tooluniverse

• tooluniverse package
  • ADMETAITool
    • ADMETAITool.__init__()
    • ADMETAITool._predict()
    • ADMETAITool.run()
  • AgenticTool
    • AgenticTool.__init__()
    • AgenticTool._format_prompt()
    • AgenticTool._get_global_fallback_chain()
    • AgenticTool._try_api()
    • AgenticTool._try_initialize_api()
    • AgenticTool._validate_arguments()
    • AgenticTool._validate_model_config()
    • AgenticTool.estimate_token_usage()
    • AgenticTool.get_availability_status()
    • AgenticTool.get_input_arguments()
    • AgenticTool.get_model_info()
    • AgenticTool.get_prompt_preview()
    • AgenticTool.get_prompt_template()
    • AgenticTool.has_any_api_keys()
    • AgenticTool.is_available()
    • AgenticTool.retry_initialization()
    • AgenticTool.run()
    • AgenticTool.validate_configuration()
  • AlphaFoldRESTTool
    • AlphaFoldRESTTool.__init__()
    • AlphaFoldRESTTool._build_url()
    • AlphaFoldRESTTool._make_request()
    • AlphaFoldRESTTool.run()
  • BaseTool
    • BaseTool.__init__()
    • BaseTool._apply_defaults()
    • BaseTool.check_function_call()
    • BaseTool.get_default_config_file()
    • BaseTool.get_required_parameters()
    • BaseTool.load_defaults_from_file()
    • BaseTool.run()
  • ChEMBLTool
    • ChEMBLTool.__init__()
    • ChEMBLTool._search_similar_molecules()
    • ChEMBLTool.get_chembl_id_by_name()
    • ChEMBLTool.get_chembl_smiles_pref_name_id_by_name()
    • ChEMBLTool.get_smiles_pref_name_by_chembl_id()
    • ChEMBLTool.run()
  • ClinicalTrialsDetailsTool
    • ClinicalTrialsDetailsTool.__init__()
    • ClinicalTrialsDetailsTool._extract_outcomes_from_output()
    • ClinicalTrialsDetailsTool._extract_safety_from_output()
    • ClinicalTrialsDetailsTool._remove_empty_values()
    • ClinicalTrialsDetailsTool._simplify_output()
    • ClinicalTrialsDetailsTool.run()
  • ClinicalTrialsSearchTool
    • ClinicalTrialsSearchTool.__init__()
    • ClinicalTrialsSearchTool._simplify_output()
    • ClinicalTrialsSearchTool.run()
  • ComposeTool
    • ComposeTool.__init__()
    • ComposeTool._call_tool()
    • ComposeTool._discover_tool_dependencies()
    • ComposeTool._execute_from_file()
    • ComposeTool._execute_inline_code()
    • ComposeTool._get_tool_category_mapping()
    • ComposeTool._load_code_from_file()
    • ComposeTool._load_missing_dependencies()
    • ComposeTool.run()
  • DatasetTool
    • DatasetTool.__init__()
    • DatasetTool._drugbank_filter()
    • DatasetTool._drugbank_search()
    • DatasetTool._load_dataset()
    • DatasetTool.get_dataset_info()
    • DatasetTool.run()
  • DiseaseTargetScoreTool
    • DiseaseTargetScoreTool.__init__()
    • DiseaseTargetScoreTool.run()
  • EFOTool
    • EFOTool.__init__()
    • EFOTool._search()
    • EFOTool.run()
  • EmbeddingDatabase
    • EmbeddingDatabase.__init__()
    • EmbeddingDatabase._add_documents()
    • EmbeddingDatabase._create_from_documents()
    • EmbeddingDatabase._database_exists()
    • EmbeddingDatabase._generate_embeddings()
    • EmbeddingDatabase._get_database_info()
    • EmbeddingDatabase._init_azure_client()
    • EmbeddingDatabase._init_database()
    • EmbeddingDatabase._init_openai_client()
    • EmbeddingDatabase._load_database()
    • EmbeddingDatabase._matches_filters()
