tooluniverse 0.2.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

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Files changed (186) hide show
  1. tooluniverse/__init__.py +340 -4
  2. tooluniverse/admetai_tool.py +84 -0
  3. tooluniverse/agentic_tool.py +563 -0
  4. tooluniverse/alphafold_tool.py +96 -0
  5. tooluniverse/base_tool.py +129 -6
  6. tooluniverse/boltz_tool.py +207 -0
  7. tooluniverse/chem_tool.py +192 -0
  8. tooluniverse/compose_scripts/__init__.py +1 -0
  9. tooluniverse/compose_scripts/biomarker_discovery.py +293 -0
  10. tooluniverse/compose_scripts/comprehensive_drug_discovery.py +186 -0
  11. tooluniverse/compose_scripts/drug_safety_analyzer.py +89 -0
  12. tooluniverse/compose_scripts/literature_tool.py +34 -0
  13. tooluniverse/compose_scripts/output_summarizer.py +279 -0
  14. tooluniverse/compose_scripts/tool_description_optimizer.py +681 -0
  15. tooluniverse/compose_scripts/tool_discover.py +705 -0
  16. tooluniverse/compose_scripts/tool_graph_composer.py +448 -0
  17. tooluniverse/compose_tool.py +371 -0
  18. tooluniverse/ctg_tool.py +1002 -0
  19. tooluniverse/custom_tool.py +81 -0
  20. tooluniverse/dailymed_tool.py +108 -0
  21. tooluniverse/data/admetai_tools.json +155 -0
  22. tooluniverse/data/adverse_event_tools.json +108 -0
  23. tooluniverse/data/agentic_tools.json +1156 -0
  24. tooluniverse/data/alphafold_tools.json +87 -0
  25. tooluniverse/data/boltz_tools.json +9 -0
  26. tooluniverse/data/chembl_tools.json +16 -0
  27. tooluniverse/data/clinicaltrials_gov_tools.json +326 -0
  28. tooluniverse/data/compose_tools.json +202 -0
  29. tooluniverse/data/dailymed_tools.json +70 -0
  30. tooluniverse/data/dataset_tools.json +646 -0
  31. tooluniverse/data/disease_target_score_tools.json +712 -0
  32. tooluniverse/data/efo_tools.json +17 -0
  33. tooluniverse/data/embedding_tools.json +319 -0
  34. tooluniverse/data/enrichr_tools.json +31 -0
  35. tooluniverse/data/europe_pmc_tools.json +22 -0
  36. tooluniverse/data/expert_feedback_tools.json +10 -0
  37. tooluniverse/data/fda_drug_adverse_event_tools.json +491 -0
  38. tooluniverse/data/fda_drug_labeling_tools.json +1 -1
  39. tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py +76929 -148860
  40. tooluniverse/data/finder_tools.json +209 -0
  41. tooluniverse/data/gene_ontology_tools.json +113 -0
  42. tooluniverse/data/gwas_tools.json +1082 -0
  43. tooluniverse/data/hpa_tools.json +333 -0
  44. tooluniverse/data/humanbase_tools.json +47 -0
  45. tooluniverse/data/idmap_tools.json +74 -0
  46. tooluniverse/data/mcp_client_tools_example.json +113 -0
  47. tooluniverse/data/mcpautoloadertool_defaults.json +28 -0
  48. tooluniverse/data/medlineplus_tools.json +141 -0
  49. tooluniverse/data/monarch_tools.json +1 -1
  50. tooluniverse/data/openalex_tools.json +36 -0
  51. tooluniverse/data/opentarget_tools.json +1 -1
  52. tooluniverse/data/output_summarization_tools.json +101 -0
  53. tooluniverse/data/packages/bioinformatics_core_tools.json +1756 -0
  54. tooluniverse/data/packages/categorized_tools.txt +206 -0
  55. tooluniverse/data/packages/cheminformatics_tools.json +347 -0
  56. tooluniverse/data/packages/earth_sciences_tools.json +74 -0
  57. tooluniverse/data/packages/genomics_tools.json +776 -0
  58. tooluniverse/data/packages/image_processing_tools.json +38 -0
  59. tooluniverse/data/packages/machine_learning_tools.json +789 -0
  60. tooluniverse/data/packages/neuroscience_tools.json +62 -0
  61. tooluniverse/data/packages/original_tools.txt +0 -0
