tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

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  1. tooluniverse/__init__.py +56 -10
  2. tooluniverse/admetai_tool.py +8 -4
  3. tooluniverse/agentic_tool.py +40 -4
  4. tooluniverse/arxiv_tool.py +2 -6
  5. tooluniverse/base_tool.py +210 -25
  6. tooluniverse/biogrid_tool.py +118 -0
  7. tooluniverse/biorxiv_tool.py +35 -16
  8. tooluniverse/build_optimizer.py +87 -0
  9. tooluniverse/cache/__init__.py +3 -0
  10. tooluniverse/cache/memory_cache.py +99 -0
  11. tooluniverse/cache/result_cache_manager.py +235 -0
  12. tooluniverse/cache/sqlite_backend.py +257 -0
  13. tooluniverse/cellosaurus_tool.py +1332 -0
  14. tooluniverse/clinvar_tool.py +90 -0
  15. tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py +310 -0
  16. tooluniverse/compose_scripts/multi_agent_literature_search.py +794 -0
  17. tooluniverse/compose_scripts/tool_graph_generation.py +68 -35
  18. tooluniverse/compose_scripts/tool_metadata_generator.py +205 -105
  19. tooluniverse/compose_tool.py +93 -8
  20. tooluniverse/core_tool.py +46 -44
  21. tooluniverse/crossref_tool.py +89 -4
  22. tooluniverse/custom_tool.py +28 -0
  23. tooluniverse/data/agentic_tools.json +1271 -1179
  24. tooluniverse/data/alphafold_tools.json +356 -105
  25. tooluniverse/data/arxiv_tools.json +85 -81
  26. tooluniverse/data/biorxiv_tools.json +69 -64
  27. tooluniverse/data/cellosaurus_tools.json +260 -0
  28. tooluniverse/data/chembl_tools.json +27 -12
  29. tooluniverse/data/clinicaltrials_gov_tools.json +377 -302
  30. tooluniverse/data/compose_tools.json +123 -16
  31. tooluniverse/data/core_tools.json +104 -99
  32. tooluniverse/data/crossref_tools.json +131 -63
  33. tooluniverse/data/dailymed_tools.json +17 -3
  34. tooluniverse/data/dataset_tools.json +1031 -588
  35. tooluniverse/data/dblp_tools.json +135 -64
  36. tooluniverse/data/disease_target_score_tools.json +20 -10
  37. tooluniverse/data/doaj_tools.json +131 -87
  38. tooluniverse/data/drug_discovery_agents.json +292 -0
  39. tooluniverse/data/embedding_tools.json +362 -299
  40. tooluniverse/data/enrichr_tools.json +34 -27
  41. tooluniverse/data/europe_pmc_tools.json +107 -16
  42. tooluniverse/data/fatcat_tools.json +71 -66
  43. tooluniverse/data/fda_drug_adverse_event_tools.json +1061 -445
  44. tooluniverse/data/fda_drug_labeling_tools.json +6858 -6901
  45. tooluniverse/data/finder_tools.json +32 -37
  46. tooluniverse/data/gene_ontology_tools.json +19 -7
  47. tooluniverse/data/genomics_tools.json +174 -0
  48. tooluniverse/data/geo_tools.json +86 -0
  49. tooluniverse/data/gwas_tools.json +1720 -959
  50. tooluniverse/data/hal_tools.json +69 -64
  51. tooluniverse/data/hpa_tools.json +53 -14
  52. tooluniverse/data/humanbase_tools.json +51 -43
  53. tooluniverse/data/idmap_tools.json +76 -70
  54. tooluniverse/data/literature_search_tools.json +306 -0
  55. tooluniverse/data/markitdown_tools.json +51 -0
  56. tooluniverse/data/mcp_client_tools_example.json +122 -107
  57. tooluniverse/data/medlineplus_tools.json +50 -10
  58. tooluniverse/data/medrxiv_tools.json +69 -64
  59. tooluniverse/data/molecule_2d_tools.json +134 -0
  60. tooluniverse/data/molecule_3d_tools.json +164 -0
  61. tooluniverse/data/monarch_tools.json +112 -110
  62. tooluniverse/data/odphp_tools.json +389 -119
  63. tooluniverse/data/openaire_tools.json +89 -79
  64. tooluniverse/data/openalex_tools.json +96 -31
  65. tooluniverse/data/opentarget_tools.json +1457 -1372
  66. tooluniverse/data/osf_preprints_tools.json +77 -73
  67. tooluniverse/data/packages/bioinformatics_core_tools.json +40 -10
  68. tooluniverse/data/packages/cheminformatics_tools.json +20 -5
  69. tooluniverse/data/packages/genomics_tools.json +36 -9
  70. tooluniverse/data/packages/machine_learning_tools.json +36 -9
  71. tooluniverse/data/packages/scientific_computing_tools.json +20 -5
  72. tooluniverse/data/packages/single_cell_tools.json +20 -5
  73. tooluniverse/data/packages/structural_biology_tools.json +16 -4
  74. tooluniverse/data/packages/visualization_tools.json +20 -5
  75. tooluniverse/data/pmc_tools.json +108 -103
  76. tooluniverse/data/ppi_tools.json +139 -0
  77. tooluniverse/data/protein_structure_3d_tools.json +138 -0
  78. tooluniverse/data/pubchem_tools.json +37 -12
  79. tooluniverse/data/pubmed_tools.json +124 -58
  80. tooluniverse/data/pubtator_tools.json +68 -60
  81. tooluniverse/data/rcsb_pdb_tools.json +1532 -1221
  82. tooluniverse/data/semantic_scholar_tools.json +54 -22
  83. tooluniverse/data/special_tools.json +8 -6
  84. tooluniverse/data/tool_composition_tools.json +112 -82
  85. tooluniverse/data/unified_guideline_tools.json +909 -0
  86. tooluniverse/data/url_fetch_tools.json +102 -82
  87. tooluniverse/data/uspto_tools.json +49 -30
  88. tooluniverse/data/wikidata_sparql_tools.json +42 -39
  89. tooluniverse/data/xml_tools.json +3274 -3113
  90. tooluniverse/data/zenodo_tools.json +83 -76
  91. tooluniverse/dblp_tool.py +76 -6
  92. tooluniverse/dbsnp_tool.py +71 -0
  93. tooluniverse/default_config.py +19 -0
  94. tooluniverse/doaj_tool.py +76 -17
  95. tooluniverse/doctor.py +48 -0
  96. tooluniverse/ensembl_tool.py +61 -0
  97. tooluniverse/europe_pmc_tool.py +132 -17
  98. tooluniverse/exceptions.py +170 -0
  99. tooluniverse/execute_function.py +930 -387
  100. tooluniverse/fatcat_tool.py +0 -1
  101. tooluniverse/generate_tools.py +481 -0
  102. tooluniverse/genomics_gene_search_tool.py +56 -0
  103. tooluniverse/geo_tool.py +116 -0
  104. tooluniverse/gnomad_tool.py +63 -0
  105. tooluniverse/hal_tool.py +1 -1
  106. tooluniverse/llm_clients.py +101 -124
  107. tooluniverse/markitdown_tool.py +159 -0
  108. tooluniverse/mcp_client_tool.py +10 -5
  109. tooluniverse/mcp_tool_registry.py +4 -1
  110. tooluniverse/medrxiv_tool.py +32 -13
  111. tooluniverse/memory_manager.py +166 -0
  112. tooluniverse/molecule_2d_tool.py +274 -0
  113. tooluniverse/molecule_3d_tool.py +441 -0
  114. tooluniverse/odphp_tool.py +49 -14
  115. tooluniverse/openaire_tool.py +5 -20
  116. tooluniverse/openalex_tool.py +34 -0
  117. tooluniverse/osf_preprints_tool.py +1 -1
  118. tooluniverse/pmc_tool.py +54 -56
  119. tooluniverse/protein_structure_3d_tool.py +295 -0
  120. tooluniverse/pubmed_tool.py +69 -6
  121. tooluniverse/remote/boltz/boltz_mcp_server.py +3 -1
  122. tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +3 -1
  123. tooluniverse/semantic_scholar_tool.py +40 -10
  124. tooluniverse/smcp.py +149 -213
  125. tooluniverse/smcp_server.py +97 -55
  126. tooluniverse/string_tool.py +112 -0
  127. tooluniverse/tool_registry.py +35 -3
  128. tooluniverse/tools/ADMETAI_predict_BBB_penetrance.py +46 -0
  129. tooluniverse/tools/ADMETAI_predict_CYP_interactions.py +46 -0
  130. tooluniverse/tools/ADMETAI_predict_bioavailability.py +46 -0
  131. tooluniverse/tools/ADMETAI_predict_clearance_distribution.py +49 -0
  132. tooluniverse/tools/ADMETAI_predict_nuclear_receptor_activity.py +49 -0
  133. tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py +49 -0
  134. tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py +49 -0
  135. tooluniverse/tools/ADMETAI_predict_stress_response.py +46 -0
  136. tooluniverse/tools/ADMETAI_predict_toxicity.py +46 -0
  137. tooluniverse/tools/ADMETAnalyzerAgent.py +59 -0
  138. tooluniverse/tools/AdvancedCodeQualityAnalyzer.py +63 -0
  139. tooluniverse/tools/AdverseEventICDMapper.py +46 -0