    • EmbeddingDatabase._search()
    • EmbeddingDatabase._substitute_env_vars()
    • EmbeddingDatabase.run()
  • EmbeddingSync
    • EmbeddingSync.__init__()
    • EmbeddingSync._download_from_huggingface()
    • EmbeddingSync._generate_readme()
    • EmbeddingSync._get_database_info()
    • EmbeddingSync._local_database_exists()
    • EmbeddingSync._merge_databases()
    • EmbeddingSync._rename_database_in_db()
    • EmbeddingSync._upload_to_huggingface()
    • EmbeddingSync.run()
  • EuropePMCTool
    • EuropePMCTool.__init__()
    • EuropePMCTool._search()
    • EuropePMCTool.run()
  • FDACountAdditiveReactionsTool
    • FDACountAdditiveReactionsTool.__init__()
    • FDACountAdditiveReactionsTool.run()
  • FDADrugAdverseEventTool
    • FDADrugAdverseEventTool.__init__()
    • FDADrugAdverseEventTool._map_value()
    • FDADrugAdverseEventTool._post_process()
    • FDADrugAdverseEventTool._search()
    • FDADrugAdverseEventTool.run()
    • FDADrugAdverseEventTool.validate_enum_arguments()
  • FDADrugLabelGetDrugGenericNameTool
    • FDADrugLabelGetDrugGenericNameTool.__init__()
    • FDADrugLabelGetDrugGenericNameTool.run()
  • FDADrugLabelSearchIDTool
    • FDADrugLabelSearchIDTool.__init__()
    • FDADrugLabelSearchIDTool.run()
  • FDADrugLabelSearchTool
    • FDADrugLabelSearchTool.__init__()
    • FDADrugLabelSearchTool.run()
  • FDADrugLabelTool
    • FDADrugLabelTool.__init__()
  • GWASAssociationByID
    • GWASAssociationByID.__init__()
    • GWASAssociationByID.run()
  • GWASAssociationSearch
    • GWASAssociationSearch.__init__()
    • GWASAssociationSearch.run()
  • GWASAssociationsForSNP
    • GWASAssociationsForSNP.__init__()
    • GWASAssociationsForSNP.run()
  • GWASAssociationsForStudy
    • GWASAssociationsForStudy.__init__()
    • GWASAssociationsForStudy.run()
  • GWASAssociationsForTrait
    • GWASAssociationsForTrait.__init__()
    • GWASAssociationsForTrait.run()
  • GWASSNPByID
    • GWASSNPByID.__init__()
    • GWASSNPByID.run()
  • GWASSNPSearch
    • GWASSNPSearch.__init__()
    • GWASSNPSearch.run()
  • GWASSNPsForGene
    • GWASSNPsForGene.__init__()
    • GWASSNPsForGene.run()
  • GWASStudiesForTrait
    • GWASStudiesForTrait.__init__()
    • GWASStudiesForTrait.run()
  • GWASStudyByID
    • GWASStudyByID.__init__()
    • GWASStudyByID.run()
  • GWASStudySearch
    • GWASStudySearch.__init__()
    • GWASStudySearch.run()
  • GWASVariantsForTrait
    • GWASVariantsForTrait.__init__()
    • GWASVariantsForTrait.run()
  • GetSPLBySetIDTool
    • GetSPLBySetIDTool.__init__()
    • GetSPLBySetIDTool.run()
  • HPAGetGeneJSONTool
    • HPAGetGeneJSONTool.run()
  • HPAGetGeneXMLTool
    • HPAGetGeneXMLTool.run()
  • MCPAutoLoaderTool
    • MCPAutoLoaderTool.__del__()
    • MCPAutoLoaderTool.__init__()
    • MCPAutoLoaderTool.auto_load_and_register()
    • MCPAutoLoaderTool.call_tool()
    • MCPAutoLoaderTool.discover_tools()
    • MCPAutoLoaderTool.generate_proxy_tool_configs()
    • MCPAutoLoaderTool.register_tools_in_engine()
    • MCPAutoLoaderTool.run()
  • MCPClientTool
    • MCPClientTool.__init__()
    • MCPClientTool._run_call_tool()
    • MCPClientTool._run_get_prompt()
    • MCPClientTool._run_list_prompts()
    • MCPClientTool._run_list_resources()
    • MCPClientTool._run_list_tools()