  62. tooluniverse/data/packages/physics_astronomy_tools.json +62 -0
  63. tooluniverse/data/packages/scientific_computing_tools.json +560 -0
  64. tooluniverse/data/packages/single_cell_tools.json +453 -0
  65. tooluniverse/data/packages/structural_biology_tools.json +396 -0
  66. tooluniverse/data/packages/visualization_tools.json +399 -0
  67. tooluniverse/data/pubchem_tools.json +215 -0
  68. tooluniverse/data/pubtator_tools.json +68 -0
  69. tooluniverse/data/rcsb_pdb_tools.json +1332 -0
  70. tooluniverse/data/reactome_tools.json +19 -0
  71. tooluniverse/data/semantic_scholar_tools.json +26 -0
  72. tooluniverse/data/special_tools.json +2 -25
  73. tooluniverse/data/tool_composition_tools.json +88 -0
  74. tooluniverse/data/toolfinderkeyword_defaults.json +34 -0
  75. tooluniverse/data/txagent_client_tools.json +9 -0
  76. tooluniverse/data/uniprot_tools.json +211 -0
  77. tooluniverse/data/url_fetch_tools.json +94 -0
  78. tooluniverse/data/uspto_downloader_tools.json +9 -0
  79. tooluniverse/data/uspto_tools.json +811 -0
  80. tooluniverse/data/xml_tools.json +3275 -0
  81. tooluniverse/dataset_tool.py +296 -0
  82. tooluniverse/default_config.py +165 -0
  83. tooluniverse/efo_tool.py +42 -0
  84. tooluniverse/embedding_database.py +630 -0
  85. tooluniverse/embedding_sync.py +396 -0
  86. tooluniverse/enrichr_tool.py +266 -0
  87. tooluniverse/europe_pmc_tool.py +52 -0
  88. tooluniverse/execute_function.py +1775 -95
  89. tooluniverse/extended_hooks.py +444 -0
  90. tooluniverse/gene_ontology_tool.py +194 -0
  91. tooluniverse/graphql_tool.py +158 -36
  92. tooluniverse/gwas_tool.py +358 -0
  93. tooluniverse/hpa_tool.py +1645 -0
  94. tooluniverse/humanbase_tool.py +389 -0
  95. tooluniverse/logging_config.py +254 -0
  96. tooluniverse/mcp_client_tool.py +764 -0
  97. tooluniverse/mcp_integration.py +413 -0
  98. tooluniverse/mcp_tool_registry.py +925 -0
  99. tooluniverse/medlineplus_tool.py +337 -0
  100. tooluniverse/openalex_tool.py +228 -0
  101. tooluniverse/openfda_adv_tool.py +283 -0
  102. tooluniverse/openfda_tool.py +393 -160
  103. tooluniverse/output_hook.py +1122 -0
  104. tooluniverse/package_tool.py +195 -0
  105. tooluniverse/pubchem_tool.py +158 -0
  106. tooluniverse/pubtator_tool.py +168 -0
  107. tooluniverse/rcsb_pdb_tool.py +38 -0
  108. tooluniverse/reactome_tool.py +108 -0
  109. tooluniverse/remote/boltz/boltz_mcp_server.py +50 -0
  110. tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py +442 -0
  111. tooluniverse/remote/expert_feedback/human_expert_mcp_tools.py +2013 -0
  112. tooluniverse/remote/expert_feedback/simple_test.py +23 -0
  113. tooluniverse/remote/expert_feedback/start_web_interface.py +188 -0
  114. tooluniverse/remote/expert_feedback/web_only_interface.py +0 -0
  115. tooluniverse/remote/immune_compass/compass_tool.py +327 -0
  116. tooluniverse/remote/pinnacle/pinnacle_tool.py +328 -0
  117. tooluniverse/remote/transcriptformer/transcriptformer_tool.py +586 -0
  118. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +61 -0
  119. tooluniverse/remote/uspto_downloader/uspto_downloader_tool.py +120 -0
  120. tooluniverse/remote_tool.py +99 -0
  121. tooluniverse/restful_tool.py +53 -30
  122. tooluniverse/scripts/generate_tool_graph.py +408 -0
  123. tooluniverse/scripts/visualize_tool_graph.py +829 -0
  124. tooluniverse/semantic_scholar_tool.py +62 -0
  125. tooluniverse/smcp.py +2452 -0
  126. tooluniverse/smcp_server.py +975 -0
  127. tooluniverse/test/mcp_server_test.py +0 -0