  140. tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py +52 -0
  141. tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py +59 -0
  142. tooluniverse/tools/ArXiv_search_papers.py +63 -0
  143. tooluniverse/tools/ArgumentDescriptionOptimizer.py +55 -0
  144. tooluniverse/tools/BioRxiv_search_preprints.py +52 -0
  145. tooluniverse/tools/BiomarkerDiscoveryWorkflow.py +55 -0
  146. tooluniverse/tools/CMA_Guidelines_Search.py +52 -0
  147. tooluniverse/tools/CORE_search_papers.py +67 -0
  148. tooluniverse/tools/CallAgent.py +46 -0
  149. tooluniverse/tools/ChEMBL_search_similar_molecules.py +59 -0
  150. tooluniverse/tools/ClinVar_search_variants.py +52 -0
  151. tooluniverse/tools/ClinicalTrialDesignAgent.py +63 -0
  152. tooluniverse/tools/CodeOptimizer.py +55 -0
  153. tooluniverse/tools/CodeQualityAnalyzer.py +71 -0
  154. tooluniverse/tools/CompoundDiscoveryAgent.py +59 -0
  155. tooluniverse/tools/ComprehensiveDrugDiscoveryPipeline.py +49 -0
  156. tooluniverse/tools/Crossref_search_works.py +55 -0
  157. tooluniverse/tools/DBLP_search_publications.py +52 -0
  158. tooluniverse/tools/DOAJ_search_articles.py +55 -0
  159. tooluniverse/tools/DailyMed_get_spl_by_setid.py +52 -0
  160. tooluniverse/tools/DailyMed_search_spls.py +79 -0
  161. tooluniverse/tools/DataAnalysisValidityReviewer.py +49 -0
  162. tooluniverse/tools/DescriptionAnalyzer.py +55 -0
  163. tooluniverse/tools/DescriptionQualityEvaluator.py +59 -0
  164. tooluniverse/tools/DiseaseAnalyzerAgent.py +52 -0
  165. tooluniverse/tools/DomainExpertValidator.py +63 -0
  166. tooluniverse/tools/DrugInteractionAnalyzerAgent.py +52 -0
  167. tooluniverse/tools/DrugOptimizationAgent.py +63 -0
  168. tooluniverse/tools/DrugSafetyAnalyzer.py +59 -0
  169. tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py +52 -0
  170. tooluniverse/tools/EthicalComplianceReviewer.py +49 -0
  171. tooluniverse/tools/EuropePMC_Guidelines_Search.py +52 -0
  172. tooluniverse/tools/EuropePMC_search_articles.py +52 -0
  173. tooluniverse/tools/ExperimentalDesignScorer.py +55 -0
  174. tooluniverse/tools/FAERS_count_additive_administration_routes.py +52 -0
  175. tooluniverse/tools/FAERS_count_additive_adverse_reactions.py +71 -0
  176. tooluniverse/tools/FAERS_count_additive_event_reports_by_country.py +63 -0
  177. tooluniverse/tools/FAERS_count_additive_reaction_outcomes.py +63 -0
  178. tooluniverse/tools/FAERS_count_additive_reports_by_reporter_country.py +63 -0
  179. tooluniverse/tools/FAERS_count_additive_seriousness_classification.py +63 -0
  180. tooluniverse/tools/FAERS_count_country_by_drug_event.py +63 -0
  181. tooluniverse/tools/FAERS_count_death_related_by_drug.py +49 -0
  182. tooluniverse/tools/FAERS_count_drug_routes_by_event.py +52 -0
  183. tooluniverse/tools/FAERS_count_drugs_by_drug_event.py +63 -0
  184. tooluniverse/tools/FAERS_count_outcomes_by_drug_event.py +63 -0
  185. tooluniverse/tools/FAERS_count_patient_age_distribution.py +49 -0
  186. tooluniverse/tools/FAERS_count_reactions_by_drug_event.py +71 -0
  187. tooluniverse/tools/FAERS_count_reportercountry_by_drug_event.py +63 -0
  188. tooluniverse/tools/FAERS_count_seriousness_by_drug_event.py +63 -0
  189. tooluniverse/tools/FDA_get_abuse_dependence_info_by_drug_name.py +55 -0
  190. tooluniverse/tools/FDA_get_abuse_info_by_drug_name.py +55 -0
  191. tooluniverse/tools/FDA_get_accessories_info_by_drug_name.py +55 -0
  192. tooluniverse/tools/FDA_get_active_ingredient_info_by_drug_name.py +55 -0
  193. tooluniverse/tools/FDA_get_adverse_reactions_by_drug_name.py +55 -0
  194. tooluniverse/tools/FDA_get_alarms_by_drug_name.py +55 -0
  195. tooluniverse/tools/FDA_get_animal_pharmacology_info_by_drug_name.py +55 -0
  196. tooluniverse/tools/FDA_get_assembly_installation_info_by_drug_name.py +55 -0
  197. tooluniverse/tools/FDA_get_boxed_warning_info_by_drug_name.py +55 -0
  198. tooluniverse/tools/FDA_get_brand_name_generic_name.py +52 -0
  199. tooluniverse/tools/FDA_get_calibration_instructions_by_drug_name.py +55 -0
  200. tooluniverse/tools/FDA_get_carcinogenic_mutagenic_fertility_by_drug_name.py +55 -0
  201. tooluniverse/tools/FDA_get_child_safety_info_by_drug_name.py +55 -0
  202. tooluniverse/tools/FDA_get_clinical_pharmacology_by_drug_name.py +55 -0
  203. tooluniverse/tools/FDA_get_clinical_studies_info_by_drug_name.py +55 -0
  204. tooluniverse/tools/FDA_get_contact_for_questions_info_by_drug_name.py +55 -0
  205. tooluniverse/tools/FDA_get_contraindications_by_drug_name.py +55 -0
  206. tooluniverse/tools/FDA_get_controlled_substance_DEA_schedule_info_by_drug_name.py +55 -0
  207. tooluniverse/tools/FDA_get_dear_health_care_provider_letter_info_by_drug_name.py +55 -0
  208. tooluniverse/tools/FDA_get_dependence_info_by_drug_name.py +55 -0
  209. tooluniverse/tools/FDA_get_disposal_info_by_drug_name.py +55 -0
  210. tooluniverse/tools/FDA_get_do_not_use_info_by_drug_name.py +55 -0
  211. tooluniverse/tools/FDA_get_document_id_by_drug_name.py +55 -0
  212. tooluniverse/tools/FDA_get_dosage_and_storage_information_by_drug_name.py +55 -0
  213. tooluniverse/tools/FDA_get_dosage_forms_and_strengths_by_drug_name.py +55 -0
  214. tooluniverse/tools/FDA_get_drug_generic_name.py +46 -0
  215. tooluniverse/tools/FDA_get_drug_interactions_by_drug_name.py +55 -0
  216. tooluniverse/tools/FDA_get_drug_name_by_SPL_ID.py +55 -0
  217. tooluniverse/tools/FDA_get_drug_name_by_adverse_reaction.py +59 -0
  218. tooluniverse/tools/FDA_get_drug_name_by_calibration_instructions.py +59 -0
  219. tooluniverse/tools/FDA_get_drug_name_by_dependence_info.py +59 -0
  220. tooluniverse/tools/FDA_get_drug_name_by_document_id.py +55 -0
  221. tooluniverse/tools/FDA_get_drug_name_by_dosage_info.py +55 -0
  222. tooluniverse/tools/FDA_get_drug_name_by_environmental_warning.py +59 -0
  223. tooluniverse/tools/FDA_get_drug_name_by_inactive_ingredient.py +59 -0
  224. tooluniverse/tools/FDA_get_drug_name_by_info_on_conditions_for_doctor_consultation.py +55 -0
  225. tooluniverse/tools/FDA_get_drug_name_by_labor_and_delivery_info.py +59 -0
  226. tooluniverse/tools/FDA_get_drug_name_by_microbiology.py +59 -0
  227. tooluniverse/tools/FDA_get_drug_name_by_other_safety_info.py +55 -0
  228. tooluniverse/tools/FDA_get_drug_name_by_pharmacodynamics.py +59 -0
  229. tooluniverse/tools/FDA_get_drug_name_by_pharmacogenomics.py +59 -0
  230. tooluniverse/tools/FDA_get_drug_name_by_precautions.py +55 -0
  231. tooluniverse/tools/FDA_get_drug_name_by_pregnancy_or_breastfeeding_info.py +59 -0
  232. tooluniverse/tools/FDA_get_drug_name_by_principal_display_panel.py +59 -0
  233. tooluniverse/tools/FDA_get_drug_name_by_reference.py +55 -0
  234. tooluniverse/tools/FDA_get_drug_name_by_set_id.py +55 -0
  235. tooluniverse/tools/FDA_get_drug_name_by_stop_use_info.py +55 -0
  236. tooluniverse/tools/FDA_get_drug_name_by_storage_and_handling_info.py +55 -0
  237. tooluniverse/tools/FDA_get_drug_name_by_warnings.py +55 -0
  238. tooluniverse/tools/FDA_get_drug_name_from_patient_package_insert.py +59 -0
  239. tooluniverse/tools/FDA_get_drug_names_by_abuse_dependence_info.py +55 -0
  240. tooluniverse/tools/FDA_get_drug_names_by_abuse_info.py +63 -0
  241. tooluniverse/tools/FDA_get_drug_names_by_accessories.py +63 -0
  242. tooluniverse/tools/FDA_get_drug_names_by_active_ingredient.py +63 -0
  243. tooluniverse/tools/FDA_get_drug_names_by_alarm.py +63 -0
  244. tooluniverse/tools/FDA_get_drug_names_by_animal_pharmacology_info.py +63 -0
