rcsb.exdb 1.31__py3-none-any.whl

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Files changed (98) hide show
  1. rcsb/__init__.py +1 -0
  2. rcsb/exdb/__init__.py +1 -0
  3. rcsb/exdb/branch/BranchedEntityExtractor.py +82 -0
  4. rcsb/exdb/branch/GlycanProvider.py +116 -0
  5. rcsb/exdb/branch/GlycanUtils.py +114 -0
  6. rcsb/exdb/branch/__init__.py +0 -0
  7. rcsb/exdb/chemref/ChemRefEtlWorker.py +118 -0
  8. rcsb/exdb/chemref/ChemRefExtractor.py +70 -0
  9. rcsb/exdb/chemref/ChemRefMappingProvider.py +139 -0
  10. rcsb/exdb/chemref/PubChemDataCacheProvider.py +372 -0
  11. rcsb/exdb/chemref/PubChemEtlWrapper.py +280 -0
  12. rcsb/exdb/chemref/PubChemIndexCacheProvider.py +638 -0
  13. rcsb/exdb/chemref/__init__.py +0 -0
  14. rcsb/exdb/citation/CitationAdapter.py +91 -0
  15. rcsb/exdb/citation/CitationExtractor.py +190 -0
  16. rcsb/exdb/citation/CitationUtils.py +51 -0
  17. rcsb/exdb/citation/__init__.py +0 -0
  18. rcsb/exdb/cli/__init__.py +0 -0
  19. rcsb/exdb/entry/EntryInfoProvider.py +148 -0
  20. rcsb/exdb/entry/__init__.py +0 -0
  21. rcsb/exdb/examples-seq/EntityInstanceExtractor.py +557 -0
  22. rcsb/exdb/examples-seq/EntityPolymerExtractor.py +544 -0
  23. rcsb/exdb/examples-seq/EntityPolymerExtractorFullTests.py +176 -0
  24. rcsb/exdb/examples-seq/ReferenceSequenceAssignmentUpdater.py +449 -0
  25. rcsb/exdb/examples-seq/ReferenceSequenceUtils.py +123 -0
  26. rcsb/exdb/examples-seq/ReferenceSequenceUtilsTests.py +109 -0
  27. rcsb/exdb/examples-seq/exampleObjectExtractor.py +109 -0
  28. rcsb/exdb/examples-seq/fixtureEntityPolymerExtractor.py +85 -0
  29. rcsb/exdb/examples-seq/testEntityInstanceExtractor.py +170 -0
  30. rcsb/exdb/examples-seq/testEntityPolymerExtractor.py +171 -0
  31. rcsb/exdb/examples-seq/testReferenceSequenceAssignmentUpdater.py +79 -0
  32. rcsb/exdb/examples-seq/testReferenceSequenceUtils.py +108 -0
  33. rcsb/exdb/seq/AnnotationExtractor.py +76 -0
  34. rcsb/exdb/seq/LigandNeighborMappingExtractor.py +84 -0
  35. rcsb/exdb/seq/LigandNeighborMappingProvider.py +106 -0
  36. rcsb/exdb/seq/PolymerEntityExtractor.py +328 -0
  37. rcsb/exdb/seq/ReferenceSequenceAnnotationAdapter.py +598 -0
  38. rcsb/exdb/seq/ReferenceSequenceAnnotationProvider.py +228 -0
  39. rcsb/exdb/seq/ReferenceSequenceAssignmentAdapter.py +534 -0
  40. rcsb/exdb/seq/ReferenceSequenceAssignmentProvider.py +388 -0
  41. rcsb/exdb/seq/ReferenceSequenceCacheProvider.py +397 -0
  42. rcsb/exdb/seq/TaxonomyExtractor.py +69 -0
  43. rcsb/exdb/seq/UniProtCoreEtlWorker.py +177 -0
  44. rcsb/exdb/seq/UniProtExtractor.py +80 -0
  45. rcsb/exdb/seq/__init__.py +0 -0
  46. rcsb/exdb/tests/TEST-EXDB-CLI-EXEC.sh +19 -0
  47. rcsb/exdb/tests/TEST-EXDB-CLI-REFSEQ-EXEC.sh +12 -0
  48. rcsb/exdb/tests/__init__.py +0 -0