    • MCPClientTool._run_read_resource()
    • MCPClientTool.call_tool()
    • MCPClientTool.get_prompt()
    • MCPClientTool.list_prompts()
    • MCPClientTool.list_resources()
    • MCPClientTool.list_tools()
    • MCPClientTool.read_resource()
    • MCPClientTool.run()
  • MedlinePlusRESTTool
    • MedlinePlusRESTTool.__init__()
    • MedlinePlusRESTTool._build_url()
    • MedlinePlusRESTTool._extract_text_content()
    • MedlinePlusRESTTool._format_response()
    • MedlinePlusRESTTool.connect_lookup_by_code()
    • MedlinePlusRESTTool.get_genetics_condition_by_name()
    • MedlinePlusRESTTool.get_genetics_gene_by_name()
    • MedlinePlusRESTTool.get_genetics_index()
    • MedlinePlusRESTTool.run()
    • MedlinePlusRESTTool.search_topics_by_keyword()
  • MonarchDiseasesForMultiplePhenoTool
    • MonarchDiseasesForMultiplePhenoTool.__init__()
    • MonarchDiseasesForMultiplePhenoTool.run()
  • MonarchTool
    • MonarchTool.__init__()
    • MonarchTool.run()
  • ODPHPItemList
    • ODPHPItemList.run()
  • ODPHPMyHealthfinder
    • ODPHPMyHealthfinder.run()
  • ODPHPOutlinkFetch
    • ODPHPOutlinkFetch.__init__()
    • ODPHPOutlinkFetch._extract_text()
    • ODPHPOutlinkFetch.run()
  • ODPHPTopicSearch
    • ODPHPTopicSearch.run()
  • OpentargetGeneticsTool
    • OpentargetGeneticsTool.__init__()
  • OpentargetTool
    • OpentargetTool.__init__()
    • OpentargetTool.run()
  • OpentargetToolDrugNameMatch
    • OpentargetToolDrugNameMatch.__init__()
    • OpentargetToolDrugNameMatch.run()
  • PackageTool
    • PackageTool.__init__()
    • PackageTool._get_installation_instructions()
    • PackageTool._get_local_info()
    • PackageTool._get_pypi_info()
    • PackageTool._get_quick_start_guide()
    • PackageTool._get_usage_example()
    • PackageTool.run()
  • PubChemRESTTool
    • PubChemRESTTool.__init__()
    • PubChemRESTTool._build_url()
    • PubChemRESTTool.run()
  • PubTatorTool
    • PubTatorTool.__init__()
    • PubTatorTool._compose_url()
    • PubTatorTool._filter_search_results()
    • PubTatorTool._query_params()
    • PubTatorTool.run()
  • RCSBTool
    • RCSBTool.__init__()
    • RCSBTool.prepare_input_ids()
    • RCSBTool.run()
    • RCSBTool.validate_params()
  • ReactomeRESTTool
    • ReactomeRESTTool.__init__()
    • ReactomeRESTTool._build_url()
    • ReactomeRESTTool.run()
  • SMCP
    • SMCP.__init__()
    • SMCP._add_search_tools()
    • SMCP._add_utility_tools()
    • SMCP._create_mcp_tool_from_tooluniverse()
    • SMCP._custom_handle_request()
    • SMCP._expose_tooluniverse_tools()
    • SMCP._get_valid_categories()
    • SMCP._handle_tools_find()
    • SMCP._init_tool_finder()
    • SMCP._perform_tool_search()
    • SMCP._register_custom_mcp_methods()
    • SMCP._select_search_tool()
    • SMCP._setup_smcp_tools()
    • SMCP.add_custom_tool()
    • SMCP.close()
    • SMCP.run_simple()
  • SearchSPLTool
    • SearchSPLTool.__init__()
    • SearchSPLTool.run()
  • SemanticScholarTool
    • SemanticScholarTool.__init__()
    • SemanticScholarTool._search()
    • SemanticScholarTool.run()
  • ToolFinderEmbedding
    • ToolFinderEmbedding.rag_model_name
    • ToolFinderEmbedding.rag_model
    • ToolFinderEmbedding.tool_desc_embedding
    • ToolFinderEmbedding.tool_name
    • ToolFinderEmbedding.tool_embedding_path