  245. tooluniverse/tools/FDA_get_drug_names_by_application_number_NDC_number.py +59 -0
  246. tooluniverse/tools/FDA_get_drug_names_by_assembly_installation_info.py +63 -0
  247. tooluniverse/tools/FDA_get_drug_names_by_boxed_warning.py +63 -0
  248. tooluniverse/tools/FDA_get_drug_names_by_child_safety_info.py +63 -0
  249. tooluniverse/tools/FDA_get_drug_names_by_clinical_pharmacology.py +63 -0
  250. tooluniverse/tools/FDA_get_drug_names_by_clinical_studies.py +63 -0
  251. tooluniverse/tools/FDA_get_drug_names_by_consulting_doctor_pharmacist_info.py +63 -0
  252. tooluniverse/tools/FDA_get_drug_names_by_contraindications.py +63 -0
  253. tooluniverse/tools/FDA_get_drug_names_by_controlled_substance_DEA_schedule.py +63 -0
  254. tooluniverse/tools/FDA_get_drug_names_by_dear_health_care_provider_letter_info.py +63 -0
  255. tooluniverse/tools/FDA_get_drug_names_by_disposal_info.py +63 -0
  256. tooluniverse/tools/FDA_get_drug_names_by_dosage_forms_and_strengths_info.py +63 -0
  257. tooluniverse/tools/FDA_get_drug_names_by_drug_interactions.py +63 -0
  258. tooluniverse/tools/FDA_get_drug_names_by_effective_time.py +63 -0
  259. tooluniverse/tools/FDA_get_drug_names_by_food_safety_warnings.py +63 -0
  260. tooluniverse/tools/FDA_get_drug_names_by_general_precautions.py +63 -0
  261. tooluniverse/tools/FDA_get_drug_names_by_geriatric_use.py +63 -0
  262. tooluniverse/tools/FDA_get_drug_names_by_health_claim.py +63 -0
  263. tooluniverse/tools/FDA_get_drug_names_by_indication.py +55 -0
  264. tooluniverse/tools/FDA_get_drug_names_by_info_for_nursing_mothers.py +63 -0
  265. tooluniverse/tools/FDA_get_drug_names_by_information_for_owners_or_caregivers.py +63 -0
  266. tooluniverse/tools/FDA_get_drug_names_by_ingredient.py +63 -0
  267. tooluniverse/tools/FDA_get_drug_names_by_instructions_for_use.py +63 -0
  268. tooluniverse/tools/FDA_get_drug_names_by_lab_test_interference.py +63 -0
  269. tooluniverse/tools/FDA_get_drug_names_by_lab_tests.py +63 -0
  270. tooluniverse/tools/FDA_get_drug_names_by_mechanism_of_action.py +63 -0
  271. tooluniverse/tools/FDA_get_drug_names_by_medication_guide.py +63 -0
  272. tooluniverse/tools/FDA_get_drug_names_by_nonclinical_toxicology_info.py +63 -0
  273. tooluniverse/tools/FDA_get_drug_names_by_nonteratogenic_effects.py +63 -0
  274. tooluniverse/tools/FDA_get_drug_names_by_overdosage_info.py +63 -0
  275. tooluniverse/tools/FDA_get_drug_names_by_pediatric_use.py +63 -0
  276. tooluniverse/tools/FDA_get_drug_names_by_pharmacokinetics.py +63 -0
  277. tooluniverse/tools/FDA_get_drug_names_by_population_use.py +63 -0
  278. tooluniverse/tools/FDA_get_drug_names_by_pregnancy_effects_info.py +63 -0
  279. tooluniverse/tools/FDA_get_drug_names_by_residue_warning.py +63 -0
  280. tooluniverse/tools/FDA_get_drug_names_by_risk.py +63 -0
  281. tooluniverse/tools/FDA_get_drug_names_by_route.py +63 -0
  282. tooluniverse/tools/FDA_get_drug_names_by_safe_handling_warning.py +63 -0
  283. tooluniverse/tools/FDA_get_drug_names_by_safety_summary.py +63 -0
  284. tooluniverse/tools/FDA_get_drug_names_by_spl_indexing_data_elements.py +63 -0
  285. tooluniverse/tools/FDA_get_drug_names_by_teratogenic_effects.py +63 -0
  286. tooluniverse/tools/FDA_get_drug_names_by_user_safety_warning.py +63 -0
  287. tooluniverse/tools/FDA_get_drug_names_by_warnings_and_cautions.py +63 -0
  288. tooluniverse/tools/FDA_get_drugs_by_carcinogenic_mutagenic_fertility.py +63 -0
  289. tooluniverse/tools/FDA_get_effective_time_by_drug_name.py +55 -0
  290. tooluniverse/tools/FDA_get_environmental_warning_by_drug_name.py +55 -0
  291. tooluniverse/tools/FDA_get_general_precautions_by_drug_name.py +55 -0
  292. tooluniverse/tools/FDA_get_geriatric_use_info_by_drug_name.py +55 -0
  293. tooluniverse/tools/FDA_get_health_claims_by_drug_name.py +55 -0
  294. tooluniverse/tools/FDA_get_inactive_ingredient_info_by_drug_name.py +55 -0
  295. tooluniverse/tools/FDA_get_indications_by_drug_name.py +55 -0
  296. tooluniverse/tools/FDA_get_info_for_nursing_mothers_by_drug_name.py +55 -0
  297. tooluniverse/tools/FDA_get_info_for_patients_by_drug_name.py +55 -0
  298. tooluniverse/tools/FDA_get_info_on_conditions_for_doctor_consultation_by_drug_name.py +55 -0
  299. tooluniverse/tools/FDA_get_info_on_consulting_doctor_pharmacist_by_drug_name.py +55 -0
  300. tooluniverse/tools/FDA_get_information_for_owners_or_caregivers_by_drug_name.py +55 -0
  301. tooluniverse/tools/FDA_get_ingredients_by_drug_name.py +55 -0
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  581. tooluniverse/tools/get_chem_comp_charge_and_ambiguity.py +46 -0
  582. tooluniverse/tools/get_chembl_webresource_client_info.py +44 -0
  583. tooluniverse/tools/get_citation_info_by_pdb_id.py +46 -0
  584. tooluniverse/tools/get_clair3_info.py +46 -0
  585. tooluniverse/tools/get_clinical_trial_conditions_and_interventions.py +55 -0
  586. tooluniverse/tools/get_clinical_trial_descriptions.py +52 -0
  587. tooluniverse/tools/get_clinical_trial_eligibility_criteria.py +55 -0
  588. tooluniverse/tools/get_clinical_trial_locations.py +52 -0
  589. tooluniverse/tools/get_clinical_trial_outcome_measures.py +52 -0
  590. tooluniverse/tools/get_clinical_trial_references.py +52 -0
  591. tooluniverse/tools/get_clinical_trial_status_and_dates.py +52 -0
  592. tooluniverse/tools/get_cobra_info.py +46 -0
  593. tooluniverse/tools/get_cobrapy_info.py +46 -0
  594. tooluniverse/tools/get_cooler_info.py +49 -0
  595. tooluniverse/tools/get_core_refinement_statistics.py +46 -0
  596. tooluniverse/tools/get_cryosparc_tools_info.py +46 -0
  597. tooluniverse/tools/get_crystal_growth_conditions_by_pdb_id.py +49 -0
  598. tooluniverse/tools/get_crystallization_ph_by_pdb_id.py +46 -0
  599. tooluniverse/tools/get_crystallographic_properties_by_pdb_id.py +49 -0
  600. tooluniverse/tools/get_cupy_info.py +44 -0
  601. tooluniverse/tools/get_cyvcf2_info.py +49 -0
  602. tooluniverse/tools/get_dask_info.py +44 -0
  603. tooluniverse/tools/get_datamol_info.py +44 -0
  604. tooluniverse/tools/get_datashader_info.py +44 -0
  605. tooluniverse/tools/get_deepchem_info.py +49 -0
  606. tooluniverse/tools/get_deeppurpose_info.py +46 -0
  607. tooluniverse/tools/get_deeptools_info.py +46 -0
  608. tooluniverse/tools/get_deepxde_info.py +49 -0
  609. tooluniverse/tools/get_dendropy_info.py +44 -0
  610. tooluniverse/tools/get_descriptastorus_info.py +46 -0
  611. tooluniverse/tools/get_diffdock_info.py +46 -0
  612. tooluniverse/tools/get_dscribe_info.py +49 -0
  613. tooluniverse/tools/get_ec_number_by_entity_id.py +46 -0
  614. tooluniverse/tools/get_elephant_info.py +44 -0
  615. tooluniverse/tools/get_em_3d_fitting_and_reconstruction_details.py +49 -0
  616. tooluniverse/tools/get_emdb_ids_by_pdb_id.py +46 -0
  617. tooluniverse/tools/get_episcanpy_info.py +44 -0
  618. tooluniverse/tools/get_ete3_info.py +44 -0
  619. tooluniverse/tools/get_faiss_info.py +46 -0
  620. tooluniverse/tools/get_fanc_info.py +46 -0
  621. tooluniverse/tools/get_flask_info.py +46 -0
  622. tooluniverse/tools/get_flowio_info.py +46 -0
  623. tooluniverse/tools/get_flowkit_info.py +46 -0
  624. tooluniverse/tools/get_flowutils_info.py +46 -0
  625. tooluniverse/tools/get_freesasa_info.py +44 -0
  626. tooluniverse/tools/get_galpy_info.py +44 -0
  627. tooluniverse/tools/get_gene_name_by_entity_id.py +46 -0
  628. tooluniverse/tools/get_geopandas_info.py +44 -0
  629. tooluniverse/tools/get_gget_info.py +46 -0