  128. tooluniverse/test/test_admetai_tool.py +370 -0
  129. tooluniverse/test/test_agentic_tool.py +129 -0
  130. tooluniverse/test/test_alphafold_tool.py +71 -0
  131. tooluniverse/test/test_chem_tool.py +37 -0
  132. tooluniverse/test/test_compose_lieraturereview.py +63 -0
  133. tooluniverse/test/test_compose_tool.py +448 -0
  134. tooluniverse/test/test_dailymed.py +69 -0
  135. tooluniverse/test/test_dataset_tool.py +200 -0
  136. tooluniverse/test/test_disease_target_score.py +56 -0
  137. tooluniverse/test/test_drugbank_filter_examples.py +179 -0
  138. tooluniverse/test/test_efo.py +31 -0
  139. tooluniverse/test/test_enrichr_tool.py +21 -0
  140. tooluniverse/test/test_europe_pmc_tool.py +20 -0
  141. tooluniverse/test/test_fda_adv.py +95 -0
  142. tooluniverse/test/test_fda_drug_labeling.py +91 -0
  143. tooluniverse/test/test_gene_ontology_tools.py +66 -0
  144. tooluniverse/test/test_gwas_tool.py +139 -0
  145. tooluniverse/test/test_hpa.py +625 -0
  146. tooluniverse/test/test_humanbase_tool.py +20 -0
  147. tooluniverse/test/test_idmap_tools.py +61 -0
  148. tooluniverse/test/test_mcp_server.py +211 -0
  149. tooluniverse/test/test_mcp_tool.py +247 -0
  150. tooluniverse/test/test_medlineplus.py +220 -0
  151. tooluniverse/test/test_openalex_tool.py +32 -0
  152. tooluniverse/test/test_opentargets.py +28 -0
  153. tooluniverse/test/test_pubchem_tool.py +116 -0
  154. tooluniverse/test/test_pubtator_tool.py +37 -0
  155. tooluniverse/test/test_rcsb_pdb_tool.py +86 -0
  156. tooluniverse/test/test_reactome.py +54 -0
  157. tooluniverse/test/test_semantic_scholar_tool.py +24 -0
  158. tooluniverse/test/test_software_tools.py +147 -0
  159. tooluniverse/test/test_tool_description_optimizer.py +49 -0
  160. tooluniverse/test/test_tool_finder.py +26 -0
  161. tooluniverse/test/test_tool_finder_llm.py +252 -0
  162. tooluniverse/test/test_tools_find.py +195 -0
  163. tooluniverse/test/test_uniprot_tools.py +74 -0
  164. tooluniverse/test/test_uspto_tool.py +72 -0
  165. tooluniverse/test/test_xml_tool.py +113 -0
  166. tooluniverse/tool_finder_embedding.py +267 -0
  167. tooluniverse/tool_finder_keyword.py +693 -0
  168. tooluniverse/tool_finder_llm.py +699 -0
  169. tooluniverse/tool_graph_web_ui.py +955 -0
  170. tooluniverse/tool_registry.py +416 -0
  171. tooluniverse/uniprot_tool.py +155 -0
  172. tooluniverse/url_tool.py +253 -0
  173. tooluniverse/uspto_tool.py +240 -0
  174. tooluniverse/utils.py +369 -41
  175. tooluniverse/xml_tool.py +369 -0
  176. tooluniverse-1.0.1.dist-info/METADATA +387 -0
  177. tooluniverse-1.0.1.dist-info/RECORD +182 -0
  178. tooluniverse-1.0.1.dist-info/entry_points.txt +9 -0
  179. tooluniverse/generate_mcp_tools.py +0 -113
  180. tooluniverse/mcp_server.py +0 -3340
  181. tooluniverse-0.2.0.dist-info/METADATA +0 -139
  182. tooluniverse-0.2.0.dist-info/RECORD +0 -21
  183. tooluniverse-0.2.0.dist-info/entry_points.txt +0 -4
  184. {tooluniverse-0.2.0.dist-info → tooluniverse-1.0.1.dist-info}/WHEEL +0 -0
  185. {tooluniverse-0.2.0.dist-info → tooluniverse-1.0.1.dist-info}/licenses/LICENSE +0 -0
  186. {tooluniverse-0.2.0.dist-info → tooluniverse-1.0.1.dist-info}/top_level.txt +0 -0
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+ from tooluniverse import ToolUniverse
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+
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+ # Step 1: Initialize tool universe
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+ tooluni = ToolUniverse()
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+ tooluni.load_tools()
