tooluniverse 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

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  1. tooluniverse/__init__.py +70 -0
  2. tooluniverse/agentic_tool.py +121 -15
  3. tooluniverse/arxiv_tool.py +109 -0
  4. tooluniverse/base_tool.py +174 -25
  5. tooluniverse/biorxiv_tool.py +116 -0
  6. tooluniverse/cellosaurus_tool.py +1332 -0
  7. tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +310 -0
  8. tooluniverse/compose_scripts/multi_agent_literature_search.py +794 -0
  9. tooluniverse/compose_scripts/tool_graph_generation.py +68 -35
  10. tooluniverse/compose_scripts/tool_metadata_generator.py +205 -105
  11. tooluniverse/compose_tool.py +93 -8
  12. tooluniverse/core_tool.py +155 -0
  13. tooluniverse/crossref_tool.py +158 -0
  14. tooluniverse/data/agentic_tools.json +1271 -1179
  15. tooluniverse/data/alphafold_tools.json +356 -105
  16. tooluniverse/data/arxiv_tools.json +94 -0
  17. tooluniverse/data/biorxiv_tools.json +75 -0
  18. tooluniverse/data/cellosaurus_tools.json +260 -0
  19. tooluniverse/data/chembl_tools.json +27 -12
  20. tooluniverse/data/clinicaltrials_gov_tools.json +377 -302
  21. tooluniverse/data/compose_tools.json +123 -16
  22. tooluniverse/data/core_tools.json +113 -0
  23. tooluniverse/data/crossref_tools.json +138 -0
  24. tooluniverse/data/dailymed_tools.json +17 -3
  25. tooluniverse/data/dataset_tools.json +1031 -588
  26. tooluniverse/data/dblp_tools.json +144 -0
  27. tooluniverse/data/disease_target_score_tools.json +20 -10
  28. tooluniverse/data/doaj_tools.json +140 -0
  29. tooluniverse/data/embedding_tools.json +362 -299
  30. tooluniverse/data/enrichr_tools.json +34 -27
  31. tooluniverse/data/europe_pmc_tools.json +108 -16
  32. tooluniverse/data/fatcat_tools.json +77 -0
  33. tooluniverse/data/fda_drug_adverse_event_tools.json +1061 -445
  34. tooluniverse/data/fda_drug_labeling_tools.json +6858 -6901
  35. tooluniverse/data/finder_tools.json +32 -37
  36. tooluniverse/data/gene_ontology_tools.json +19 -7
  37. tooluniverse/data/gwas_tools.json +1720 -959
  38. tooluniverse/data/hal_tools.json +75 -0
  39. tooluniverse/data/hpa_tools.json +53 -14
  40. tooluniverse/data/humanbase_tools.json +51 -43
  41. tooluniverse/data/idmap_tools.json +76 -70
  42. tooluniverse/data/literature_search_tools.json +306 -0
  43. tooluniverse/data/mcp_client_tools_example.json +122 -107
  44. tooluniverse/data/medlineplus_tools.json +50 -10
  45. tooluniverse/data/medrxiv_tools.json +75 -0
  46. tooluniverse/data/molecule_2d_tools.json +134 -0
  47. tooluniverse/data/molecule_3d_tools.json +164 -0
  48. tooluniverse/data/monarch_tools.json +112 -110
  49. tooluniverse/data/odphp_tools.json +389 -119
  50. tooluniverse/data/openaire_tools.json +95 -0
  51. tooluniverse/data/openalex_tools.json +100 -31
  52. tooluniverse/data/opentarget_tools.json +1457 -1372
  53. tooluniverse/data/osf_preprints_tools.json +81 -0
  54. tooluniverse/data/packages/bioinformatics_core_tools.json +40 -10
  55. tooluniverse/data/packages/cheminformatics_tools.json +20 -5
  56. tooluniverse/data/packages/genomics_tools.json +36 -9
  57. tooluniverse/data/packages/machine_learning_tools.json +36 -9
  58. tooluniverse/data/packages/scientific_computing_tools.json +20 -5
  59. tooluniverse/data/packages/single_cell_tools.json +20 -5
  60. tooluniverse/data/packages/structural_biology_tools.json +16 -4
  61. tooluniverse/data/packages/visualization_tools.json +20 -5
  62. tooluniverse/data/pmc_tools.json +117 -0
  63. tooluniverse/data/protein_structure_3d_tools.json +138 -0
  64. tooluniverse/data/pubchem_tools.json +37 -12
  65. tooluniverse/data/pubmed_tools.json +133 -0
  66. tooluniverse/data/pubtator_tools.json +68 -60
  67. tooluniverse/data/rcsb_pdb_tools.json +1532 -1221
  68. tooluniverse/data/semantic_scholar_tools.json +55 -22
  69. tooluniverse/data/special_tools.json +8 -6
  70. tooluniverse/data/tool_composition_tools.json +112 -82