  630. tooluniverse/tools/get_googlesearch_python_info.py +46 -0
  631. tooluniverse/tools/get_gseapy_info.py +49 -0
  632. tooluniverse/tools/get_h5py_info.py +46 -0
  633. tooluniverse/tools/get_harmony_pytorch_info.py +46 -0
  634. tooluniverse/tools/get_hmmlearn_info.py +46 -0
  635. tooluniverse/tools/get_holoviews_info.py +44 -0
  636. tooluniverse/tools/get_host_organism_by_pdb_id.py +46 -0
  637. tooluniverse/tools/get_htmd_info.py +44 -0
  638. tooluniverse/tools/get_hyperopt_info.py +49 -0
  639. tooluniverse/tools/get_igraph_info.py +49 -0
  640. tooluniverse/tools/get_imageio_info.py +44 -0
  641. tooluniverse/tools/get_imbalanced_learn_info.py +44 -0
  642. tooluniverse/tools/get_jcvi_info.py +46 -0
  643. tooluniverse/tools/get_joblib_info.py +44 -0
  644. tooluniverse/tools/get_joint_associated_diseases_by_HPO_ID_list.py +55 -0
  645. tooluniverse/tools/get_khmer_info.py +46 -0
  646. tooluniverse/tools/get_kipoiseq_info.py +44 -0
  647. tooluniverse/tools/get_lifelines_info.py +49 -0
  648. tooluniverse/tools/get_ligand_bond_count_by_pdb_id.py +46 -0
  649. tooluniverse/tools/get_ligand_smiles_by_chem_comp_id.py +49 -0
  650. tooluniverse/tools/get_lightgbm_info.py +44 -0
  651. tooluniverse/tools/get_loompy_info.py +46 -0
  652. tooluniverse/tools/get_mageck_info.py +46 -0
  653. tooluniverse/tools/get_matplotlib_info.py +49 -0
  654. tooluniverse/tools/get_mdanalysis_info.py +46 -0
  655. tooluniverse/tools/get_mdtraj_info.py +44 -0
  656. tooluniverse/tools/get_mne_info.py +44 -0
  657. tooluniverse/tools/get_molfeat_info.py +44 -0
  658. tooluniverse/tools/get_molvs_info.py +44 -0
  659. tooluniverse/tools/get_mordred_info.py +44 -0
  660. tooluniverse/tools/get_msprime_info.py +49 -0
  661. tooluniverse/tools/get_mudata_info.py +49 -0
  662. tooluniverse/tools/get_mutation_annotations_by_pdb_id.py +46 -0
  663. tooluniverse/tools/get_neo_info.py +44 -0
  664. tooluniverse/tools/get_netcdf4_info.py +44 -0
  665. tooluniverse/tools/get_networkx_info.py +46 -0
  666. tooluniverse/tools/get_nglview_info.py +44 -0
  667. tooluniverse/tools/get_nilearn_info.py +44 -0
  668. tooluniverse/tools/get_numba_info.py +46 -0
  669. tooluniverse/tools/get_numpy_info.py +46 -0
  670. tooluniverse/tools/get_oligosaccharide_descriptors_by_entity_id.py +49 -0
  671. tooluniverse/tools/get_openbabel_info.py +49 -0
  672. tooluniverse/tools/get_openchem_info.py +46 -0
  673. tooluniverse/tools/get_opencv_info.py +49 -0
  674. tooluniverse/tools/get_openmm_info.py +49 -0
  675. tooluniverse/tools/get_optlang_info.py +46 -0
  676. tooluniverse/tools/get_optuna_info.py +44 -0
  677. tooluniverse/tools/get_palantir_info.py +44 -0
  678. tooluniverse/tools/get_pandas_info.py +49 -0
  679. tooluniverse/tools/get_patsy_info.py +44 -0
  680. tooluniverse/tools/get_pdbfixer_info.py +46 -0
  681. tooluniverse/tools/get_phenotype_by_HPO_ID.py +46 -0
  682. tooluniverse/tools/get_pillow_info.py +44 -0
  683. tooluniverse/tools/get_plantcv_info.py +46 -0
  684. tooluniverse/tools/get_plip_info.py +46 -0
  685. tooluniverse/tools/get_plotly_info.py +44 -0
  686. tooluniverse/tools/get_poliastro_info.py +46 -0
  687. tooluniverse/tools/get_polymer_entity_annotations.py +49 -0
  688. tooluniverse/tools/get_polymer_entity_count_by_pdb_id.py +46 -0
  689. tooluniverse/tools/get_polymer_entity_ids_by_pdb_id.py +46 -0
  690. tooluniverse/tools/get_polymer_entity_type_by_entity_id.py +49 -0
  691. tooluniverse/tools/get_polymer_molecular_weight_by_entity_id.py +49 -0
  692. tooluniverse/tools/get_poretools_info.py +44 -0
  693. tooluniverse/tools/get_prody_info.py +46 -0
  694. tooluniverse/tools/get_protein_classification_by_pdb_id.py +49 -0
  695. tooluniverse/tools/get_protein_metadata_by_pdb_id.py +46 -0
  696. tooluniverse/tools/get_pubchempy_info.py +44 -0
  697. tooluniverse/tools/get_pybedtools_info.py +49 -0
  698. tooluniverse/tools/get_pybigwig_info.py +46 -0
  699. tooluniverse/tools/get_pydeseq2_info.py +46 -0
  700. tooluniverse/tools/get_pyensembl_info.py +44 -0
  701. tooluniverse/tools/get_pyephem_info.py +44 -0
  702. tooluniverse/tools/get_pyfaidx_info.py +49 -0
  703. tooluniverse/tools/get_pyfasta_info.py +44 -0
  704. tooluniverse/tools/get_pykalman_info.py +46 -0
  705. tooluniverse/tools/get_pyliftover_info.py +49 -0
  706. tooluniverse/tools/get_pymassspec_info.py +46 -0
  707. tooluniverse/tools/get_pymed_info.py +46 -0
  708. tooluniverse/tools/get_pymzml_info.py +46 -0
  709. tooluniverse/tools/get_pypdf2_info.py +46 -0
  710. tooluniverse/tools/get_pyranges_info.py +49 -0
  711. tooluniverse/tools/get_pyrosetta_info.py +44 -0
  712. tooluniverse/tools/get_pysam_info.py +46 -0
  713. tooluniverse/tools/get_pyscenic_info.py +46 -0
  714. tooluniverse/tools/get_pyscf_info.py +46 -0
  715. tooluniverse/tools/get_pyscreener_info.py +46 -0
  716. tooluniverse/tools/get_pytdc_info.py +46 -0
  717. tooluniverse/tools/get_python_libsbml_info.py +46 -0
  718. tooluniverse/tools/get_pytorch_info.py +49 -0
  719. tooluniverse/tools/get_pyvcf_info.py +44 -0
  720. tooluniverse/tools/get_pyvis_info.py +44 -0
  721. tooluniverse/tools/get_qutip_info.py +44 -0
  722. tooluniverse/tools/get_rasterio_info.py +44 -0
  723. tooluniverse/tools/get_rdkit_info.py +46 -0
  724. tooluniverse/tools/get_refinement_resolution_by_pdb_id.py +49 -0
  725. tooluniverse/tools/get_release_deposit_dates_by_pdb_id.py +49 -0
  726. tooluniverse/tools/get_reportlab_info.py +49 -0
  727. tooluniverse/tools/get_requests_info.py +49 -0
  728. tooluniverse/tools/get_ruptures_info.py +46 -0
  729. tooluniverse/tools/get_scanorama_info.py +44 -0
  730. tooluniverse/tools/get_scanpy_info.py +49 -0
  731. tooluniverse/tools/get_schnetpack_info.py +49 -0
  732. tooluniverse/tools/get_scholarly_info.py +46 -0
  733. tooluniverse/tools/get_scikit_bio_info.py +49 -0
  734. tooluniverse/tools/get_scikit_image_info.py +46 -0
  735. tooluniverse/tools/get_scikit_learn_info.py +49 -0
  736. tooluniverse/tools/get_scipy_info.py +46 -0
  737. tooluniverse/tools/get_scrublet_info.py +49 -0
  738. tooluniverse/tools/get_scvelo_info.py +49 -0
  739. tooluniverse/tools/get_scvi_tools_info.py +44 -0
  740. tooluniverse/tools/get_seaborn_info.py +49 -0
  741. tooluniverse/tools/get_sequence_by_pdb_id.py +46 -0
  742. tooluniverse/tools/get_sequence_lengths_by_pdb_id.py +46 -0
  743. tooluniverse/tools/get_sequence_positional_features_by_instance_id.py +49 -0
  744. tooluniverse/tools/get_skopt_info.py +44 -0
  745. tooluniverse/tools/get_souporcell_info.py +46 -0
  746. tooluniverse/tools/get_source_organism_by_pdb_id.py +46 -0
  747. tooluniverse/tools/get_space_group_by_pdb_id.py +46 -0
  748. tooluniverse/tools/get_statsmodels_info.py +49 -0
  749. tooluniverse/tools/get_structure_determination_software_by_pdb_id.py +49 -0
  750. tooluniverse/tools/get_structure_title_by_pdb_id.py +46 -0
  751. tooluniverse/tools/get_structure_validation_metrics_by_pdb_id.py +49 -0
  752. tooluniverse/tools/get_sunpy_info.py +44 -0
  753. tooluniverse/tools/get_sympy_info.py +46 -0
  754. tooluniverse/tools/get_target_cofactor_info.py +46 -0
  755. tooluniverse/tools/get_taxonomy_by_pdb_id.py +46 -0
  756. tooluniverse/tools/get_tiledb_info.py +46 -0
  757. tooluniverse/tools/get_tiledbsoma_info.py +46 -0
  758. tooluniverse/tools/get_torch_geometric_info.py +49 -0
  759. tooluniverse/tools/get_tqdm_info.py +46 -0
  760. tooluniverse/tools/get_trackpy_info.py +46 -0