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+
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+ # Standard testing
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+ test_queries = [
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+ {
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+ "name": "ADMETAI_predict_physicochemical_properties",
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+ "arguments": {
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+ "smiles": [
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+ ]
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+ "CCC(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
311
+ "CC[C@H](C)C(=O)O[C@@H]1C[C@H](C)C=C2C=C[C@H](C)[C@@H](CC[C@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
312
+ "CC[C@@H](C)C(=O)O[C@@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@@H](CC[C@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
313
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)C21",
314
+ "CC[C@H](C)C(=O)O[C@H]1C[C@H](O)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
315
+ "CC(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)C21",
316
+ "C[C@H]1C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]2[C@@H](OC(=O)[C@@H](C)CCO)C1",
317
+ "CC(O)[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
318
+ ]
319
+ },
320
+ },
321
+ {
322
+ "name": "ADMETAI_predict_solubility_lipophilicity_hydration",
323
+ "arguments": {
324
+ "smiles": [
325
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)O)[C@H]21",
326
+ "CC[C@H](C)C(=O)O[C@@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@H](O)CC(=O)[O-])C21.[Na+]",
327
+ "CC[C@@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)O)[C@H]21",
328
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)[O-])[C@H]21.[Na+]",
329
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)[O-])[C@H]21.[K+]",
330
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CCC(O)C[C@@H](O)CC(=O)O)[C@H]21",
331
+ "CC[C@H](C)C(=O)O[C@@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@H](O)CC(=O)O)C21",
332
+ "CCC(C)C(=O)OC1CC(C)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)O)C21",
333
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CCC(O)C[C@@H](O)CC(=O)[O-])[C@H]21.[Na+]",
334
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](O)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)[O-])[C@H]21.[Na+]",
335
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](O)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)O)[C@H]21",
336
+ "CCC(C)C(=O)OC1CC(O)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)O)C21",
337
+ "CCC(C)C(=O)OC1CC(O)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)[O-])C21.[Na+]",
338
+ "CC[C@H](C)C(=O)O[C@H]1C[C@H](O)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)O)[C@H]21",
339
+ "CC[C@H](C)C(=O)O[C@H]1C[C@H](O)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)[O-])[C@H]21.[Na+]",
340
+ "CCC(C)C(=O)OC1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)NO)[C@H]21",
341
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)NO)[C@H]21",
342
+ "CC(O)[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(=O)O)[C@H]21",
343
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CCCC[C@@H](O)CC(=O)O)[C@H]21",
344
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CCCC[C@@H](O)CC(=O)[O-])[C@H]21.[Na+]",
345
+ "CC[C@@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
346
+ "CC[C@H](C)C(=O)O[C@H]1C[C@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