    • ToolFinderEmbedding.special_tools_name
    • ToolFinderEmbedding.tooluniverse
    • ToolFinderEmbedding.__init__()
    • ToolFinderEmbedding.find_tools()
    • ToolFinderEmbedding.load_rag_model()
    • ToolFinderEmbedding.load_tool_desc_embedding()
    • ToolFinderEmbedding.rag_infer()
    • ToolFinderEmbedding.run()
  • ToolFinderKeyword
    • ToolFinderKeyword.STEMMING_RULES
    • ToolFinderKeyword.STOP_WORDS
    • ToolFinderKeyword.__init__()
    • ToolFinderKeyword._apply_stemming()
    • ToolFinderKeyword._build_tool_index()
    • ToolFinderKeyword._calculate_exact_match_bonus()
    • ToolFinderKeyword._calculate_tfidf_score()
    • ToolFinderKeyword._extract_parameter_text()
    • ToolFinderKeyword._extract_phrases()
    • ToolFinderKeyword._run_json_search()
    • ToolFinderKeyword._tokenize_and_normalize()
    • ToolFinderKeyword.find_tools()
    • ToolFinderKeyword.run()
  • ToolFinderLLM
    • ToolFinderLLM.__init__()
    • ToolFinderLLM._format_as_json()
    • ToolFinderLLM._format_tools_for_prompt()
    • ToolFinderLLM._get_available_tools()
    • ToolFinderLLM._get_tool_selection_prompt()
    • ToolFinderLLM._init_agentic_tool()
    • ToolFinderLLM._prefilter_tools_by_keywords()
    • ToolFinderLLM.clear_cache()
    • ToolFinderLLM.find_tools()
    • ToolFinderLLM.find_tools_legacy()
    • ToolFinderLLM.find_tools_llm()
    • ToolFinderLLM.get_tool_stats()
    • ToolFinderLLM.run()
  • ToolUniverse
    • ToolUniverse.all_tools
    • ToolUniverse.all_tool_dict
    • ToolUniverse.tool_category_dicts
    • ToolUniverse.tool_files
    • ToolUniverse.callable_functions
    • ToolUniverse.__init__()
    • ToolUniverse._check_api_key_requirements()
    • ToolUniverse._create_hook_config_from_type()
    • ToolUniverse._filter_and_deduplicate_tools()
    • ToolUniverse._get_api_key()
    • ToolUniverse._load_auto_discovered_configs()
    • ToolUniverse._load_tool_names_from_file()
    • ToolUniverse._load_tools_from_mcp_server()
    • ToolUniverse._process_mcp_auto_loaders()
    • ToolUniverse._scan_all_json_files()
    • ToolUniverse._scan_predefined_files()
    • ToolUniverse.call_id_gen()
    • ToolUniverse.check_function_call()
    • ToolUniverse.discover_mcp_tools()
    • ToolUniverse.export_tool_names()
    • ToolUniverse.extract_function_call_json()
    • ToolUniverse.filter_tool_lists()
    • ToolUniverse.find_tools_by_pattern()
    • ToolUniverse.force_full_discovery()
    • ToolUniverse.generate_env_template()
    • ToolUniverse.get_available_tools()
    • ToolUniverse.get_lazy_loading_status()
    • ToolUniverse.get_one_tool_by_one_name()
    • ToolUniverse.get_tool_by_name()
    • ToolUniverse.get_tool_description()
    • ToolUniverse.get_tool_specification_by_names()
    • ToolUniverse.get_tool_type_by_name()
    • ToolUniverse.get_tool_types()
    • ToolUniverse.init_tool()
    • ToolUniverse.list_built_in_tools()
    • ToolUniverse.list_mcp_connections()
    • ToolUniverse.load_mcp_tools()
    • ToolUniverse.load_tools()
    • ToolUniverse.load_tools_from_names_list()
    • ToolUniverse.prepare_one_tool_prompt()
    • ToolUniverse.prepare_tool_examples()
    • ToolUniverse.prepare_tool_prompts()
    • ToolUniverse.refresh_tool_name_desc()
    • ToolUniverse.register_custom_tool()
    • ToolUniverse.remove_keys()