  761. tooluniverse/tools/get_tskit_info.py +46 -0
  762. tooluniverse/tools/get_umap_learn_info.py +49 -0
  763. tooluniverse/tools/get_uniprot_accession_by_entity_id.py +49 -0
  764. tooluniverse/tools/get_velocyto_info.py +44 -0
  765. tooluniverse/tools/get_viennarna_info.py +49 -0
  766. tooluniverse/tools/get_webpage_text_from_url.py +52 -0
  767. tooluniverse/tools/get_webpage_title.py +49 -0
  768. tooluniverse/tools/get_xarray_info.py +44 -0
  769. tooluniverse/tools/get_xesmf_info.py +44 -0
  770. tooluniverse/tools/get_xgboost_info.py +44 -0
  771. tooluniverse/tools/get_zarr_info.py +44 -0
  772. tooluniverse/tools/gnomAD_query_variant.py +52 -0
  773. tooluniverse/tools/gwas_get_association_by_id.py +49 -0
  774. tooluniverse/tools/gwas_get_associations_for_snp.py +67 -0
  775. tooluniverse/tools/gwas_get_associations_for_study.py +55 -0
  776. tooluniverse/tools/gwas_get_associations_for_trait.py +55 -0
  777. tooluniverse/tools/gwas_get_snp_by_id.py +46 -0
  778. tooluniverse/tools/gwas_get_snps_for_gene.py +55 -0
  779. tooluniverse/tools/gwas_get_studies_for_trait.py +75 -0
  780. tooluniverse/tools/gwas_get_study_by_id.py +46 -0
  781. tooluniverse/tools/gwas_get_variants_for_trait.py +55 -0
  782. tooluniverse/tools/gwas_search_associations.py +75 -0
  783. tooluniverse/tools/gwas_search_snps.py +63 -0
  784. tooluniverse/tools/gwas_search_studies.py +75 -0
  785. tooluniverse/tools/humanbase_ppi_analysis.py +67 -0
  786. tooluniverse/tools/mesh_get_subjects_by_pharmacological_action.py +63 -0
  787. tooluniverse/tools/mesh_get_subjects_by_subject_id.py +63 -0
  788. tooluniverse/tools/mesh_get_subjects_by_subject_name.py +63 -0
  789. tooluniverse/tools/mesh_get_subjects_by_subject_scope_or_definition.py +63 -0
  790. tooluniverse/tools/odphp_itemlist.py +49 -0
  791. tooluniverse/tools/odphp_myhealthfinder.py +67 -0
  792. tooluniverse/tools/odphp_outlink_fetch.py +59 -0
  793. tooluniverse/tools/odphp_topicsearch.py +67 -0
  794. tooluniverse/tools/openalex_literature_search.py +67 -0
  795. tooluniverse/tools/reactome_disease_target_score.py +52 -0
  796. tooluniverse/tools/search_clinical_trials.py +67 -0
  797. tooluniverse/tools/visualize_molecule_2d.py +83 -0
  798. tooluniverse/tools/visualize_molecule_3d.py +91 -0
  799. tooluniverse/tools/visualize_protein_structure_3d.py +79 -0
  800. tooluniverse/ucsc_tool.py +60 -0
  801. tooluniverse/unified_guideline_tools.py +2328 -0
  802. tooluniverse/unpaywall_tool.py +0 -1
  803. tooluniverse/utils.py +122 -6
  804. tooluniverse/visualization_tool.py +897 -0
  805. tooluniverse/wikidata_sparql_tool.py +1 -2
  806. tooluniverse/zenodo_tool.py +3 -4
  807. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/METADATA +19 -4
  808. tooluniverse-1.0.8.dist-info/RECORD +891 -0
  809. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/entry_points.txt +3 -0
  810. tooluniverse/test/list_azure_openai_models.py +0 -210
  811. tooluniverse/test/mcp_server_test.py +0 -0
  812. tooluniverse/test/test_admetai_tool.py +0 -370
  813. tooluniverse/test/test_agentic_tool.py +0 -129
  814. tooluniverse/test/test_agentic_tool_azure_models.py +0 -91
  815. tooluniverse/test/test_alphafold_tool.py +0 -108
  816. tooluniverse/test/test_api_key_validation_min.py +0 -64
  817. tooluniverse/test/test_chem_tool.py +0 -37
  818. tooluniverse/test/test_claude_sdk.py +0 -93
  819. tooluniverse/test/test_compose_lieraturereview.py +0 -63
  820. tooluniverse/test/test_compose_tool.py +0 -448
  821. tooluniverse/test/test_dailymed.py +0 -69
  822. tooluniverse/test/test_dataset_tool.py +0 -200
  823. tooluniverse/test/test_disease_target_score.py +0 -56
  824. tooluniverse/test/test_drugbank_filter_examples.py +0 -179
  825. tooluniverse/test/test_efo.py +0 -31
  826. tooluniverse/test/test_enrichr_tool.py +0 -21
  827. tooluniverse/test/test_europe_pmc_tool.py +0 -20
  828. tooluniverse/test/test_fda_adv.py +0 -95
  829. tooluniverse/test/test_fda_drug_labeling.py +0 -91
  830. tooluniverse/test/test_gene_ontology_tools.py +0 -66
  831. tooluniverse/test/test_global_fallback.py +0 -288
  832. tooluniverse/test/test_gwas_tool.py +0 -139
  833. tooluniverse/test/test_hooks_direct.py +0 -219
  834. tooluniverse/test/test_hpa.py +0 -625
  835. tooluniverse/test/test_humanbase_tool.py +0 -20
  836. tooluniverse/test/test_idmap_tools.py +0 -61
  837. tooluniverse/test/test_list_built_in_tools.py +0 -33
  838. tooluniverse/test/test_mcp_server.py +0 -211
  839. tooluniverse/test/test_mcp_tool.py +0 -247
  840. tooluniverse/test/test_medlineplus.py +0 -220
  841. tooluniverse/test/test_odphp_tool.py +0 -166
  842. tooluniverse/test/test_openalex_tool.py +0 -32
  843. tooluniverse/test/test_openrouter_client.py +0 -288
  844. tooluniverse/test/test_opentargets.py +0 -28
  845. tooluniverse/test/test_pubchem_tool.py +0 -116
  846. tooluniverse/test/test_pubtator_tool.py +0 -37
  847. tooluniverse/test/test_rcsb_pdb_tool.py +0 -86
  848. tooluniverse/test/test_reactome.py +0 -54
  849. tooluniverse/test/test_semantic_scholar_tool.py +0 -24
  850. tooluniverse/test/test_software_tools.py +0 -147
  851. tooluniverse/test/test_stdio_hooks.py +0 -285
  852. tooluniverse/test/test_tool_description_optimizer.py +0 -49
  853. tooluniverse/test/test_tool_finder.py +0 -26
  854. tooluniverse/test/test_tool_finder_llm.py +0 -252
  855. tooluniverse/test/test_tools_find.py +0 -195
  856. tooluniverse/test/test_uniprot_tools.py +0 -74
  857. tooluniverse/test/test_uspto_tool.py +0 -72
  858. tooluniverse/test/test_xml_tool.py +0 -113
  859. tooluniverse-1.0.6.dist-info/RECORD +0 -230
  860. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/WHEEL +0 -0
  861. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/licenses/LICENSE +0 -0
  862. {tooluniverse-1.0.6.dist-info → tooluniverse-1.0.8.dist-info}/top_level.txt +0 -0
tooluniverse/visualization_tool.py ADDED
@@ -0,0 +1,897 @@
1
+ """
2
+ Visualization Tool Base Class for ToolUniverse
3
+ ==============================================
4
+
5
+ This module provides the base VisualizationTool class that all visualization
6
+ tools inherit from. It provides common functionality for HTML generation,
7
+ image conversion, error handling, and output formatting.
8
+ """
9
+
10
+ import base64
11
+ from typing import Any, Dict, Optional
12
+ from .base_tool import BaseTool
13
+ from .tool_registry import register_tool
14
+
15
+
16
+ @register_tool("VisualizationTool")
17
+ class VisualizationTool(BaseTool):
18
+ """
19
+ Base class for all visualization tools in ToolUniverse.
20
+
21
+ Provides common functionality for:
22
+ - HTML generation and embedding
23
+ - Static image conversion
24
+ - Error handling
25
+ - Output formatting
26
+ """
27
+
28
+ def __init__(self, tool_config):
29
+ super().__init__(tool_config)
30
+ self.name = tool_config.get("name")
31
+ self.description = tool_config.get("description")
32
+
33
+ # Default visualization settings
34
+ self.default_width = tool_config.get("default_width", 800)
35
+ self.default_height = tool_config.get("default_height", 600)
36
+ self.default_style = tool_config.get("default_style", {})
37
+
38
+ def create_visualization_response(
39
+ self,
40
+ html_content: str,
41
+ viz_type: str,
42
+ data: Optional[Dict] = None,
43
+ static_image: Optional[str] = None,
44
+ metadata: Optional[Dict] = None,
45
+ ) -> Dict[str, Any]:
46
+ """Create a standardized visualization response."""