  71. tooluniverse/data/unified_guideline_tools.json +707 -0
  72. tooluniverse/data/unpaywall_tools.json +86 -0
  73. tooluniverse/data/url_fetch_tools.json +102 -82
  74. tooluniverse/data/uspto_tools.json +49 -30
  75. tooluniverse/data/wikidata_sparql_tools.json +45 -0
  76. tooluniverse/data/xml_tools.json +3274 -3113
  77. tooluniverse/data/zenodo_tools.json +90 -0
  78. tooluniverse/dblp_tool.py +132 -0
  79. tooluniverse/default_config.py +30 -0
  80. tooluniverse/doaj_tool.py +183 -0
  81. tooluniverse/doctor.py +48 -0
  82. tooluniverse/europe_pmc_tool.py +132 -17
  83. tooluniverse/exceptions.py +170 -0
  84. tooluniverse/execute_function.py +825 -342
  85. tooluniverse/fatcat_tool.py +65 -0
  86. tooluniverse/generate_tools.py +198 -0
  87. tooluniverse/hal_tool.py +77 -0
  88. tooluniverse/llm_clients.py +283 -20
  89. tooluniverse/mcp_tool_registry.py +4 -1
  90. tooluniverse/medrxiv_tool.py +116 -0
  91. tooluniverse/memory_manager.py +166 -0
  92. tooluniverse/molecule_2d_tool.py +274 -0
  93. tooluniverse/molecule_3d_tool.py +441 -0
  94. tooluniverse/odphp_tool.py +49 -14
  95. tooluniverse/openaire_tool.py +130 -0
  96. tooluniverse/openalex_tool.py +34 -0
  97. tooluniverse/osf_preprints_tool.py +67 -0
  98. tooluniverse/pmc_tool.py +179 -0
  99. tooluniverse/protein_structure_3d_tool.py +295 -0
  100. tooluniverse/pubmed_tool.py +173 -0
  101. tooluniverse/remote/boltz/boltz_mcp_server.py +3 -1
  102. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -1
  103. tooluniverse/semantic_scholar_tool.py +40 -10
  104. tooluniverse/smcp.py +228 -263
  105. tooluniverse/smcp_server.py +97 -55
  106. tooluniverse/tool_registry.py +35 -3
  107. tooluniverse/tools/ADMETAI_predict_BBB_penetrance.py +46 -0
  108. tooluniverse/tools/ADMETAI_predict_CYP_interactions.py +46 -0
  109. tooluniverse/tools/ADMETAI_predict_bioavailability.py +46 -0
  110. tooluniverse/tools/ADMETAI_predict_clearance_distribution.py +49 -0
  111. tooluniverse/tools/ADMETAI_predict_nuclear_receptor_activity.py +49 -0
  112. tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py +49 -0
  113. tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py +49 -0
  114. tooluniverse/tools/ADMETAI_predict_stress_response.py +46 -0
  115. tooluniverse/tools/ADMETAI_predict_toxicity.py +46 -0
  116. tooluniverse/tools/AdvancedCodeQualityAnalyzer.py +63 -0
  117. tooluniverse/tools/AdverseEventICDMapper.py +46 -0
  118. tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py +52 -0
  119. tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py +59 -0
  120. tooluniverse/tools/ArXiv_search_papers.py +63 -0
  121. tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
  122. tooluniverse/tools/BioRxiv_search_preprints.py +52 -0
  123. tooluniverse/tools/BiomarkerDiscoveryWorkflow.py +55 -0
  124. tooluniverse/tools/CORE_search_papers.py +67 -0
  125. tooluniverse/tools/CallAgent.py +46 -0
  126. tooluniverse/tools/ChEMBL_search_similar_molecules.py +59 -0
  127. tooluniverse/tools/CodeOptimizer.py +55 -0
  128. tooluniverse/tools/CodeQualityAnalyzer.py +71 -0
  129. tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py +49 -0
  130. tooluniverse/tools/Crossref_search_works.py +55 -0
  131. tooluniverse/tools/DBLP_search_publications.py +52 -0
  132. tooluniverse/tools/DOAJ_search_articles.py +55 -0
  133. tooluniverse/tools/DailyMed_get_spl_by_setid.py +52 -0
  134. tooluniverse/tools/DailyMed_search_spls.py +79 -0
  135. tooluniverse/tools/DataAnalysisValidityReviewer.py +49 -0
  136. tooluniverse/tools/DescriptionAnalyzer.py +55 -0
  137. tooluniverse/tools/DescriptionQualityEvaluator.py +59 -0
  138. tooluniverse/tools/DomainExpertValidator.py +63 -0
  139. tooluniverse/tools/DrugSafetyAnalyzer.py +59 -0
  140. tooluniverse/tools/EthicalComplianceReviewer.py +49 -0
  141. tooluniverse/tools/EuropePMC_Guidelines_Search.py +52 -0
  142. tooluniverse/tools/EuropePMC_search_articles.py +52 -0