    • ToolUniverse.return_all_loaded_tools()
    • ToolUniverse.run()
    • ToolUniverse.run_one_function()
    • ToolUniverse.select_tools()
    • ToolUniverse.toggle_hooks()
    • ToolUniverse.tool_specification()
    • ToolUniverse.tool_to_str()
  • URLHTMLTagTool
    • URLHTMLTagTool.__init__()
    • URLHTMLTagTool.run()
  • URLToPDFTextTool
    • URLToPDFTextTool.__init__()
    • URLToPDFTextTool._ensure_playwright_browsers()
    • URLToPDFTextTool.run()
  • USPTOOpenDataPortalTool
    • USPTOOpenDataPortalTool.__init__()
    • USPTOOpenDataPortalTool.assign_by_path()
    • USPTOOpenDataPortalTool.get_by_path()
    • USPTOOpenDataPortalTool.prune_item()
    • USPTOOpenDataPortalTool.run()
  • UniProtRESTTool
    • UniProtRESTTool.__init__()
    • UniProtRESTTool._build_url()
    • UniProtRESTTool._extract_data()
    • UniProtRESTTool.get_disease_variants_by_accession()
    • UniProtRESTTool.get_entry_by_accession()
    • UniProtRESTTool.get_function_by_accession()
    • UniProtRESTTool.get_names_taxonomy_by_accession()
    • UniProtRESTTool.get_ptm_processing_by_accession()
    • UniProtRESTTool.get_sequence_isoforms_by_accession()
    • UniProtRESTTool.get_subcellular_location_by_accession()
    • UniProtRESTTool.run()
  • XMLDatasetTool
    • XMLDatasetTool.__init__()
    • XMLDatasetTool._extract_field_value()
    • XMLDatasetTool._extract_record_data()
    • XMLDatasetTool._filter()
    • XMLDatasetTool._find_matches()
    • XMLDatasetTool._get_all_records_data()
    • XMLDatasetTool._get_dataset_path()
    • XMLDatasetTool._get_filter_description()
    • XMLDatasetTool._get_filter_function()
    • XMLDatasetTool._get_searchable_value()
    • XMLDatasetTool._is_match()
    • XMLDatasetTool._load_dataset()
    • XMLDatasetTool._search()
    • XMLDatasetTool.get_dataset_info()
    • XMLDatasetTool.run()
  • create_smcp_server()
  • get_tool_registry()
  • register_tool()
  • Subpackages
    • tooluniverse.data package
      • Submodules
        • tooluniverse.data.fda_drugs_with_brand_generic_names_for_tool module
  • Submodules
    • tooluniverse.agentic_tool module
      • AgenticTool
        • AgenticTool.__init__()
        • AgenticTool._format_prompt()
        • AgenticTool._get_global_fallback_chain()
        • AgenticTool._try_api()
        • AgenticTool._try_initialize_api()
        • AgenticTool._validate_arguments()
        • AgenticTool._validate_model_config()
        • AgenticTool.estimate_token_usage()
        • AgenticTool.get_availability_status()
        • AgenticTool.get_input_arguments()
        • AgenticTool.get_model_info()
        • AgenticTool.get_prompt_preview()
        • AgenticTool.get_prompt_template()
        • AgenticTool.has_any_api_keys()
        • AgenticTool.is_available()
        • AgenticTool.retry_initialization()
        • AgenticTool.run()
        • AgenticTool.validate_configuration()
    • tooluniverse.base_tool module
      • AuthenticationError
      • BaseTool
        • BaseTool.__init__()
        • BaseTool._apply_defaults()
        • BaseTool.check_function_call()
        • BaseTool.get_default_config_file()
        • BaseTool.get_required_parameters()
        • BaseTool.load_defaults_from_file()
        • BaseTool.run()
      • RateLimitError
      • ToolExecutionError