47
+ response = {
48
+ "success": True,
49
+ "visualization": {
50
+ "html": html_content,
51
+ "type": viz_type,
52
+ "data": data or {},
53
+ "metadata": metadata or {},
54
+ },
55
+ }
56
+
57
+ if static_image:
58
+ response["visualization"]["static_image"] = static_image
59
+
60
+ return response
61
+
62
+ def create_error_response(
63
+ self, error_message: str, error_type: str = "VisualizationError"
64
+ ) -> Dict[str, Any]:
65
+ """Create a standardized error response."""
66
+ return {
67
+ "success": False,
68
+ "error": error_message,
69
+ "error_type": error_type,
70
+ "visualization": {
71
+ "html": f"<div class='error'>Error: {error_message}</div>",
72
+ "type": "error",
73
+ "data": {},
74
+ "metadata": {},
75
+ },
76
+ }
77
+
78
+ def convert_to_base64_image(self, image_data: bytes, format: str = "PNG") -> str:
79
+ """Convert image data to base64 string."""
80
+ return base64.b64encode(image_data).decode("utf-8")
81
+
82
+ def create_plotly_html(
83
+ self,
84
+ fig,
85
+ width: Optional[int] = None,
86
+ height: Optional[int] = None,
87
+ include_plotlyjs: str = "cdn",
88
+ ) -> str:
89
+ """Create HTML from Plotly figure."""
90
+ if width is None:
91
+ width = self.default_width
92
+ if height is None:
93
+ height = self.default_height
94
+
95
+ return fig.to_html(
96
+ include_plotlyjs=include_plotlyjs,
97
+ div_id=f"{self.name}_plot",
98
+ config={
99
+ "displayModeBar": True,
100
+ "displaylogo": False,
101
+ "modeBarButtonsToRemove": ["pan2d", "lasso2d", "select2d"],
102
+ },
103
+ )
104
+
105
+ def create_py3dmol_html(
106
+ self,
107
+ viewer_html: str,
108
+ width: Optional[int] = None,
109
+ height: Optional[int] = None,
110
+ title: str = None,
111
+ info_cards: str = "",
112
+ control_panel: str = "",
113
+ toolbar: str = "",
114
+ ) -> str:
115
+ """Create modern HTML wrapper for py3Dmol viewer."""
116
+ if width is None:
117
+ width = self.default_width
118
+ if height is None:
119
+ height = self.default_height
120
+ if title is None:
121
+ title = f"{self.name} Visualization"
122
+
123
+ return f"""
124
+ <!DOCTYPE html>
125
+ <html>
126
+ <head>
127
+ <meta charset="utf-8">
128
+ <title>{title}</title>
129
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
130
+ <style>
131
+ * {{
132
+ margin: 0;
133
+ padding: 0;
134
+ box-sizing: border-box;
135
+ }}
136
+
137
+ body {{
138
+ font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
139
+ background: linear-gradient(135deg, #f0f4f8 0%, #ffffff 100%);
140
+ min-height: 100vh;
141
+ color: #2c3e50;
142
+ line-height: 1.6;
143
+ }}
144
+
145
+ .container {{
146
+ max-width: 1400px;
147
+ margin: 0 auto;
148
+ padding: 20px;
149
+ }}
150
+
151
+ .header {{
152
+ text-align: center;
153
+ margin-bottom: 30px;
154
+ }}
155
+
156
+ .title {{
157
+ font-size: 2.5rem;
158
+ font-weight: 300;
159
+ color: #4A90E2;
160
+ margin-bottom: 10px;
161
+ text-shadow: 0 2px 4px rgba(0,0,0,0.1);
162
+ }}
163
+
164
+ .subtitle {{
165
+ font-size: 1.1rem;
166
+ color: #7f8c8d;
167
+ font-weight: 300;
168
+ }}
169
+
170
+ .main-content {{
171
+ display: grid;
172
+ grid-template-columns: 1fr 300px;
173
+ gap: 30px;
174
+ margin-bottom: 30px;
175
+ }}
176
+
177
+ .viewer-section {{
178
+ position: relative;
179
+ }}
180
+
181
+ .viewer-container {{
182
+ background: white;
183
+ border-radius: 16px;
184
+ box-shadow: 0 8px 32px rgba(0,0,0,0.1);
185
+ overflow: hidden;
186
+ position: relative;
187
+ }}
188
+
189
+ .viewer-wrapper {{
190
+ position: relative;
191
+ width: 100%;
192
+ height: {height}px;
193
+ }}
194
+
195
+ .control-panel {{
196
+ position: absolute;
197
+ top: 20px;
198
+ right: 20px;
199
+ background: rgba(255,255,255,0.95);
200
+ backdrop-filter: blur(10px);
201
+ border-radius: 12px;
202
+ padding: 20px;
203
+ box-shadow: 0 8px 16px rgba(0,0,0,0.15);
204
+ z-index: 1000;
205
+ min-width: 200px;
206
+ }}
207
+
208
+ .control-group {{
209
+ margin-bottom: 15px;
210
+ }}
211
+
212
+ .control-group:last-child {{
213
+ margin-bottom: 0;
214
+ }}
215
+
216
+ .control-label {{
217
+ font-size: 0.9rem;
218
+ font-weight: 600;
219
+ color: #34495e;
220
+ margin-bottom: 8px;
221
+ display: block;
222
+ }}
223
+
224
+ .control-select {{
225
+ width: 100%;
226
+ padding: 8px 12px;
227
+ border: 1px solid #ddd;
228
+ border-radius: 8px;
229
+ background: white;
230
+ font-size: 0.9rem;
231
+ color: #2c3e50;
232
+ cursor: pointer;
233
+ transition: all 0.2s;
234
+ }}
235
+
236
+ .control-select:hover {{
237
+ border-color: #4A90E2;
238
+ }}
239
+
240
+ .control-select:focus {{
241
+ outline: none;
242
+ border-color: #4A90E2;
243
+ box-shadow: 0 0 0 3px rgba(74, 144, 226, 0.1);
244
+ }}
245
+
246
+ .toolbar {{
247
+ position: absolute;
248
+ bottom: 20px;
249
+ left: 20px;
250
+ display: flex;
251
+ gap: 10px;
252
+ z-index: 1000;
253
+ }}
254
+
255
+ .btn {{
256
+ background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
257
+ border: none;
258
+ border-radius: 8px;
259
+ color: white;
260
+ padding: 10px 16px;
261
+ cursor: pointer;
262
+ font-size: 0.9rem;
263
+ font-weight: 500;
264
+ transition: all 0.2s;
265
+ box-shadow: 0 2px 8px rgba(0,0,0,0.15);
266
+ }}
267
+
268
+ .btn:hover {{
269
+ transform: translateY(-2px);
270
+ box-shadow: 0 4px 12px rgba(0,0,0,0.2);
271
+ }}
272
+
273
+ .btn:active {{
274
+ transform: translateY(0);
275
+ }}
276
+
277
+ .btn-secondary {{
278
+ background: linear-gradient(135deg, #50C878 0%, #4A90E2 100%);
279
+ }}
280
+
281
+ .btn-outline {{
282
+ background: transparent;
283
+ border: 2px solid #4A90E2;
284
+ color: #4A90E2;
285
+ }}
286
+
287
+ .btn-outline:hover {{
288
+ background: #4A90E2;
289
+ color: white;
290
+ }}
291
+
292
+ .info-section {{
293
+ display: flex;
294
+ flex-direction: column;
295
+ gap: 20px;
296
+ }}
297
+
298
+ .card {{
299
+ background: white;
300
+ border-radius: 12px;
301
+ box-shadow: 0 4px 6px rgba(0,0,0,0.1);
302
+ padding: 20px;
303
+ transition: transform 0.2s;
304
+ }}
305
+
306
+ .card:hover {{
307
+ transform: translateY(-2px);
308
+ box-shadow: 0 8px 16px rgba(0,0,0,0.15);
309
+ }}
310
+
311
+ .card-title {{
312
+ font-size: 1.2rem;
313
+ font-weight: 600;
314
+ color: #2c3e50;
315
+ margin-bottom: 15px;
316
+ display: flex;
317
+ align-items: center;
318
+ gap: 8px;
319
+ }}
320
+
321
+ .card-icon {{
322
+ width: 20px;
323
+ height: 20px;
324
+ fill: #4A90E2;
325
+ }}
326
+
327
+ .info-grid {{
328
+ display: grid;
329
+ grid-template-columns: 1fr 1fr;
330
+ gap: 10px;
331
+ }}
332
+
333
+ .info-item {{
334
+ display: flex;
335
+ justify-content: space-between;
336
+ padding: 8px 0;
337
+ border-bottom: 1px solid #ecf0f1;
338
+ }}
339
+
340
+ .info-item:last-child {{
341
+ border-bottom: none;
342
+ }}
343
+
344
+ .info-label {{
345
+ font-weight: 500;
346
+ color: #7f8c8d;
347
+ }}
348
+
349
+ .info-value {{
350
+ font-weight: 600;
351
+ color: #2c3e50;
352
+ }}
353
+
354
+ .interaction-hints {{
355
+ background: linear-gradient(135deg, #f8f9fa 0%, #e9ecef 100%);
356
+ border-radius: 8px;
357
+ padding: 15px;
358
+ font-size: 0.9rem;
359
+ color: #6c757d;
360
+ text-align: center;
361
+ border-left: 4px solid #4A90E2;
362
+ }}
363
+
364
+ .hint-icon {{
365
+ display: inline-block;
366
+ margin-right: 5px;
367
+ }}
368
+
369
+ @media (max-width: 768px) {{
370
+ .main-content {{
371
+ grid-template-columns: 1fr;
372
+ }}
373
+
374
+ .control-panel {{
375
+ position: relative;
376
+ top: auto;
377
+ right: auto;
378
+ margin-bottom: 20px;
379
+ }}
380
+
381
+ .toolbar {{
382
+ position: relative;
383
+ bottom: auto;
384
+ left: auto;
385
+ margin-top: 20px;
386
+ justify-content: center;
387
+ }}
388
+
389
+ .title {{
390
+ font-size: 2rem;
391
+ }}
392
+
393
+ .info-grid {{
394
+ grid-template-columns: 1fr;
395
+ }}
396
+ }}
397
+ </style>
398
+ </head>
399
+ <body>
400
+ <div class="container">
401
+ <div class="header">
402
+ <h1 class="title">{title}</h1>
403
+ <p class="subtitle">Interactive 3D Molecular Visualization</p>
404
+ </div>
405
+
406
+ <div class="main-content">
407
+ <div class="viewer-section">
408
+ <div class="viewer-container">
409
+ {control_panel}
410
+ <div class="viewer-wrapper">
411
+ {viewer_html}
412
+ </div>
413
+ {toolbar}
414
+ </div>
415
+ </div>
416
+
417
+ <div class="info-section">
418
+ {info_cards}
419
+ <div class="card">
420
+ <h3 class="card-title">
421
+ <svg class="card-icon" viewBox="0 0 24 24">
422
+ <path d="M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M12,4A8,8 0 0,1 20,12A8,8 0 0,1 12,20A8,8 0 0,1 4,12A8,8 0 0,1 12,4M12,6A6,6 0 0,0 6,12A6,6 0 0,0 12,18A6,6 0 0,0 18,12A6,6 0 0,0 12,6M12,8A4,4 0 0,1 16,12A4,4 0 0,1 12,16A4,4 0 0,1 8,12A4,4 0 0,1 12,8Z"/>
423
+ </svg>
424
+ Interaction Guide
425
+ </h3>
426
+ <div class="interaction-hints">
427
+ <span class="hint-icon">🖱️</span> Drag to rotate |
428
+ <span class="hint-icon">🔍</span> Scroll to zoom |
429
+ <span class="hint-icon">✋</span> Right-click to pan
430
+ </div>
431
+ </div>
432
+ </div>
433
+ </div>
434
+ </div>
435
+ </body>
436
+ </html>
437
+ """
438
+
439
+ def add_3d_controls_script(self) -> str:
440
+ """Add JavaScript for 3D viewer controls."""