  49. rcsb/exdb/tests/fixtureDictMethodResourceProvider.py +104 -0
  50. rcsb/exdb/tests/fixturePdbxLoader.py +298 -0
  51. rcsb/exdb/tests/test-data/components-abbrev.cif +2739 -0
  52. rcsb/exdb/tests/test-data/prdcc-abbrev.cif +9171 -0
  53. rcsb/exdb/tests/testAnnotationExtractor.py +79 -0
  54. rcsb/exdb/tests/testBranchedEntityExtractor.py +81 -0
  55. rcsb/exdb/tests/testChemRefLoader.py +106 -0
  56. rcsb/exdb/tests/testChemRefMappingProvider.py +95 -0
  57. rcsb/exdb/tests/testCitationAdapter.py +97 -0
  58. rcsb/exdb/tests/testCitationExtractor.py +93 -0
  59. rcsb/exdb/tests/testCitationUtils.py +92 -0
  60. rcsb/exdb/tests/testEntryInfoEtlWorkflow.py +70 -0
  61. rcsb/exdb/tests/testEntryInfoProvider.py +97 -0
  62. rcsb/exdb/tests/testGlycanEtlWorkflow.py +70 -0
  63. rcsb/exdb/tests/testGlycanProvider.py +98 -0
  64. rcsb/exdb/tests/testGlycanUtils.py +64 -0
  65. rcsb/exdb/tests/testLigandNeighborMappingProvider.py +90 -0
  66. rcsb/exdb/tests/testObjectExtractor.py +342 -0
  67. rcsb/exdb/tests/testObjectTransformer.py +83 -0
  68. rcsb/exdb/tests/testObjectUpdater.py +120 -0
  69. rcsb/exdb/tests/testPolymerEntityExtractor.py +93 -0
  70. rcsb/exdb/tests/testPubChemDataCacheProvider.py +124 -0
  71. rcsb/exdb/tests/testPubChemEtlWorkflow.py +134 -0
  72. rcsb/exdb/tests/testPubChemEtlWrapper.py +155 -0
  73. rcsb/exdb/tests/testPubChemIndexCacheProvider.py +123 -0
  74. rcsb/exdb/tests/testReferenceSequenceAnnotationAdapter.py +106 -0
  75. rcsb/exdb/tests/testReferenceSequenceAssignmentAdapter.py +121 -0
  76. rcsb/exdb/tests/testReferenceSequenceAssignmentAdapterValidate.py +122 -0
  77. rcsb/exdb/tests/testReferenceSequenceAssignmentProvider.py +117 -0
  78. rcsb/exdb/tests/testReferenceSequenceCacheProvider.py +94 -0
  79. rcsb/exdb/tests/testTaxonomyExtractor.py +75 -0
  80. rcsb/exdb/tests/testTreeNodeListWorker.py +111 -0
  81. rcsb/exdb/tests/testUniProtCoreEtlWorker.py +99 -0
  82. rcsb/exdb/tests/testUniProtExtractor.py +77 -0
  83. rcsb/exdb/tree/TreeNodeListWorker.py +228 -0
  84. rcsb/exdb/tree/__init__.py +0 -0
  85. rcsb/exdb/utils/ObjectAdapterBase.py +22 -0
  86. rcsb/exdb/utils/ObjectExtractor.py +286 -0
  87. rcsb/exdb/utils/ObjectTransformer.py +124 -0
  88. rcsb/exdb/utils/ObjectUpdater.py +121 -0
  89. rcsb/exdb/utils/ObjectValidator.py +160 -0
  90. rcsb/exdb/utils/__init__.py +0 -0
  91. rcsb/exdb/wf/EntryInfoEtlWorkflow.py +71 -0
  92. rcsb/exdb/wf/GlycanEtlWorkflow.py +76 -0
  93. rcsb/exdb/wf/PubChemEtlWorkflow.py +240 -0
  94. rcsb/exdb/wf/__init__.py +0 -0
  95. rcsb_exdb-1.31.dist-info/METADATA +103 -0
  96. rcsb_exdb-1.31.dist-info/RECORD +98 -0
  97. rcsb_exdb-1.31.dist-info/WHEEL +4 -0
  98. rcsb_exdb-1.31.dist-info/licenses/LICENSE +201 -0

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