      • ValidationError
    • tooluniverse.chem_tool module
      • ChEMBLTool
        • ChEMBLTool.__init__()
        • ChEMBLTool._search_similar_molecules()
        • ChEMBLTool.get_chembl_id_by_name()
        • ChEMBLTool.get_chembl_smiles_pref_name_id_by_name()
        • ChEMBLTool.get_smiles_pref_name_by_chembl_id()
        • ChEMBLTool.run()
    • tooluniverse.ctg_tool module
      • ClinicalTrialsDetailsTool
        • ClinicalTrialsDetailsTool.__init__()
        • ClinicalTrialsDetailsTool._extract_outcomes_from_output()
        • ClinicalTrialsDetailsTool._extract_safety_from_output()
        • ClinicalTrialsDetailsTool._remove_empty_values()
        • ClinicalTrialsDetailsTool._simplify_output()
        • ClinicalTrialsDetailsTool.run()
      • ClinicalTrialsSearchTool
        • ClinicalTrialsSearchTool.__init__()
        • ClinicalTrialsSearchTool._simplify_output()
        • ClinicalTrialsSearchTool.run()
      • ClinicalTrialsTool
        • ClinicalTrialsTool.__init__()
        • ClinicalTrialsTool._format_endpoint_url()
        • ClinicalTrialsTool._map_param_names()
        • ClinicalTrialsTool._prepare_api_params()
        • ClinicalTrialsTool.run()
    • tooluniverse.dataset_tool module
      • DatasetTool
        • DatasetTool.__init__()
        • DatasetTool._drugbank_filter()
        • DatasetTool._drugbank_search()
        • DatasetTool._load_dataset()
        • DatasetTool.get_dataset_info()
        • DatasetTool.run()
    • tooluniverse.efo_tool module
      • EFOTool
        • EFOTool.__init__()
        • EFOTool._search()
        • EFOTool.run()
    • tooluniverse.enrichr_tool module
      • EnrichrTool
        • EnrichrTool.__init__()
        • EnrichrTool.build_graph()
        • EnrichrTool.enrichr_api()
        • EnrichrTool.get_enrichment_results()
        • EnrichrTool.get_official_gene_name()
        • EnrichrTool.rank_paths_by_weight()
        • EnrichrTool.rank_paths_to_term()
        • EnrichrTool.run()
        • EnrichrTool.submit_gene_list()
    • tooluniverse.europe_pmc_tool module
      • EuropePMCTool
        • EuropePMCTool.__init__()
        • EuropePMCTool._search()
        • EuropePMCTool.run()
    • tooluniverse.execute_function module
      • ToolUniverse
        • ToolUniverse.all_tools
        • ToolUniverse.all_tool_dict
        • ToolUniverse.tool_category_dicts
        • ToolUniverse.tool_files
        • ToolUniverse.callable_functions
        • ToolUniverse.__init__()
        • ToolUniverse._check_api_key_requirements()
        • ToolUniverse._create_hook_config_from_type()
        • ToolUniverse._filter_and_deduplicate_tools()
        • ToolUniverse._get_api_key()
        • ToolUniverse._load_auto_discovered_configs()
        • ToolUniverse._load_tool_names_from_file()
        • ToolUniverse._load_tools_from_mcp_server()
        • ToolUniverse._process_mcp_auto_loaders()
        • ToolUniverse._scan_all_json_files()
        • ToolUniverse._scan_predefined_files()
        • ToolUniverse.call_id_gen()
        • ToolUniverse.check_function_call()
        • ToolUniverse.discover_mcp_tools()
        • ToolUniverse.export_tool_names()
        • ToolUniverse.extract_function_call_json()
        • ToolUniverse.filter_tool_lists()
        • ToolUniverse.find_tools_by_pattern()