441
+ return """
442
+ <script>
443
+ let viewer = null;
444
+
445
+ // Wait for 3Dmol to load
446
+ function waitFor3Dmol() {
447
+ if (typeof $3Dmol !== 'undefined') {
448
+ // Find the viewer element
449
+ const viewerElements = document.querySelectorAll('[id^="3dmolviewer_"]');
450
+ if (viewerElements.length > 0) {
451
+ const viewerId = viewerElements[0].id;
452
+ viewer = window[viewerId.replace('3dmolviewer_', 'viewer_')];
453
+ if (viewer) {
454
+ console.log('3Dmol viewer found:', viewer);
455
+ }
456
+ }
457
+ } else {
458
+ setTimeout(waitFor3Dmol, 100);
459
+ }
460
+ }
461
+
462
+ // Style change function
463
+ function changeStyle() {
464
+ if (!viewer) return;
465
+ const style = document.getElementById('styleSelect').value;
466
+ const color = document.getElementById('colorSelect').value;
467
+
468
+ viewer.setStyle({}, {}); // Clear current style
469
+
470
+ if (style === 'cartoon') {
471
+ viewer.setStyle({cartoon: {color: color}});
472
+ } else if (style === 'stick') {
473
+ viewer.setStyle({stick: {color: color}});
474
+ } else if (style === 'sphere') {
475
+ viewer.setStyle({sphere: {color: color}});
476
+ } else if (style === 'line') {
477
+ viewer.setStyle({line: {color: color}});
478
+ } else if (style === 'surface') {
479
+ viewer.addSurface($3Dmol.VDW, {opacity: 0.7, color: 'white'});
480
+ }
481
+
482
+ viewer.render();
483
+ }
484
+
485
+ // Color change function
486
+ function changeColor() {
487
+ if (!viewer) return;
488
+ const style = document.getElementById('styleSelect').value;
489
+ const color = document.getElementById('colorSelect').value;
490
+
491
+ viewer.setStyle({}, {}); // Clear current style
492
+
493
+ if (style === 'cartoon') {
494
+ viewer.setStyle({cartoon: {color: color}});
495
+ } else if (style === 'stick') {
496
+ viewer.setStyle({stick: {color: color}});
497
+ } else if (style === 'sphere') {
498
+ viewer.setStyle({sphere: {color: color}});
499
+ } else if (style === 'line') {
500
+ viewer.setStyle({line: {color: color}});
501
+ }
502
+
503
+ viewer.render();
504
+ }
505
+
506
+ // Background change function
507
+ function changeBackground() {
508
+ if (!viewer) return;
509
+ const bg = document.getElementById('bgSelect').value;
510
+ viewer.setBackgroundColor(bg);
511
+ }
512
+
513
+ // Reset view function
514
+ function resetView() {
515
+ if (!viewer) return;
516
+ viewer.zoomTo();
517
+ viewer.render();
518
+ }
519
+
520
+ // Screenshot function
521
+ function downloadScreenshot() {
522
+ if (!viewer) return;
523
+ const img = viewer.pngURI();
524
+ const link = document.createElement('a');
525
+ link.download = 'protein_structure.png';
526
+ link.href = img;
527
+ link.click();
528
+ }
529
+
530
+ // Fullscreen function
531
+ function toggleFullscreen() {
532
+ const container = document.querySelector('.viewer-container');
533
+ if (!document.fullscreenElement) {
534
+ container.requestFullscreen().catch(err => {
535
+ console.log('Error attempting to enable fullscreen:', err);
536
+ });
537
+ } else {
538
+ document.exitFullscreen();
539
+ }
540
+ }
541
+
542
+ // Initialize when page loads
543
+ document.addEventListener('DOMContentLoaded', function() {
544
+ waitFor3Dmol();
545
+ });
546
+ </script>
547
+ """
548
+
549
+ def create_molecule_2d_html(
550
+ self,
551
+ molecule_image: str,
552
+ molecule_info: Dict[str, Any],
553
+ width: Optional[int] = None,
554
+ height: Optional[int] = None,
555
+ title: str = None,
556
+ ) -> str:
557
+ """Create modern HTML for 2D molecule visualization."""
558
+ if width is None:
559
+ width = self.default_width
560
+ if height is None:
561
+ height = self.default_height
562
+ if title is None:
563
+ title = f"{self.name} Visualization"
564
+
565
+ # Extract molecule properties
566
+ smiles = molecule_info.get("smiles", "N/A")
567
+ mol_weight = molecule_info.get("molecular_weight", 0)
568
+ logp = molecule_info.get("logp", 0)
569
+ hbd = molecule_info.get("hbd", 0)
570
+ hba = molecule_info.get("hba", 0)
571
+ tpsa = molecule_info.get("tpsa", 0)
572
+ rotatable_bonds = molecule_info.get("rotatable_bonds", 0)
573
+ aromatic_rings = molecule_info.get("aromatic_rings", 0)
574
+ heavy_atoms = molecule_info.get("heavy_atoms", 0)
575
+ formal_charge = molecule_info.get("formal_charge", 0)
576
+
577
+ return f"""
578
+ <!DOCTYPE html>
579
+ <html>
580
+ <head>
581
+ <meta charset="utf-8">
582
+ <title>{title}</title>
583
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
584
+ <style>
585
+ * {{
586
+ margin: 0;
587
+ padding: 0;
588
+ box-sizing: border-box;
589
+ }}
590
+
591
+ body {{
592
+ font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
593
+ background: linear-gradient(135deg, #f0f4f8 0%, #ffffff 100%);
594
+ min-height: 100vh;
595
+ color: #2c3e50;
596
+ line-height: 1.6;
597
+ }}
598
+
599
+ .container {{
600
+ max-width: 1200px;
601
+ margin: 0 auto;
602
+ padding: 20px;
603
+ }}
604
+
605
+ .header {{
606
+ text-align: center;
607
+ margin-bottom: 30px;
608
+ }}
609
+
610
+ .title {{
611
+ font-size: 2.5rem;
612
+ font-weight: 300;
613
+ color: #4A90E2;
614
+ margin-bottom: 10px;
615
+ text-shadow: 0 2px 4px rgba(0,0,0,0.1);
616
+ }}
617
+
618
+ .subtitle {{
619
+ font-size: 1.1rem;
620
+ color: #7f8c8d;
621
+ font-weight: 300;
622
+ }}
623
+
624
+ .main-content {{
625
+ display: grid;
626
+ grid-template-columns: 1fr 1fr;
627
+ gap: 30px;
628
+ margin-bottom: 30px;
629
+ }}
630
+
631
+ .molecule-section {{
632
+ background: white;
633
+ border-radius: 16px;
634
+ box-shadow: 0 8px 32px rgba(0,0,0,0.1);
635
+ padding: 30px;
636
+ text-align: center;
637
+ }}
638
+
639
+ .molecule-image {{
640
+ margin: 20px 0;
641
+ padding: 20px;
642
+ background: linear-gradient(135deg, #f8f9fa 0%, #ffffff 100%);
643
+ border-radius: 12px;
644
+ box-shadow: 0 4px 12px rgba(0,0,0,0.1);
645
+ }}
646
+
647
+ .molecule-image img {{
648
+ max-width: 100%;
649
+ height: auto;
650
+ border-radius: 8px;
651
+ }}
652
+
653
+ .properties-section {{
654
+ display: flex;
655
+ flex-direction: column;
656
+ gap: 20px;
657
+ }}
658
+
659
+ .card {{
660
+ background: white;
661
+ border-radius: 12px;
662
+ box-shadow: 0 4px 6px rgba(0,0,0,0.1);
663
+ padding: 20px;
664
+ transition: transform 0.2s;
665
+ }}
666
+
667
+ .card:hover {{
668
+ transform: translateY(-2px);
669
+ box-shadow: 0 8px 16px rgba(0,0,0,0.15);
670
+ }}
671
+
672
+ .card-title {{
673
+ font-size: 1.2rem;
674
+ font-weight: 600;
675
+ color: #2c3e50;
676
+ margin-bottom: 15px;
677
+ display: flex;
678
+ align-items: center;
679
+ gap: 8px;
680
+ }}
681
+
682
+ .card-icon {{
683
+ width: 20px;
684
