cdxml-toolkit 0.5.0__py3-none-any.whl

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Files changed (91) hide show
  1. cdxml_toolkit/__init__.py +18 -0
  2. cdxml_toolkit/_jre/__init__.py +2 -0
  3. cdxml_toolkit/_jre/temurin-21-jre-win-x64.zip +0 -0
  4. cdxml_toolkit/analysis/__init__.py +35 -0
  5. cdxml_toolkit/analysis/deterministic/__init__.py +12 -0
  6. cdxml_toolkit/analysis/deterministic/discover_experiment_files.py +413 -0
  7. cdxml_toolkit/analysis/deterministic/lab_book_formatter.py +701 -0
  8. cdxml_toolkit/analysis/deterministic/lcms_file_categorizer.py +928 -0
  9. cdxml_toolkit/analysis/deterministic/lcms_identifier.py +598 -0
  10. cdxml_toolkit/analysis/deterministic/mass_resolver.py +654 -0
  11. cdxml_toolkit/analysis/deterministic/multi_lcms_analyzer.py +1412 -0
  12. cdxml_toolkit/analysis/deterministic/procedure_writer.py +446 -0
  13. cdxml_toolkit/analysis/extract_nmr.py +47 -0
  14. cdxml_toolkit/analysis/format_procedure_entry.py +479 -0
  15. cdxml_toolkit/analysis/lcms_analyzer.py +1299 -0
  16. cdxml_toolkit/analysis/parse_analysis_file.py +134 -0
  17. cdxml_toolkit/cdxml_builder.py +920 -0
  18. cdxml_toolkit/cdxml_utils.py +342 -0
  19. cdxml_toolkit/chemdraw/__init__.py +5 -0
  20. cdxml_toolkit/chemdraw/_chemscript_server.py +562 -0
  21. cdxml_toolkit/chemdraw/cdx_converter.py +527 -0
  22. cdxml_toolkit/chemdraw/cdxml_to_image.py +262 -0
  23. cdxml_toolkit/chemdraw/cdxml_to_image_rdkit.py +296 -0
  24. cdxml_toolkit/chemdraw/chemscript_bridge.py +901 -0
  25. cdxml_toolkit/constants.py +304 -0
  26. cdxml_toolkit/coord_normalizer.py +438 -0
  27. cdxml_toolkit/deterministic_pipeline/__init__.py +6 -0
  28. cdxml_toolkit/deterministic_pipeline/legacy/__init__.py +5 -0
  29. cdxml_toolkit/deterministic_pipeline/legacy/eln_cdx_cleanup.py +509 -0
  30. cdxml_toolkit/deterministic_pipeline/legacy/eln_enrichment.py +1394 -0
  31. cdxml_toolkit/deterministic_pipeline/legacy/scheme_aligner.py +428 -0
  32. cdxml_toolkit/deterministic_pipeline/legacy/scheme_polisher.py +1337 -0
  33. cdxml_toolkit/deterministic_pipeline/legacy/scheme_polisher_v2.py +1340 -0
  34. cdxml_toolkit/deterministic_pipeline/scheme_reader_audit.py +931 -0
  35. cdxml_toolkit/deterministic_pipeline/scheme_reader_verify.py +1160 -0
  36. cdxml_toolkit/image/__init__.py +15 -0
  37. cdxml_toolkit/image/reaction_from_image.py +2103 -0
  38. cdxml_toolkit/image/structure_from_image.py +1711 -0
  39. cdxml_toolkit/layout/__init__.py +5 -0
  40. cdxml_toolkit/layout/alignment.py +1642 -0
  41. cdxml_toolkit/layout/reaction_cleanup.py +1002 -0
  42. cdxml_toolkit/layout/scheme_merger.py +2260 -0
  43. cdxml_toolkit/mcp_server/__init__.py +0 -0
  44. cdxml_toolkit/mcp_server/__main__.py +5 -0
  45. cdxml_toolkit/mcp_server/server.py +1567 -0
  46. cdxml_toolkit/naming/__init__.py +6 -0
  47. cdxml_toolkit/naming/aligned_namer.py +2342 -0
  48. cdxml_toolkit/naming/mol_builder.py +3722 -0