        • ToolUniverse.force_full_discovery()
        • ToolUniverse.generate_env_template()
        • ToolUniverse.get_available_tools()
        • ToolUniverse.get_lazy_loading_status()
        • ToolUniverse.get_one_tool_by_one_name()
        • ToolUniverse.get_tool_by_name()
        • ToolUniverse.get_tool_description()
        • ToolUniverse.get_tool_specification_by_names()
        • ToolUniverse.get_tool_type_by_name()
        • ToolUniverse.get_tool_types()
        • ToolUniverse.init_tool()
        • ToolUniverse.list_built_in_tools()
        • ToolUniverse.list_mcp_connections()
        • ToolUniverse.load_mcp_tools()
        • ToolUniverse.load_tools()
        • ToolUniverse.load_tools_from_names_list()
        • ToolUniverse.prepare_one_tool_prompt()
        • ToolUniverse.prepare_tool_examples()
        • ToolUniverse.prepare_tool_prompts()
        • ToolUniverse.refresh_tool_name_desc()
        • ToolUniverse.register_custom_tool()
        • ToolUniverse.remove_keys()
        • ToolUniverse.return_all_loaded_tools()
        • ToolUniverse.run()
        • ToolUniverse.run_one_function()
        • ToolUniverse.select_tools()
        • ToolUniverse.toggle_hooks()
        • ToolUniverse.tool_specification()
        • ToolUniverse.tool_to_str()
    • tooluniverse.graphql_tool module
      • DiseaseTargetScoreTool
        • DiseaseTargetScoreTool.__init__()
        • DiseaseTargetScoreTool.run()
      • GraphQLTool
        • GraphQLTool.__init__()
        • GraphQLTool.run()
      • OpentargetGeneticsTool
        • OpentargetGeneticsTool.__init__()
      • OpentargetTool
        • OpentargetTool.__init__()
        • OpentargetTool.run()
      • OpentargetToolDrugNameMatch
        • OpentargetToolDrugNameMatch.__init__()
        • OpentargetToolDrugNameMatch.run()
      • execute_query()
      • remove_none_and_empty_values()
      • validate_query()
    • tooluniverse.humanbase_tool module
      • HumanBaseTool
        • HumanBaseTool.__init__()
        • HumanBaseTool._convert_to_string()
        • HumanBaseTool._get_current_timestamp()
        • HumanBaseTool.get_entrez_ids()
        • HumanBaseTool.get_official_gene_name()
        • HumanBaseTool.humanbase_ppi_retrieve()
        • HumanBaseTool.run()
    • tooluniverse.mcp_client_tool module
      • BaseMCPClient
        • BaseMCPClient.__init__()
        • BaseMCPClient._close_session()
        • BaseMCPClient._ensure_session()
        • BaseMCPClient._get_mcp_endpoint()
        • BaseMCPClient._initialize_mcp_session()
        • BaseMCPClient._make_mcp_request()
        • BaseMCPClient._run_with_cleanup()
      • MCPAutoLoaderTool
        • MCPAutoLoaderTool.__del__()
        • MCPAutoLoaderTool.__init__()
        • MCPAutoLoaderTool.auto_load_and_register()
        • MCPAutoLoaderTool.call_tool()
        • MCPAutoLoaderTool.discover_tools()
        • MCPAutoLoaderTool.generate_proxy_tool_configs()
        • MCPAutoLoaderTool.register_tools_in_engine()
        • MCPAutoLoaderTool.run()
      • MCPClientTool
        • MCPClientTool.__init__()
        • MCPClientTool._run_call_tool()
        • MCPClientTool._run_get_prompt()
        • MCPClientTool._run_list_prompts()
        • MCPClientTool._run_list_resources()
        • MCPClientTool._run_list_tools()