  143. tooluniverse/tools/ExperimentalDesignScorer.py +55 -0
  144. tooluniverse/tools/FAERS_count_additive_administration_routes.py +52 -0
  145. tooluniverse/tools/FAERS_count_additive_adverse_reactions.py +71 -0
  146. tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py +63 -0
  147. tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py +63 -0
  148. tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py +63 -0
  149. tooluniverse/tools/FAERS_count_additive_seriousness_classification.py +63 -0
  150. tooluniverse/tools/FAERS_count_country_by_drug_event.py +63 -0
  151. tooluniverse/tools/FAERS_count_death_related_by_drug.py +49 -0
  152. tooluniverse/tools/FAERS_count_drug_routes_by_event.py +52 -0
  153. tooluniverse/tools/FAERS_count_drugs_by_drug_event.py +63 -0
  154. tooluniverse/tools/FAERS_count_outcomes_by_drug_event.py +63 -0
  155. tooluniverse/tools/FAERS_count_patient_age_distribution.py +49 -0
  156. tooluniverse/tools/FAERS_count_reactions_by_drug_event.py +71 -0
  157. tooluniverse/tools/FAERS_count_reportercountry_by_drug_event.py +63 -0
  158. tooluniverse/tools/FAERS_count_seriousness_by_drug_event.py +63 -0
  159. tooluniverse/tools/FDA_get_abuse_dependence_info_by_drug_name.py +55 -0
  160. tooluniverse/tools/FDA_get_abuse_info_by_drug_name.py +55 -0
  161. tooluniverse/tools/FDA_get_accessories_info_by_drug_name.py +55 -0
  162. tooluniverse/tools/FDA_get_active_ingredient_info_by_drug_name.py +55 -0
  163. tooluniverse/tools/FDA_get_adverse_reactions_by_drug_name.py +55 -0
  164. tooluniverse/tools/FDA_get_alarms_by_drug_name.py +55 -0
  165. tooluniverse/tools/FDA_get_animal_pharmacology_info_by_drug_name.py +55 -0
  166. tooluniverse/tools/FDA_get_assembly_installation_info_by_drug_name.py +55 -0
  167. tooluniverse/tools/FDA_get_boxed_warning_info_by_drug_name.py +55 -0
  168. tooluniverse/tools/FDA_get_brand_name_generic_name.py +52 -0
  169. tooluniverse/tools/FDA_get_calibration_instructions_by_drug_name.py +55 -0
  170. tooluniverse/tools/FDA_get_carcinogenic_mutagenic_fertility_by_drug_name.py +55 -0
  171. tooluniverse/tools/FDA_get_child_safety_info_by_drug_name.py +55 -0
  172. tooluniverse/tools/FDA_get_clinical_pharmacology_by_drug_name.py +55 -0
  173. tooluniverse/tools/FDA_get_clinical_studies_info_by_drug_name.py +55 -0
  174. tooluniverse/tools/FDA_get_contact_for_questions_info_by_drug_name.py +55 -0
  175. tooluniverse/tools/FDA_get_contraindications_by_drug_name.py +55 -0
  176. tooluniverse/tools/FDA_get_controlled_substance_DEA_schedule_info_by_drug_name.py +55 -0
  177. tooluniverse/tools/FDA_get_dear_health_care_provider_letter_info_by_drug_name.py +55 -0
  178. tooluniverse/tools/FDA_get_dependence_info_by_drug_name.py +55 -0
  179. tooluniverse/tools/FDA_get_disposal_info_by_drug_name.py +55 -0
  180. tooluniverse/tools/FDA_get_do_not_use_info_by_drug_name.py +55 -0
  181. tooluniverse/tools/FDA_get_document_id_by_drug_name.py +55 -0
  182. tooluniverse/tools/FDA_get_dosage_and_storage_information_by_drug_name.py +55 -0
  183. tooluniverse/tools/FDA_get_dosage_forms_and_strengths_by_drug_name.py +55 -0
  184. tooluniverse/tools/FDA_get_drug_generic_name.py +46 -0
  185. tooluniverse/tools/FDA_get_drug_interactions_by_drug_name.py +55 -0
  186. tooluniverse/tools/FDA_get_drug_name_by_SPL_ID.py +55 -0
  187. tooluniverse/tools/FDA_get_drug_name_by_adverse_reaction.py +59 -0
  188. tooluniverse/tools/FDA_get_drug_name_by_calibration_instructions.py +59 -0
  189. tooluniverse/tools/FDA_get_drug_name_by_dependence_info.py +59 -0
  190. tooluniverse/tools/FDA_get_drug_name_by_document_id.py +55 -0
  191. tooluniverse/tools/FDA_get_drug_name_by_dosage_info.py +55 -0
  192. tooluniverse/tools/FDA_get_drug_name_by_environmental_warning.py +59 -0
  193. tooluniverse/tools/FDA_get_drug_name_by_inactive_ingredient.py +59 -0
  194. tooluniverse/tools/FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation.py +55 -0