+ height: 20px;
685
+ fill: #4A90E2;
686
+ }}
687
+
688
+ .property-grid {{
689
+ display: grid;
690
+ grid-template-columns: 1fr 1fr;
691
+ gap: 12px;
692
+ }}
693
+
694
+ .property-item {{
695
+ display: flex;
696
+ justify-content: space-between;
697
+ align-items: center;
698
+ padding: 12px 16px;
699
+ background: linear-gradient(135deg, #f8f9fa 0%, #ffffff 100%);
700
+ border-radius: 8px;
701
+ border-left: 4px solid #4A90E2;
702
+ transition: all 0.2s;
703
+ }}
704
+
705
+ .property-item:hover {{
706
+ background: linear-gradient(135deg, #e3f2fd 0%, #f8f9fa 100%);
707
+ transform: translateX(4px);
708
+ }}
709
+
710
+ .property-label {{
711
+ font-weight: 500;
712
+ color: #7f8c8d;
713
+ font-size: 0.9rem;
714
+ }}
715
+
716
+ .property-value {{
717
+ font-weight: 600;
718
+ color: #2c3e50;
719
+ font-size: 1rem;
720
+ }}
721
+
722
+ .property-unit {{
723
+ font-size: 0.8rem;
724
+ color: #95a5a6;
725
+ margin-left: 4px;
726
+ }}
727
+
728
+ .smiles-display {{
729
+ background: linear-gradient(135deg, #e8f5e8 0%, #f0f8f0 100%);
730
+ border-radius: 8px;
731
+ padding: 15px;
732
+ font-family: 'Courier New', monospace;
733
+ font-size: 0.9rem;
734
+ color: #2c3e50;
735
+ border-left: 4px solid #50C878;
736
+ word-break: break-all;
737
+ }}
738
+
739
+ .download-section {{
740
+ text-align: center;
741
+ margin-top: 20px;
742
+ }}
743
+
744
+ .btn {{
745
+ background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
746
+ border: none;
747
+ border-radius: 8px;
748
+ color: white;
749
+ padding: 12px 24px;
750
+ cursor: pointer;
751
+ font-size: 1rem;
752
+ font-weight: 500;
753
+ transition: all 0.2s;
754
+ box-shadow: 0 2px 8px rgba(0,0,0,0.15);
755
+ margin: 0 10px;
756
+ }}
757
+
758
+ .btn:hover {{
759
+ transform: translateY(-2px);
760
+ box-shadow: 0 4px 12px rgba(0,0,0,0.2);
761
+ }}
762
+
763
+ .btn-secondary {{
764
+ background: linear-gradient(135deg, #50C878 0%, #4A90E2 100%);
765
+ }}
766
+
767
+ @media (max-width: 768px) {{
768
+ .main-content {{
769
+ grid-template-columns: 1fr;
770
+ }}
771
+
772
+ .property-grid {{
773
+ grid-template-columns: 1fr;
774
+ }}
775
+
776
+ .title {{
777
+ font-size: 2rem;
778
+ }}
779
+
780
+ .molecule-section {{
781
+ padding: 20px;
782
+ }}
783
+ }}
784
+ </style>
785
+ </head>
786
+ <body>
787
+ <div class="container">
788
+ <div class="header">
789
+ <h1 class="title">{title}</h1>
790
+ <p class="subtitle">2D Molecular Structure Analysis</p>
791
+ </div>
792
+
793
+ <div class="main-content">
794
+ <div class="molecule-section">
795
+ <h3 style="color: #2c3e50; margin-bottom: 20px;">Molecular Structure</h3>
796
+ <div class="molecule-image">
797
+ <img src="data:image/png;base64,{molecule_image}"
798
+ alt="2D Molecular Structure"
799
+ style="max-width: 100%; height: auto;">
800
+ </div>
801
+ <div class="download-section">
802
+ <button class="btn" onclick="downloadImage()">Download PNG</button>
803
+ <button class="btn btn-secondary" onclick="copySMILES()">Copy SMILES</button>
804
+ </div>
805
+ </div>
806
+
807
+ <div class="properties-section">
808
+ <div class="card">
809
+ <h3 class="card-title">
810
+ <svg class="card-icon" viewBox="0 0 24 24">
811
+ <path d="M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M12,4A8,8 0 0,1 20,12A8,8 0 0,1 12,20A8,8 0 0,1 4,12A8,8 0 0,1 12,4M12,6A6,6 0 0,0 6,12A6,6 0 0,0 12,18A6,6 0 0,0 18,12A6,6 0 0,0 12,6M12,8A4,4 0 0,1 16,12A4,4 0 0,1 12,16A4,4 0 0,1 8,12A4,4 0 0,1 12,8Z"/>
812
+ </svg>
813
+ Basic Properties
814
+ </h3>
815
+ <div class="property-grid">
816
+ <div class="property-item">
817
+ <span class="property-label">Molecular Weight</span>
818
+ <span class="property-value">{mol_weight:.2f}<span class="property-unit">Da</span></span>
819
+ </div>
820
+ <div class="property-item">
821
+ <span class="property-label">Heavy Atoms</span>
822
+ <span class="property-value">{heavy_atoms}</span>
823
+ </div>
824
+ <div class="property-item">
825
+ <span class="property-label">Formal Charge</span>
826
+ <span class="property-value">{formal_charge}</span>
827
+ </div>
828
+ <div class="property-item">
829
+ <span class="property-label">Aromatic Rings</span>
830
+ <span class="property-value">{aromatic_rings}</span>
831
+ </div>
832
+ </div>
833
+ </div>
834
+
835
+ <div class="card">
836
+ <h3 class="card-title">
837
+ <svg class="card-icon" viewBox="0 0 24 24">
838
+ <path d="M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M12,4A8,8 0 0,1 20,12A8,8 0 0,1 12,20A8,8 0 0,1 4,12A8,8 0 0,1 12,4M12,6A6,6 0 0,0 6,12A6,6 0 0,0 12,18A6,6 0 0,0 18,12A6,6 0 0,0 12,6M12,8A4,4 0 0,1 16,12A4,4 0 0,1 12,16A4,4 0 0,1 8,12A4,4 0 0,1 12,8Z"/>
839
+ </svg>
840
+ Drug Properties
841
+ </h3>
842
+ <div class="property-grid">
843
+ <div class="property-item">
844
+ <span class="property-label">LogP</span>
845
+ <span class="property-value">{logp:.2f}</span>
846
+ </div>
847
+ <div class="property-item">
848
+ <span class="property-label">TPSA</span>
849
+ <span class="property-value">{tpsa:.2f}<span class="property-unit">Ų</span></span>
850
+ </div>
851
+ <div class="property-item">
852
+ <span class="property-label">H-Bond Donors</span>
853
+ <span class="property-value">{hbd}</span>
854
+ </div>
855
+ <div class="property-item">
856
+ <span class="property-label">H-Bond Acceptors</span>
857
+ <span class="property-value">{hba}</span>
858
+ </div>
859
+ <div class="property-item">
860
+ <span class="property-label">Rotatable Bonds</span>
861
+ <span class="property-value">{rotatable_bonds}</span>
862
+ </div>
863
+ </div>
864
+ </div>
865
+
866
+ <div class="card">
867
+ <h3 class="card-title">
868
+ <svg class="card-icon" viewBox="0 0 24 24">
869
+ <path d="M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M12,4A8,8 0 0,1 20,12A8,8 0 0,1 12,20A8,8 0 0,1 4,12A8,8 0 0,1 12,4M12,6A6,6 0 0,0 6,12A6,6 0 0,0 12,18A6,6 0 0,0 18,12A6,6 0 0,0 12,6M12,8A4,4 0 0,1 16,12A4,4 0 0,1 12,16A4,4 0 0,1 8,12A4,4 0 0,1 12,8Z"/>
870
+ </svg>
871
+ SMILES Notation
872
+ </h3>
873
+ <div class="smiles-display">{smiles}</div>
874
+ </div>
875
+ </div>
876
+ </div>
877
+ </div>
878
+
879
+ <script>
880
+ function downloadImage() {{
881
+ const img = document.querySelector('.molecule-image img');
882
+ const link = document.createElement('a');
883
+ link.download = 'molecule_structure.png';
884
+ link.href = img.src;
885
+ link.click();
886
+ }}
887
+
888
+ function copySMILES() {{
889
+ const smiles = '{smiles}';
890
+ navigator.clipboard.writeText(smiles).then(function() {{
891
+ alert('SMILES copied to clipboard!');
892
+ }});
893
+ }}
894
+ </script>
895
+ </body>
896
+ </html>
897
+ """