347
+ "CCC(C)C(=O)OC1CC(C)C=C2C=CC(C)C(CCC3CC(O)CC(=O)O3)C21",
348
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)C21.[NaH]",
349
+ "CCC(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
350
+ "CC[C@H](C)C(=O)O[C@@H]1C[C@H](C)C=C2C=C[C@H](C)[C@@H](CC[C@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
351
+ "CC[C@@H](C)C(=O)O[C@@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@@H](CC[C@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
352
+ "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)C21",
353
+ "CC[C@H](C)C(=O)O[C@H]1C[C@H](O)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
354
+ "CC(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)C21",
355
+ "C[C@H]1C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]2[C@@H](OC(=O)[C@@H](C)CCO)C1",
356
+ "CC(O)[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21",
357
+ ]
358
+ },
359
+ },
360
+ ]
361
+
362
+ for idx, query in enumerate(test_queries):
363
+ print(
364
+ f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
365
+ )
366
+ result = tooluni.run(query)
367
+ print("✅ Success. Output:")
368
+ print(
369
+ result if isinstance(result, dict) else str(result)
370
+ ) # Print snippet if result is big
@@ -0,0 +1,129 @@
1
+ from tooluniverse import ToolUniverse
2
+ from typing import Any, Dict, List
3
+
4
+ # Step 1: Initialize tool universe and load available tools
5
+ tooluni = ToolUniverse()
6
+ tooluni.load_tools()
7
+
8
+ # Sample biomedical text for testing
9
+ sample_abstract = """
10
+ Background: Drug-drug interactions (DDIs) are a major cause of adverse drug reactions and
11
+ represent a significant public health concern. This study aimed to develop and validate a
12
+ machine learning approach for predicting potential DDIs using molecular descriptors and
13
+ pharmacokinetic properties.
14
+
15
+ Methods: We collected data on 15,000 drug pairs from DrugBank and FDA databases. Molecular
16
+ descriptors were computed using RDKit, and pharmacokinetic parameters were extracted from
17
+ literature. A gradient boosting classifier was trained to predict DDI severity levels.
18
+
19
+ Results: The model achieved an accuracy of 89.2% with a precision of 0.91 and recall of 0.87
20
+ for high-severity DDI prediction. Feature importance analysis revealed that CYP450 enzyme
21
+ inhibition patterns and protein binding affinity were the most predictive features.
22
+
23
+ Conclusions: Our machine learning approach demonstrates high accuracy in predicting DDIs and
24
+ could serve as a valuable tool for clinical decision support and drug safety assessment.
25
+ """
26
+
27
+ # Define test queries based on the agentic_tools.json configuration
28
+ test_queries: List[Dict[str, Any]] = [
29
+ # {
30
+ # "name": "BiomedicalTextSummarizer",
31
+ # "arguments": {
32
+ # "text": sample_abstract,
33
+ # "summary_length": "100 words",
34
+ # "focus_area": "methodology and results"
35
+ # }
36
+ # },
37
+ # {
38
+ # "name": "BiomedicalTextSummarizer",
39
+ # "arguments": {
40
+ # "text": "Metformin is a first-line treatment for type 2 diabetes that works by reducing glucose production in the liver.",
41
+ # "summary_length": "25 words",
42
+ # "focus_area": "mechanism of action"
43
+ # }
44
+ # },
45
+ # {
46
+ # "name": "MedicalLiteratureReviewer",
47
+ # "arguments": {
48
+ # "research_topic": "Immunotherapy efficacy in triple-negative breast cancer",
49
+ # "literature_content": "Study 1: Pembrolizumab showed 23% response rate (n=150). Study 2: Atezolizumab combined with chemotherapy improved progression-free survival (HR=0.62, p=0.002).",