  195. tooluniverse/tools/FDA_get_drug_name_by_labor_and_delivery_info.py +59 -0
  196. tooluniverse/tools/FDA_get_drug_name_by_microbiology.py +59 -0
  197. tooluniverse/tools/FDA_get_drug_name_by_other_safety_info.py +55 -0
  198. tooluniverse/tools/FDA_get_drug_name_by_pharmacodynamics.py +59 -0
  199. tooluniverse/tools/FDA_get_drug_name_by_pharmacogenomics.py +59 -0
  200. tooluniverse/tools/FDA_get_drug_name_by_precautions.py +55 -0
  201. tooluniverse/tools/FDA_get_drug_name_by_pregnancy_or_breastfeeding_info.py +59 -0
  202. tooluniverse/tools/FDA_get_drug_name_by_principal_display_panel.py +59 -0
  203. tooluniverse/tools/FDA_get_drug_name_by_reference.py +55 -0
  204. tooluniverse/tools/FDA_get_drug_name_by_set_id.py +55 -0
  205. tooluniverse/tools/FDA_get_drug_name_by_stop_use_info.py +55 -0
  206. tooluniverse/tools/FDA_get_drug_name_by_storage_and_handling_info.py +55 -0
  207. tooluniverse/tools/FDA_get_drug_name_by_warnings.py +55 -0
  208. tooluniverse/tools/FDA_get_drug_name_from_patient_package_insert.py +59 -0
  209. tooluniverse/tools/FDA_get_drug_names_by_abuse_dependence_info.py +55 -0
  210. tooluniverse/tools/FDA_get_drug_names_by_abuse_info.py +63 -0
  211. tooluniverse/tools/FDA_get_drug_names_by_accessories.py +63 -0
  212. tooluniverse/tools/FDA_get_drug_names_by_active_ingredient.py +63 -0
  213. tooluniverse/tools/FDA_get_drug_names_by_alarm.py +63 -0
  214. tooluniverse/tools/FDA_get_drug_names_by_animal_pharmacology_info.py +63 -0
  215. tooluniverse/tools/FDA_get_drug_names_by_application_number_NDC_number.py +59 -0
  216. tooluniverse/tools/FDA_get_drug_names_by_assembly_installation_info.py +63 -0
  217. tooluniverse/tools/FDA_get_drug_names_by_boxed_warning.py +63 -0
  218. tooluniverse/tools/FDA_get_drug_names_by_child_safety_info.py +63 -0
  219. tooluniverse/tools/FDA_get_drug_names_by_clinical_pharmacology.py +63 -0
  220. tooluniverse/tools/FDA_get_drug_names_by_clinical_studies.py +63 -0
  221. tooluniverse/tools/FDA_get_drug_names_by_consulting_doctor_pharmacist_info.py +63 -0
  222. tooluniverse/tools/FDA_get_drug_names_by_contraindications.py +63 -0
  223. tooluniverse/tools/FDA_get_drug_names_by_controlled_substance_DEA_schedule.py +63 -0
  224. tooluniverse/tools/FDA_get_drug_names_by_dear_health_care_provider_letter_info.py +63 -0
  225. tooluniverse/tools/FDA_get_drug_names_by_disposal_info.py +63 -0
  226. tooluniverse/tools/FDA_get_drug_names_by_dosage_forms_and_strengths_info.py +63 -0
  227. tooluniverse/tools/FDA_get_drug_names_by_drug_interactions.py +63 -0
  228. tooluniverse/tools/FDA_get_drug_names_by_effective_time.py +63 -0
  229. tooluniverse/tools/FDA_get_drug_names_by_food_safety_warnings.py +63 -0
  230. tooluniverse/tools/FDA_get_drug_names_by_general_precautions.py +63 -0
  231. tooluniverse/tools/FDA_get_drug_names_by_geriatric_use.py +63 -0
  232. tooluniverse/tools/FDA_get_drug_names_by_health_claim.py +63 -0
  233. tooluniverse/tools/FDA_get_drug_names_by_indication.py +55 -0
  234. tooluniverse/tools/FDA_get_drug_names_by_info_for_nursing_mothers.py +63 -0
  235. tooluniverse/tools/FDA_get_drug_names_by_information_for_owners_or_caregivers.py +63 -0
  236. tooluniverse/tools/FDA_get_drug_names_by_ingredient.py +63 -0
  237. tooluniverse/tools/FDA_get_drug_names_by_instructions_for_use.py +63 -0
  238. tooluniverse/tools/FDA_get_drug_names_by_lab_test_interference.py +63 -0
  239. tooluniverse/tools/FDA_get_drug_names_by_lab_tests.py +63 -0
  240. tooluniverse/tools/FDA_get_drug_names_by_mechanism_of_action.py +63 -0
  241. tooluniverse/tools/FDA_get_drug_names_by_medication_guide.py +63 -0
  242. tooluniverse/tools/FDA_get_drug_names_by_nonclinical_toxicology_info.py +63 -0
  243. tooluniverse/tools/FDA_get_drug_names_by_nonteratogenic_effects.py +63 -0
  244. tooluniverse/tools/FDA_get_drug_names_by_overdosage_info.py +63 -0
  245. tooluniverse/tools/FDA_get_drug_names_by_pediatric_use.py +63 -0
