload :Electron, 'chemicalml/cml/schema3/electron'
45
+ autoload :Fragment, 'chemicalml/cml/schema3/fragment'
46
+ autoload :FragmentList, 'chemicalml/cml/schema3/fragment_list'
47
+ autoload :Gradient, 'chemicalml/cml/schema3/gradient'
48
+ autoload :Isotope, 'chemicalml/cml/schema3/isotope'
49
+ autoload :IsotopeList, 'chemicalml/cml/schema3/isotope_list'
50
+ autoload :Join, 'chemicalml/cml/schema3/join'
51
+ autoload :Kpoint, 'chemicalml/cml/schema3/kpoint'
52
+ autoload :KpointList, 'chemicalml/cml/schema3/kpoint_list'
53
+ autoload :Lattice, 'chemicalml/cml/schema3/lattice'
54
+ autoload :LatticeVector, 'chemicalml/cml/schema3/lattice_vector'
55
+ autoload :Length, 'chemicalml/cml/schema3/length'
56
+ autoload :Line3, 'chemicalml/cml/schema3/line3'
57
+ autoload :Link, 'chemicalml/cml/schema3/link'
58
+ autoload :Map, 'chemicalml/cml/schema3/map'
59
+ autoload :Mechanism, 'chemicalml/cml/schema3/mechanism'
60
+ autoload :MechanismComponent, 'chemicalml/cml/schema3/mechanism_component'
61
+ autoload :MoleculeList, 'chemicalml/cml/schema3/molecule_list'
62
+ autoload :Object, 'chemicalml/cml/schema3/object'
63
+ autoload :Observation, 'chemicalml/cml/schema3/observation'
64
+ autoload :Particle, 'chemicalml/cml/schema3/particle'
65
+ autoload :Peak, 'chemicalml/cml/schema3/peak'
66
+ autoload :PeakGroup, 'chemicalml/cml/schema3/peak_group'
67
+ autoload :PeakList, 'chemicalml/cml/schema3/peak_list'
68
+ autoload :PeakStructure, 'chemicalml/cml/schema3/peak_structure'
69
+ autoload :Plane3, 'chemicalml/cml/schema3/plane3'
70
+ autoload :Point3, 'chemicalml/cml/schema3/point3'
71
+ autoload :Potential, 'chemicalml/cml/schema3/potential'
72
+ autoload :PotentialForm, 'chemicalml/cml/schema3/potential_form'
73
+ autoload :PotentialList, 'chemicalml/cml/schema3/potential_list'
74
+ autoload :ReactionScheme, 'chemicalml/cml/schema3/reaction_scheme'
75
+ autoload :ReactionStep, 'chemicalml/cml/schema3/reaction_step'
76
+ autoload :ReactionStepList, 'chemicalml/cml/schema3/reaction_step_list'
77
+ autoload :ReactiveCentre, 'chemicalml/cml/schema3/reactive_centre'
78
+ autoload :Region, 'chemicalml/cml/schema3/region'
79
+ autoload :Sample, 'chemicalml/cml/schema3/sample'
80
+ autoload :Spectator, 'chemicalml/cml/schema3/spectator'
81
+ autoload :SpectatorList, 'chemicalml/cml/schema3/spectator_list'
82
+ autoload :Spectrum, 'chemicalml/cml/schema3/spectrum'
83
+ autoload :SpectrumData, 'chemicalml/cml/schema3/spectrum_data'
84
+ autoload :SpectrumList, 'chemicalml/cml/schema3/spectrum_list'
85
+ autoload :Sphere3, 'chemicalml/cml/schema3/sphere3'
86
+ autoload :Stmml, 'chemicalml/cml/schema3/stmml'
87
+ autoload :SubstanceList, 'chemicalml/cml/schema3/substance_list'
88
+ autoload :Symmetry, 'chemicalml/cml/schema3/symmetry'
89
+ autoload :System, 'chemicalml/cml/schema3/system'
90
+ autoload :Table, 'chemicalml/cml/schema3/table'
91
+ autoload :TableCell, 'chemicalml/cml/schema3/table_cell'
92
+ autoload :TableContent, 'chemicalml/cml/schema3/table_content'
93
+ autoload :TableHeader, 'chemicalml/cml/schema3/table_header'
94
+ autoload :TableHeaderCell, 'chemicalml/cml/schema3/table_header_cell'
95
+ autoload :TableRow, 'chemicalml/cml/schema3/table_row'
96
+ autoload :TableRowList, 'chemicalml/cml/schema3/table_row_list'
97
+ autoload :Torsion, 'chemicalml/cml/schema3/torsion'
98
+ autoload :Transform3, 'chemicalml/cml/schema3/transform3'
99
+ autoload :TransitionState, 'chemicalml/cml/schema3/transition_state'
100
+ autoload :Vector3, 'chemicalml/cml/schema3/vector3'
101
+ autoload :Xaxis, 'chemicalml/cml/schema3/xaxis'
102
+ autoload :Yaxis, 'chemicalml/cml/schema3/yaxis'
103
+ autoload :ZMatrix, 'chemicalml/cml/schema3/z_matrix'
104
104
 