        • MCPClientTool._run_read_resource()
        • MCPClientTool.call_tool()
        • MCPClientTool.get_prompt()
        • MCPClientTool.list_prompts()
        • MCPClientTool.list_resources()
        • MCPClientTool.list_tools()
        • MCPClientTool.read_resource()
        • MCPClientTool.run()
      • MCPProxyTool
        • MCPProxyTool.__init__()
        • MCPProxyTool.run()
      • MCPServerDiscovery
        • MCPServerDiscovery.create_mcp_tools_config()
        • MCPServerDiscovery.discover_server_tools()
    • tooluniverse.openalex_tool module
      • OpenAlexTool
        • OpenAlexTool.__init__()
        • OpenAlexTool._extract_paper_info()
        • OpenAlexTool.get_paper_by_doi()
        • OpenAlexTool.get_papers_by_author()
        • OpenAlexTool.run()
        • OpenAlexTool.search_literature()
    • tooluniverse.openfda_adv_tool module
      • FDACountAdditiveReactionsTool
        • FDACountAdditiveReactionsTool.__init__()
        • FDACountAdditiveReactionsTool.run()
      • FDADrugAdverseEventTool
        • FDADrugAdverseEventTool.__init__()
        • FDADrugAdverseEventTool._map_value()
        • FDADrugAdverseEventTool._post_process()
        • FDADrugAdverseEventTool._search()
        • FDADrugAdverseEventTool.run()
        • FDADrugAdverseEventTool.validate_enum_arguments()
    • tooluniverse.openfda_tool module
      • FDADrugLabelGetDrugGenericNameTool
        • FDADrugLabelGetDrugGenericNameTool.__init__()
        • FDADrugLabelGetDrugGenericNameTool.run()
      • FDADrugLabelSearchIDTool
        • FDADrugLabelSearchIDTool.__init__()
        • FDADrugLabelSearchIDTool.run()
      • FDADrugLabelSearchTool
        • FDADrugLabelSearchTool.__init__()
        • FDADrugLabelSearchTool.run()
      • FDADrugLabelTool
        • FDADrugLabelTool.__init__()
      • FDATool
        • FDATool.__init__()
        • FDATool.run()
      • check_keys_present()
      • extract_nested_fields()
      • extract_sentences_with_keywords()
      • map_properties_to_openfda_fields()
      • search_openfda()
    • tooluniverse.pubtator_tool module
      • PubTatorTool
        • PubTatorTool.__init__()
        • PubTatorTool._compose_url()
        • PubTatorTool._filter_search_results()
        • PubTatorTool._query_params()
        • PubTatorTool.run()
    • tooluniverse.restful_tool module
      • MonarchDiseasesForMultiplePhenoTool
        • MonarchDiseasesForMultiplePhenoTool.__init__()
        • MonarchDiseasesForMultiplePhenoTool.run()
      • MonarchTool
        • MonarchTool.__init__()
        • MonarchTool.run()
      • RESTfulTool
        • RESTfulTool.__init__()
        • RESTfulTool.run()
      • execute_RESTful_query()
    • tooluniverse.semantic_scholar_tool module
      • SemanticScholarTool
        • SemanticScholarTool.__init__()
        • SemanticScholarTool._search()
        • SemanticScholarTool.run()
    • tooluniverse.utils module
      • compare_function_calls()
      • download_from_hf()
      • evaluate_function_call()
      • evaluate_function_call_from_toolbox()
      • extract_function_call_json()
      • format_api_response()
      • get_md5()
      • normalize_gene_symbol()
      • read_json_list()
      • validate_hook_conditions()
      • validate_hook_config()
      • validate_query()
      • yaml_to_dict()