  246. tooluniverse/tools/FDA_get_drug_names_by_pharmacokinetics.py +63 -0
  247. tooluniverse/tools/FDA_get_drug_names_by_population_use.py +63 -0
  248. tooluniverse/tools/FDA_get_drug_names_by_pregnancy_effects_info.py +63 -0
  249. tooluniverse/tools/FDA_get_drug_names_by_residue_warning.py +63 -0
  250. tooluniverse/tools/FDA_get_drug_names_by_risk.py +63 -0
  251. tooluniverse/tools/FDA_get_drug_names_by_route.py +63 -0
  252. tooluniverse/tools/FDA_get_drug_names_by_safe_handling_warning.py +63 -0
  253. tooluniverse/tools/FDA_get_drug_names_by_safety_summary.py +63 -0
  254. tooluniverse/tools/FDA_get_drug_names_by_spl_indexing_data_elements.py +63 -0
  255. tooluniverse/tools/FDA_get_drug_names_by_teratogenic_effects.py +63 -0
  256. tooluniverse/tools/FDA_get_drug_names_by_user_safety_warning.py +63 -0
  257. tooluniverse/tools/FDA_get_drug_names_by_warnings_and_cautions.py +63 -0
  258. tooluniverse/tools/FDA_get_drugs_by_carcinogenic_mutagenic_fertility.py +63 -0
  259. tooluniverse/tools/FDA_get_effective_time_by_drug_name.py +55 -0
  260. tooluniverse/tools/FDA_get_environmental_warning_by_drug_name.py +55 -0
  261. tooluniverse/tools/FDA_get_general_precautions_by_drug_name.py +55 -0
  262. tooluniverse/tools/FDA_get_geriatric_use_info_by_drug_name.py +55 -0
  263. tooluniverse/tools/FDA_get_health_claims_by_drug_name.py +55 -0
  264. tooluniverse/tools/FDA_get_inactive_ingredient_info_by_drug_name.py +55 -0
  265. tooluniverse/tools/FDA_get_indications_by_drug_name.py +55 -0
  266. tooluniverse/tools/FDA_get_info_for_nursing_mothers_by_drug_name.py +55 -0
  267. tooluniverse/tools/FDA_get_info_for_patients_by_drug_name.py +55 -0
  268. tooluniverse/tools/FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name.py +55 -0
  269. tooluniverse/tools/FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name.py +55 -0
  270. tooluniverse/tools/FDA_get_information_for_owners_or_caregivers_by_drug_name.py +55 -0
  271. tooluniverse/tools/FDA_get_ingredients_by_drug_name.py +55 -0
  272. tooluniverse/tools/FDA_get_instructions_for_use_by_drug_name.py +55 -0
  273. tooluniverse/tools/FDA_get_lab_test_interference_info_by_drug_name.py +55 -0
  274. tooluniverse/tools/FDA_get_lab_tests_by_drug_name.py +55 -0
  275. tooluniverse/tools/FDA_get_labor_and_delivery_info_by_drug_name.py +55 -0
  276. tooluniverse/tools/FDA_get_manufacturer_name_NDC_number_by_drug_name.py +55 -0
  277. tooluniverse/tools/FDA_get_mechanism_of_action_by_drug_name.py +55 -0
  278. tooluniverse/tools/FDA_get_medication_guide_info_by_drug_name.py +55 -0
  279. tooluniverse/tools/FDA_get_microbiology_info_by_drug_name.py +55 -0
  280. tooluniverse/tools/FDA_get_nonclinical_toxicology_info_by_drug_name.py +55 -0
  281. tooluniverse/tools/FDA_get_nonteratogenic_effects_by_drug_name.py +55 -0
  282. tooluniverse/tools/FDA_get_other_safety_info_by_drug_name.py +55 -0
  283. tooluniverse/tools/FDA_get_overdosage_info_by_drug_name.py +55 -0
  284. tooluniverse/tools/FDA_get_patient_package_insert_from_drug_name.py +55 -0
  285. tooluniverse/tools/FDA_get_pediatric_use_info_by_drug_name.py +55 -0
  286. tooluniverse/tools/FDA_get_pharmacodynamics_by_drug_name.py +55 -0
  287. tooluniverse/tools/FDA_get_pharmacogenomics_info_by_drug_name.py +55 -0
  288. tooluniverse/tools/FDA_get_pharmacokinetics_by_drug_name.py +55 -0
  289. tooluniverse/tools/FDA_get_population_use_info_by_drug_name.py +55 -0
  290. tooluniverse/tools/FDA_get_precautions_by_drug_name.py +55 -0
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  592. tooluniverse/tools/get_geopandas_info.py +44 -0
  593. tooluniverse/tools/get_gget_info.py +46 -0
  594. tooluniverse/tools/get_googlesearch_python_info.py +46 -0
  595. tooluniverse/tools/get_gseapy_info.py +49 -0
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  597. tooluniverse/tools/get_harmony_pytorch_info.py +46 -0
  598. tooluniverse/tools/get_hmmlearn_info.py +46 -0
  599. tooluniverse/tools/get_holoviews_info.py +44 -0