105
105
  SCHEMA = Chemicalml::Schema::Registry.lookup(:schema3)
106
106
 
107
- autoload :Configuration, "chemicalml/cml/schema3/configuration"
108
- autoload :Context, "chemicalml/cml/schema3/context"
109
- autoload :Array, "chemicalml/cml/schema3/array"
110
- autoload :Atom, "chemicalml/cml/schema3/atom"
111
- autoload :AtomArray, "chemicalml/cml/schema3/atom_array"
112
- autoload :AtomParity, "chemicalml/cml/schema3/atom_parity"
113
- autoload :Bond, "chemicalml/cml/schema3/bond"
114
- autoload :BondArray, "chemicalml/cml/schema3/bond_array"
115
- autoload :BondStereo, "chemicalml/cml/schema3/bond_stereo"
116
- autoload :Dictionary, "chemicalml/cml/schema3/dictionary"
117
- autoload :DictionaryEntry, "chemicalml/cml/schema3/dictionary_entry"
118
- autoload :Document, "chemicalml/cml/schema3/document"
119
- autoload :Formula, "chemicalml/cml/schema3/formula"
120
- autoload :Identifier, "chemicalml/cml/schema3/identifier"
121
- autoload :Label, "chemicalml/cml/schema3/label"
122
- autoload :List, "chemicalml/cml/schema3/list"
123
- autoload :Matrix, "chemicalml/cml/schema3/matrix"
124
- autoload :Metadata, "chemicalml/cml/schema3/metadata"
125
- autoload :MetadataList, "chemicalml/cml/schema3/metadata_list"
126
- autoload :Module, "chemicalml/cml/schema3/cml_module"
127
- autoload :Molecule, "chemicalml/cml/schema3/molecule"
128
- autoload :Name, "chemicalml/cml/schema3/name"
129
- autoload :Parameter, "chemicalml/cml/schema3/parameter"
130
- autoload :ParameterList, "chemicalml/cml/schema3/parameter_list"
131
- autoload :Product, "chemicalml/cml/schema3/product"
132
- autoload :ProductList, "chemicalml/cml/schema3/product_list"
133
- autoload :Property, "chemicalml/cml/schema3/property"
134
- autoload :PropertyList, "chemicalml/cml/schema3/property_list"
135
- autoload :Reaction, "chemicalml/cml/schema3/reaction"
136
- autoload :ReactionList, "chemicalml/cml/schema3/reaction_list"
137
- autoload :Reactant, "chemicalml/cml/schema3/reactant"
138
- autoload :ReactantList, "chemicalml/cml/schema3/reactant_list"
139
- autoload :Scalar, "chemicalml/cml/schema3/scalar"
140
- autoload :Substance, "chemicalml/cml/schema3/substance"
141
- autoload :Unit, "chemicalml/cml/schema3/unit"
142
- autoload :UnitList, "chemicalml/cml/schema3/unit_list"
143
- autoload :UnitType, "chemicalml/cml/schema3/unit_type"
144
- autoload :UnitTypeList, "chemicalml/cml/schema3/unit_type_list"
107
+ autoload :Configuration, 'chemicalml/cml/schema3/configuration'
108
+ autoload :Context, 'chemicalml/cml/schema3/context'
109
+ autoload :Array, 'chemicalml/cml/schema3/array'
110
+ autoload :Atom, 'chemicalml/cml/schema3/atom'
111
+ autoload :AtomArray, 'chemicalml/cml/schema3/atom_array'
112
+ autoload :AtomParity, 'chemicalml/cml/schema3/atom_parity'
113
+ autoload :Bond, 'chemicalml/cml/schema3/bond'
114
+ autoload :BondArray, 'chemicalml/cml/schema3/bond_array'
115
+ autoload :BondStereo, 'chemicalml/cml/schema3/bond_stereo'
116
+ autoload :Dictionary, 'chemicalml/cml/schema3/dictionary'
117
+ autoload :DictionaryEntry, 'chemicalml/cml/schema3/dictionary_entry'
118
+ autoload :Document, 'chemicalml/cml/schema3/document'
119
+ autoload :Formula, 'chemicalml/cml/schema3/formula'
120
+ autoload :Identifier, 'chemicalml/cml/schema3/identifier'
121
+ autoload :Label, 'chemicalml/cml/schema3/label'
122
+ autoload :List, 'chemicalml/cml/schema3/list'
123
+ autoload :Matrix, 'chemicalml/cml/schema3/matrix'
124
+ autoload :Metadata, 'chemicalml/cml/schema3/metadata'
125
+ autoload :MetadataList, 'chemicalml/cml/schema3/metadata_list'
126
+ autoload :Module, 'chemicalml/cml/schema3/cml_module'
127
+ autoload :Molecule, 'chemicalml/cml/schema3/molecule'
128
+ autoload :Name, 'chemicalml/cml/schema3/name'
129
+ autoload :Parameter, 'chemicalml/cml/schema3/parameter'
130
+ autoload :ParameterList, 'chemicalml/cml/schema3/parameter_list'
131
+ autoload :Product, 'chemicalml/cml/schema3/product'
132
+ autoload :ProductList, 'chemicalml/cml/schema3/product_list'
133
+ autoload :Property, 'chemicalml/cml/schema3/property'
134
+ autoload :PropertyList, 'chemicalml/cml/schema3/property_list'
135
+ autoload :Reaction, 'chemicalml/cml/schema3/reaction'
136
+ autoload :ReactionList, 'chemicalml/cml/schema3/reaction_list'
137
+ autoload :Reactant, 'chemicalml/cml/schema3/reactant'
138
+ autoload :ReactantList, 'chemicalml/cml/schema3/reactant_list'
139
+ autoload :Scalar, 'chemicalml/cml/schema3/scalar'
140
+ autoload :Substance, 'chemicalml/cml/schema3/substance'
141
+ autoload :Unit, 'chemicalml/cml/schema3/unit'
142
+ autoload :UnitList, 'chemicalml/cml/schema3/unit_list'
143
+ autoload :UnitType, 'chemicalml/cml/schema3/unit_type'
144
+ autoload :UnitTypeList, 'chemicalml/cml/schema3/unit_type_list'
145
145
 
146
146
  def self.schema
147
147
  SCHEMA