  49. cdxml_toolkit/naming/name_decomposer.py +2843 -0
  50. cdxml_toolkit/naming/reactions_datamol.json +2414 -0
  51. cdxml_toolkit/office/__init__.py +5 -0
  52. cdxml_toolkit/office/doc_from_template.py +722 -0
  53. cdxml_toolkit/office/ole_embedder.py +808 -0
  54. cdxml_toolkit/office/ole_extractor.py +272 -0
  55. cdxml_toolkit/perception/__init__.py +10 -0
  56. cdxml_toolkit/perception/compound_search.py +229 -0
  57. cdxml_toolkit/perception/eln_csv_parser.py +240 -0
  58. cdxml_toolkit/perception/rdf_parser.py +664 -0
  59. cdxml_toolkit/perception/reactant_heuristic.py +1045 -0
  60. cdxml_toolkit/perception/reaction_parser.py +2150 -0
  61. cdxml_toolkit/perception/scheme_reader.py +2948 -0
  62. cdxml_toolkit/perception/scheme_refine.py +1404 -0
  63. cdxml_toolkit/perception/scheme_segmenter.py +619 -0
  64. cdxml_toolkit/perception/spatial_assignment.py +1013 -0
  65. cdxml_toolkit/rdkit_utils.py +605 -0
  66. cdxml_toolkit/render/__init__.py +17 -0
  67. cdxml_toolkit/render/auto_layout.py +229 -0
  68. cdxml_toolkit/render/compact_parser.py +632 -0
  69. cdxml_toolkit/render/parser.py +706 -0
  70. cdxml_toolkit/render/render_scheme.py +267 -0
  71. cdxml_toolkit/render/renderer.py +2387 -0
  72. cdxml_toolkit/render/schema.py +90 -0
  73. cdxml_toolkit/render/scheme_maker.py +1043 -0
  74. cdxml_toolkit/render/scheme_yaml_writer.py +1487 -0
  75. cdxml_toolkit/resolve/__init__.py +13 -0
  76. cdxml_toolkit/resolve/cas_resolver.py +430 -0
  77. cdxml_toolkit/resolve/chemscanner_abbreviations.json +28813 -0
  78. cdxml_toolkit/resolve/condensed_formula.py +493 -0
  79. cdxml_toolkit/resolve/jre_manager.py +195 -0
  80. cdxml_toolkit/resolve/reagent_abbreviations.json +1046 -0
  81. cdxml_toolkit/resolve/reagent_db.py +285 -0
  82. cdxml_toolkit/resolve/superatom_data.json +2856 -0
  83. cdxml_toolkit/resolve/superatom_table.py +146 -0
  84. cdxml_toolkit/text_formatting.py +298 -0
  85. cdxml_toolkit-0.5.0.dist-info/METADATA +318 -0
  86. cdxml_toolkit-0.5.0.dist-info/RECORD +91 -0
  87. cdxml_toolkit-0.5.0.dist-info/WHEEL +5 -0
  88. cdxml_toolkit-0.5.0.dist-info/entry_points.txt +17 -0
  89. cdxml_toolkit-0.5.0.dist-info/licenses/LICENSE +21 -0
  90. cdxml_toolkit-0.5.0.dist-info/licenses/NOTICE.md +37 -0
  91. cdxml_toolkit-0.5.0.dist-info/top_level.txt +1 -0
cdxml_toolkit/naming/__init__.py ADDED
@@ -0,0 +1,6 @@
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+ """Naming — IUPAC name analysis, alignment, and LLM-assisted construction.
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+
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+ IUPAC name decomposition (ChemScript-based), multi-step aligned naming
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+ using Viterbi dynamic programming, and composable tools for LLM-driven
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+ molecule construction via name manipulation.
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+ """