  600. tooluniverse/tools/get_host_organism_by_pdb_id.py +46 -0
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  605. tooluniverse/tools/get_imbalanced_learn_info.py +44 -0
  606. tooluniverse/tools/get_jcvi_info.py +46 -0
  607. tooluniverse/tools/get_joblib_info.py +44 -0
  608. tooluniverse/tools/get_joint_associated_diseases_by_HPO_ID_list.py +55 -0
  609. tooluniverse/tools/get_khmer_info.py +46 -0
  610. tooluniverse/tools/get_kipoiseq_info.py +44 -0
  611. tooluniverse/tools/get_lifelines_info.py +49 -0
  612. tooluniverse/tools/get_ligand_bond_count_by_pdb_id.py +46 -0
  613. tooluniverse/tools/get_ligand_smiles_by_chem_comp_id.py +49 -0
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  615. tooluniverse/tools/get_loompy_info.py +46 -0
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  620. tooluniverse/tools/get_mne_info.py +44 -0
  621. tooluniverse/tools/get_molfeat_info.py +44 -0
  622. tooluniverse/tools/get_molvs_info.py +44 -0
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  625. tooluniverse/tools/get_mudata_info.py +49 -0
  626. tooluniverse/tools/get_mutation_annotations_by_pdb_id.py +46 -0
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  628. tooluniverse/tools/get_netcdf4_info.py +44 -0
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  630. tooluniverse/tools/get_nglview_info.py +44 -0
  631. tooluniverse/tools/get_nilearn_info.py +44 -0
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  644. tooluniverse/tools/get_pdbfixer_info.py +46 -0
  645. tooluniverse/tools/get_phenotype_by_HPO_ID.py +46 -0
  646. tooluniverse/tools/get_pillow_info.py +44 -0
  647. tooluniverse/tools/get_plantcv_info.py +46 -0
  648. tooluniverse/tools/get_plip_info.py +46 -0
  649. tooluniverse/tools/get_plotly_info.py +44 -0
  650. tooluniverse/tools/get_poliastro_info.py +46 -0
  651. tooluniverse/tools/get_polymer_entity_annotations.py +49 -0
  652. tooluniverse/tools/get_polymer_entity_count_by_pdb_id.py +46 -0
  653. tooluniverse/tools/get_polymer_entity_ids_by_pdb_id.py +46 -0
  654. tooluniverse/tools/get_polymer_entity_type_by_entity_id.py +49 -0
  655. tooluniverse/tools/get_polymer_molecular_weight_by_entity_id.py +49 -0
  656. tooluniverse/tools/get_poretools_info.py +44 -0
  657. tooluniverse/tools/get_prody_info.py +46 -0
  658. tooluniverse/tools/get_protein_classification_by_pdb_id.py +49 -0
  659. tooluniverse/tools/get_protein_metadata_by_pdb_id.py +46 -0
  660. tooluniverse/tools/get_pubchempy_info.py +44 -0
  661. tooluniverse/tools/get_pybedtools_info.py +49 -0
  662. tooluniverse/tools/get_pybigwig_info.py +46 -0
  663. tooluniverse/tools/get_pydeseq2_info.py +46 -0
  664. tooluniverse/tools/get_pyensembl_info.py +44 -0
  665. tooluniverse/tools/get_pyephem_info.py +44 -0
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  669. tooluniverse/tools/get_pyliftover_info.py +49 -0
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  671. tooluniverse/tools/get_pymed_info.py +46 -0
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  712. tooluniverse/tools/get_statsmodels_info.py +49 -0
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  729. tooluniverse/tools/get_viennarna_info.py +49 -0
  730. tooluniverse/tools/get_webpage_text_from_url.py +52 -0
  731. tooluniverse/tools/get_webpage_title.py +49 -0
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  733. tooluniverse/tools/get_xesmf_info.py +44 -0
  734. tooluniverse/tools/get_xgboost_info.py +44 -0
  735. tooluniverse/tools/get_zarr_info.py +44 -0
  736. tooluniverse/tools/gwas_get_association_by_id.py +49 -0
  737. tooluniverse/tools/gwas_get_associations_for_snp.py +67 -0
  738. tooluniverse/tools/gwas_get_associations_for_study.py +55 -0
  739. tooluniverse/tools/gwas_get_associations_for_trait.py +55 -0
  740. tooluniverse/tools/gwas_get_snp_by_id.py +46 -0
  741. tooluniverse/tools/gwas_get_snps_for_gene.py +55 -0