50
+ # "focus_area": "treatment efficacy",
51
+ # "study_types": "randomized controlled trials",
52
+ # "quality_level": "moderate and above",
53
+ # "review_scope": "rapid review"
54
+ # }
55
+ # },
56
+ # {
57
+ # "name": "HypothesisGenerator",
58
+ # "arguments": {
59
+ # "context": "Recent studies have shown that patients with Alzheimer's disease have altered gut microbiome composition. Additionally, inflammation markers in the brain correlate with cognitive decline. Some research suggests that certain probiotics can cross the blood-brain barrier and influence neuroinflammation.",
60
+ # "domain": "neuroscience",
61
+ # "number_of_hypotheses": "3",
62
+ # "hypothesis_format": "If-then statements"
63
+ # }
64
+ # },
65
+ # {
66
+ # "name": "HypothesisGenerator",
67
+ # "arguments": {
68
+ # "context": "Machine learning models trained on electronic health records show promise in predicting drug adverse events. However, most models focus on single drugs rather than drug combinations. Polypharmacy is common in elderly patients and drug-drug interactions are poorly understood.",
69
+ # "domain": "pharmacology",
70
+ # "number_of_hypotheses": "2"
71
+ # }
72
+ # },
73
+ {
74
+ "name": "ExperimentalDesignScorer",
75
+ "arguments": {
76
+ "hypothesis": "Daily high-intensity interval training (HIIT) for 8 weeks will improve insulin sensitivity in overweight adults compared to moderate-intensity continuous training (MICT).",
77
+ "design_description": """
78
+ Study Design: Randomized, parallel-group clinical trial
79
+
80
+ Participants: 120 overweight adults (BMI 25–30) aged 30–50, sedentary lifestyle
81
+ Inclusion: No history of diabetes, stable weight for 3 months
82
+ Exclusion: Cardiovascular disease, musculoskeletal injuries, current exercise regimen
83
+
84
+ Interventions:
85
+ - HIIT group (n=60): 4×4-minute intervals at 90% HRmax with 3-minute active recovery, 3×/week
86
+ - MICT group (n=60): 40 minutes at 60% HRmax, 3×/week
87
+
88
+ Randomization: Computer-generated simple randomization
89
+ Blinding: Outcome assessors blinded
90
+
91
+ Primary Outcome: Change in HOMA-IR from baseline to 8 weeks
92
+ Secondary Outcomes: VO₂max, body composition (DXA), fasting glucose and insulin
93
+
94
+ Data Collection: Baseline, 4 weeks, 8 weeks
95
+ Sample Size Justification: 90% power to detect a 15% change in HOMA-IR (SD=20%), α=0.05, 15% dropout
96
+
97
+ Statistical Analysis: ANCOVA adjusting for baseline values, intention-to-treat
98
+ """,
99
+ },
100
+ },
101
+ ]
102
+
103
+ # Run individual test queries
104
+ for idx, query in enumerate(test_queries):
105
+ # try:
106
+ print(
107
+ f"\n[{idx+1}] Running tool: {query['name']} with arguments: {list(query['arguments'].keys())}"
108
+ )
109
+ result = tooluni.run(query)
110
+ print("✅ Success. Output snippet:")
111
+ if isinstance(result, dict):
112
+ if result.get("success"):
113
+ result_text = result["result"]
114
+ print(
115
+ f"Result: {result_text[:2000]}..."
116
+ if len(result_text) > 2000
117
+ else f"Result: {result_text}"
118
+ )
119
+ print(
120
+ f"Model used: {result.get('metadata', {}).get('model_info', {}).get('model_id', 'unknown')}"
121
+ )
122
+ else:
123
+ print(f"Failed: {result.get('error', 'Unknown error')}")
124
+ else:
125
+ print(str(result)[:5000])
126
+ # except Exception as e:
127
+ # print(f"❌ Failed running {query['name']}. Error: {e}")
128
+
129
+ print("\n🏁 Agentic tool tests completed!")