  742. tooluniverse/tools/gwas_get_studies_for_trait.py +75 -0
  743. tooluniverse/tools/gwas_get_study_by_id.py +46 -0
  744. tooluniverse/tools/gwas_get_variants_for_trait.py +55 -0
  745. tooluniverse/tools/gwas_search_associations.py +75 -0
  746. tooluniverse/tools/gwas_search_snps.py +63 -0
  747. tooluniverse/tools/gwas_search_studies.py +75 -0
  748. tooluniverse/tools/humanbase_ppi_analysis.py +67 -0
  749. tooluniverse/tools/mesh_get_subjects_by_pharmacological_action.py +63 -0
  750. tooluniverse/tools/mesh_get_subjects_by_subject_id.py +63 -0
  751. tooluniverse/tools/mesh_get_subjects_by_subject_name.py +63 -0
  752. tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py +63 -0
  753. tooluniverse/tools/odphp_itemlist.py +49 -0
  754. tooluniverse/tools/odphp_myhealthfinder.py +67 -0
  755. tooluniverse/tools/odphp_outlink_fetch.py +59 -0
  756. tooluniverse/tools/odphp_topicsearch.py +67 -0
  757. tooluniverse/tools/openalex_literature_search.py +67 -0
  758. tooluniverse/tools/reactome_disease_target_score.py +52 -0
  759. tooluniverse/tools/search_clinical_trials.py +67 -0
  760. tooluniverse/tools/visualize_molecule_2d.py +83 -0
  761. tooluniverse/tools/visualize_molecule_3d.py +91 -0
  762. tooluniverse/tools/visualize_protein_structure_3d.py +79 -0
  763. tooluniverse/unified_guideline_tools.py +1210 -0
  764. tooluniverse/unpaywall_tool.py +62 -0
  765. tooluniverse/utils.py +71 -2
  766. tooluniverse/visualization_tool.py +897 -0
  767. tooluniverse/wikidata_sparql_tool.py +60 -0
  768. tooluniverse/zenodo_tool.py +72 -0
  769. {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/METADATA +12 -2
  770. tooluniverse-1.0.7.dist-info/RECORD +855 -0
  771. {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/entry_points.txt +4 -0
  772. tooluniverse/test/list_azure_openai_models.py +0 -210
  773. tooluniverse/test/mcp_server_test.py +0 -0
  774. tooluniverse/test/test_admetai_tool.py +0 -370
  775. tooluniverse/test/test_agentic_tool.py +0 -129
  776. tooluniverse/test/test_agentic_tool_azure_models.py +0 -91
  777. tooluniverse/test/test_alphafold_tool.py +0 -108
  778. tooluniverse/test/test_api_key_validation_min.py +0 -64
  779. tooluniverse/test/test_chem_tool.py +0 -37
  780. tooluniverse/test/test_claude_sdk.py +0 -86
  781. tooluniverse/test/test_compose_lieraturereview.py +0 -63
  782. tooluniverse/test/test_compose_tool.py +0 -448
  783. tooluniverse/test/test_dailymed.py +0 -69
  784. tooluniverse/test/test_dataset_tool.py +0 -200
  785. tooluniverse/test/test_disease_target_score.py +0 -56
  786. tooluniverse/test/test_drugbank_filter_examples.py +0 -179
  787. tooluniverse/test/test_efo.py +0 -31
  788. tooluniverse/test/test_enrichr_tool.py +0 -21
  789. tooluniverse/test/test_europe_pmc_tool.py +0 -20
  790. tooluniverse/test/test_fda_adv.py +0 -95
  791. tooluniverse/test/test_fda_drug_labeling.py +0 -91
  792. tooluniverse/test/test_gene_ontology_tools.py +0 -66
  793. tooluniverse/test/test_global_fallback.py +0 -288
  794. tooluniverse/test/test_gwas_tool.py +0 -139
  795. tooluniverse/test/test_hooks_direct.py +0 -219
  796. tooluniverse/test/test_hpa.py +0 -625
  797. tooluniverse/test/test_humanbase_tool.py +0 -20
  798. tooluniverse/test/test_idmap_tools.py +0 -61
  799. tooluniverse/test/test_list_built_in_tools.py +0 -33
  800. tooluniverse/test/test_mcp_server.py +0 -211
  801. tooluniverse/test/test_mcp_tool.py +0 -247
  802. tooluniverse/test/test_medlineplus.py +0 -220
  803. tooluniverse/test/test_odphp_tool.py +0 -166
  804. tooluniverse/test/test_openalex_tool.py +0 -32
  805. tooluniverse/test/test_openrouter_client.py +0 -288
  806. tooluniverse/test/test_opentargets.py +0 -28
  807. tooluniverse/test/test_pubchem_tool.py +0 -116
  808. tooluniverse/test/test_pubtator_tool.py +0 -37
  809. tooluniverse/test/test_rcsb_pdb_tool.py +0 -86
  810. tooluniverse/test/test_reactome.py +0 -54
  811. tooluniverse/test/test_semantic_scholar_tool.py +0 -24
  812. tooluniverse/test/test_software_tools.py +0 -147
  813. tooluniverse/test/test_stdio_hooks.py +0 -285
  814. tooluniverse/test/test_tool_description_optimizer.py +0 -49
  815. tooluniverse/test/test_tool_finder.py +0 -26
  816. tooluniverse/test/test_tool_finder_llm.py +0 -252
  817. tooluniverse/test/test_tools_find.py +0 -195
  818. tooluniverse/test/test_uniprot_tools.py +0 -74
  819. tooluniverse/test/test_uspto_tool.py +0 -72
  820. tooluniverse/test/test_xml_tool.py +0 -113
  821. tooluniverse-1.0.5.dist-info/RECORD +0 -198
  822. {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/WHEEL +0 -0
  823. {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/licenses/LICENSE +0 -0
  824. {tooluniverse-1.0.5.dist-info → tooluniverse-1.0.7.dist-info}/top_level.txt +0 -0
tooluniverse-1.0.7.dist-info/RECORD ADDED
@@ -0,0 +1,855 @@
1
+ tooluniverse/__init__.py,sha256=V8tmwPEEdlQ6H7WItWDVW0aiqD-xG40RpbsBV3VZqPI,16819
2
+ tooluniverse/admetai_tool.py,sha256=nEfq7dwvFqjDryKv3nivGoBSRap6LT7_m76iMu72Q6E,3009
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+ tooluniverse/agentic_tool.py,sha256=i0TEs6WhF21B4gs5k7DM67qTND4qDMPD2lUzLyEWnnM,25627
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+ tooluniverse/alphafold_tool.py,sha256=NkKQttC0MfuetCTTcWTFEG2MdhyKwy3jb5TR4odiqAw,4658
5
+ tooluniverse/arxiv_tool.py,sha256=60e5moGt3XnwZeKx_nrvRZrwAavE11ok0j78AI5F6Xs,3610
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+ tooluniverse/base_tool.py,sha256=wX2D5JumEhYmpqOQRjjtLW8AzFTkutpvCGo3j1IvECo,11174
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+ tooluniverse/biorxiv_tool.py,sha256=uffhxXMOWR6b2jzxka-Qss1LjliQTuX-skIIc7RAaPs,4133
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+ tooluniverse/boltz_tool.py,sha256=Kfcymeu6FRRpWLw7dWhEON4PUBTsHuBiTAPJlYH5ZGs,7930
9
+ tooluniverse/cellosaurus_tool.py,sha256=W_npl3ga45-Hpsdq7YyGsD5_DnR2AmyaQVYNjiZoNOs,47902
10
+ tooluniverse/chem_tool.py,sha256=tJusjamWNp0x8Ke-cvVgKB7-clvD6LXTaXA0Q0fqQv4,8336
11
+ tooluniverse/compose_tool.py,sha256=f_3X_fbdrzogBdKJXoXXpxVvdb1OWt7KMxhpPUtEu24,17109
12
+ tooluniverse/core_tool.py,sha256=hHD8nVSIy6lK2vF3ygKz73gsDEPYEL-otXZXeR7M2SY,5083
13
+ tooluniverse/crossref_tool.py,sha256=oba0kkWI9m9dugf_th1nEXPWPF4onJkFUyhp5h5H4pM,5736
14
+ tooluniverse/ctg_tool.py,sha256=3nR_F-YGpxVmTa6u5xi-mrTmLSH7OBehP4EJo-CQS0Y,46053
15
+ tooluniverse/custom_tool.py,sha256=w2LMMRT82byxSNYPBKmuEJ2lbKktDJt_iW0Ew24M5VY,2701
16
+ tooluniverse/dailymed_tool.py,sha256=sxIs0xYwX0CVlkhHaPwvGV-Oo1OW2tvsWZypAWujt9k,3800
17
+ tooluniverse/dataset_tool.py,sha256=cmcCz_SFs7V78EZDNLesnQ2Qe9fVz1jOLghrpwe8hM8,11371
18
+ tooluniverse/dblp_tool.py,sha256=aPyEivx5TYUxws7zOsHswQtkVphblMsVPw0lSpyoIQA,4488
19
+ tooluniverse/default_config.py,sha256=81nZu2AiFaXXKCNLeunY_T7GpO0z_SuFHSHQLGIf2_4,9103
20
+ tooluniverse/doaj_tool.py,sha256=mzpnUwYfXdqvyn-txbV1cdWNS7Ty8g6fbvWgF2JN30I,7032
21
+ tooluniverse/doctor.py,sha256=QQ6LiV3HPkWljVKh52QptQmV3xFj53_2yo-A_n8NQ5Y,1326
22
+ tooluniverse/efo_tool.py,sha256=J4tjPFlNa9KhmQTEToBZN-m8jMuF1IKf2yQb1dyTeXI,1394
23
+ tooluniverse/embedding_database.py,sha256=ua-yIyv3dPq2GHdyZmiwZyaUlkKYyV3nslB4H9asvDo,24682
24
+ tooluniverse/embedding_sync.py,sha256=Cq3g64MjNXXpiImrzPMNsCTvGZeEI9009OlHOD3EloI,14669
25
+ tooluniverse/enrichr_tool.py,sha256=YXuHwoG_Hi-kUWK7cY_X21b5pbqoREdG7fJxKq050Jg,9472
26
+ tooluniverse/europe_pmc_tool.py,sha256=-3CAq5tDhS5NoeHifevadBgP_MHDZJdwNmM5SvjbAa8,6080
27
+ tooluniverse/exceptions.py,sha256=3svVCG7H_G_8E1mco74KWi44u1M7V1JojVycSEWdi_o,5386
28
+ tooluniverse/execute_function.py,sha256=Lj5v3t23An6FNbfGZxUMdkfqOF9gqzMVrZbzuiCElG0,101216
29
+ tooluniverse/extended_hooks.py,sha256=1Cg0rETh6_D21YFVqD-FhL7y4inZAGyQ6vMtHyugueg,15376
30
+ tooluniverse/fatcat_tool.py,sha256=-QEOYbv6KEcrOiOa27Ms1xm0sySB-vW4rWEinsS6EDw,2051
31
+ tooluniverse/gene_ontology_tool.py,sha256=l89XYdBEBm3eN3dG0lR4oV01H16_9IUB6a2c7W_c7Lg,7180
32
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