@@ -0,0 +1,71 @@
1
+ import json
2
+ from typing import Any, Dict, List
3
+ import os
4
+ from tooluniverse import ToolUniverse
5
+
6
+ # Load expected schema fields dynamically from the JSON definition
7
+ schema_path = os.path.join(
8
+ os.path.dirname(__file__), "..", "data", "alphafold_tools.json"
9
+ )
10
+ with open(schema_path) as f:
11
+ schema = json.load(f)[0]["return_schema"]["properties"]
12
+
13
+ tooluni = ToolUniverse()
14
+ tooluni.load_tools()
15
+
16
+ # Test cases: 3 valid, 1 invalid UniProt ID, and 1 missing parameter
17
+ test_queries: List[Dict[str, Any]] = [
18
+ {
19
+ "name": "alphafold_get_prediction_by_uniprot_id",
20
+ "arguments": {"uniprot_id": "Q14596"},
21
+ },
22
+ {
23
+ "name": "alphafold_get_prediction_by_uniprot_id",
24
+ "arguments": {"uniprot_id": "Q9BUR4"},
25
+ },
26
+ {
27
+ "name": "alphafold_get_prediction_by_uniprot_id",
28
+ "arguments": {"uniprot_id": "Q8W3K0"},
29
+ },
30
+ {
31
+ "name": "alphafold_get_prediction_by_uniprot_id",
32
+ "arguments": {"uniprot_id": "XXX123"},
33
+ }, # invalid
34
+ {
35
+ "name": "alphafold_get_prediction_by_uniprot_id",
36
+ "arguments": {},
37
+ }, # missing param
38
+ ]
39
+
40
+ for idx, query in enumerate(test_queries, 1):
41
+ uid = query["arguments"].get("uniprot_id")
42
+ label = f"UniProt ID: {uid}" if uid else "No UniProt ID"
43
+ print(f"\n[{idx}] Running {query['name']} with {label}")
44
+ result = tooluni.run(query)
45
+
46
+ # Handle errors
47
+ if isinstance(result, dict) and "error" in result:
48
+ print(f"INVALID: {result['error']}")
49
+ if "detail" in result:
50
+ print(f" Detail: {result['detail']}")
51
+ continue
52
+
53
+ # Handle success
54
+ data = result.get("data", [])
55
+ if not data:
56
+ print("No data returned.")
57
+ continue
58
+
59
+ first = data[0]
60
+ print("SUCCESS")
61
+ print(f" {first.get('uniprotDescription')} ({first.get('uniprotAccession')})")
62
+ print(f" Organism: {first.get('organismScientificName')}")
63
+ print(f" Avg pLDDT: {first.get('globalMetricValue')}")
64
+ print(f" Structure (PDB): {first.get('pdbUrl')}")
65
+
66
+ # Schema validation
67
+ missing = [k for k in schema.keys() if k not in first]
68
+ if missing:
69
+ print(f" INVALID Missing expected fields: {missing}")
70
+ else:
71
+ print(" All expected schema fields present")
@@ -0,0 +1,37 @@
1
+ from tooluniverse import ToolUniverse
2
+
3
+ # Step 1: Initialize tool universe
4
+ tooluni = ToolUniverse()
5
+ tooluni.load_tools()
6
+
7
+ # Step 2: Define test queries for the ChEMBLTool
8
+ test_queries = [
9
+ # {"name": "ChEMBL_search_similar_molecules", "arguments": {"query": "aspirin"}},
10
+ # {"name": "ChEMBL_search_similar_molecules", "arguments": {"query": "aspirin", "similarity_threshold": 90}},
11
+ # {"name": "ChEMBL_search_similar_molecules", "arguments": {"query": "aspirin", "max_results": 5}},
12
+ # {"name": "ChEMBL_search_similar_molecules", "arguments": {"query": "aspirin", "similarity_threshold": 85, "max_results": 3}},
13
+ # {"name": "ChEMBL_search_similar_molecules", "arguments": {"query": "CC(=O)OC1=CC=CC=C1C(=O)O", "similarity_threshold": 80, "max_results": 10}}, # SMILES for aspirin
14
+ # {'name': 'ChEMBL_search_similar_molecules', 'arguments': {'query': 'FENOFIBRATE', 'similarity_threshold': 70, 'max_results': 20}}
15
+ {
16
+ "name": "ChEMBL_search_similar_molecules",
17
+ "arguments": {
18
+ "query": "Gadavist",
19
+ "similarity_threshold": 70,
20
+ "max_results": 20,
21
+ },
22
+ }
23
+ ]
24
+
25
+ # Step 3: Run all test queries
26
+ for idx, query in enumerate(test_queries):
27
+ # try:
28
+ print(
29
+ f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
30
+ )
31
+ result = tooluni.run(query)
32
+ print("✅ Success. Example output snippet:")
33
+ print(
34
+ result if isinstance(result, dict) else str(result)
35
+ ) # Print snippet if result is big
36
+ # except Exception as e:
37
+ # print(f"❌ Failed. Error: {str(e)}")