Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y _ __add__() (tooluniverse.tool_finder_keyword.Counter method) __and__() (tooluniverse.tool_finder_keyword.Counter method) __call__() (tooluniverse.tool_graph_web_ui.Flask method) __del__() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) __delitem__() (tooluniverse.tool_finder_keyword.Counter method) __eq__() (tooluniverse.tool_finder_keyword.Counter method) __ge__() (tooluniverse.tool_finder_keyword.Counter method) __getattr__() (tooluniverse.utils.ModelMetaclass method) __gt__() (tooluniverse.tool_finder_keyword.Counter method) __iadd__() (tooluniverse.tool_finder_keyword.Counter method) __iand__() (tooluniverse.tool_finder_keyword.Counter method) __init__() (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.admetai_tool.ADMETModel method) (tooluniverse.admetai_tool.BaseTool method) (tooluniverse.ADMETAITool method) (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.agentic_tool.AzureOpenAIClient method) (tooluniverse.agentic_tool.BaseTool method) (tooluniverse.agentic_tool.GeminiClient method) (tooluniverse.AgenticTool method) (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.alphafold_tool.BaseTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.boltz_tool.BaseTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) (tooluniverse.chem_tool.BaseTool method) (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.chem_tool.Indigo method) (tooluniverse.ChEMBLTool method) (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.compose_tool.BaseTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) (tooluniverse.ctg_tool.RESTfulTool method) (tooluniverse.custom_tool.BaseTool method) (tooluniverse.custom_tool.CustomTool method) (tooluniverse.dailymed_tool.BaseTool method) (tooluniverse.dailymed_tool.GetSPLBySetIDTool method) (tooluniverse.dailymed_tool.SearchSPLTool method) (tooluniverse.dataset_tool.BaseTool method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.efo_tool.BaseTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.embedding_database.AzureOpenAI method) (tooluniverse.embedding_database.BaseTool method) (tooluniverse.embedding_database.EmbeddingDatabase method) (tooluniverse.embedding_database.OpenAI method) (tooluniverse.embedding_sync.BaseTool method) (tooluniverse.embedding_sync.EmbeddingSync method) (tooluniverse.embedding_sync.HfApi method) (tooluniverse.embedding_sync.HfHubHTTPError method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.enrichr_tool.BaseTool method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.europe_pmc_tool.BaseTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.execute_function.HookManager method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.extended_hooks.FilteringHook method) (tooluniverse.extended_hooks.FormattingHook method) (tooluniverse.extended_hooks.LoggingHook method) (tooluniverse.extended_hooks.OutputHook method) (tooluniverse.extended_hooks.ValidationHook method) (tooluniverse.FDACountAdditiveReactionsTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.FDADrugLabelSearchIDTool method) (tooluniverse.FDADrugLabelSearchTool method) (tooluniverse.FDADrugLabelTool method) (tooluniverse.gene_ontology_tool.BaseTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.GetSPLBySetIDTool method) (tooluniverse.graphql_tool.BaseTool method) (tooluniverse.graphql_tool.DiseaseTargetScoreTool method) (tooluniverse.graphql_tool.GraphQLTool method) (tooluniverse.graphql_tool.OpentargetGeneticsTool method) (tooluniverse.graphql_tool.OpentargetTool method) (tooluniverse.graphql_tool.OpentargetToolDrugNameMatch method) (tooluniverse.gwas_tool.BaseTool method) (tooluniverse.gwas_tool.GWASAssociationByID method) (tooluniverse.gwas_tool.GWASAssociationSearch method) (tooluniverse.gwas_tool.GWASAssociationsForSNP method) (tooluniverse.gwas_tool.GWASAssociationsForStudy method) (tooluniverse.gwas_tool.GWASAssociationsForTrait method) (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.gwas_tool.GWASSNPByID method) (tooluniverse.gwas_tool.GWASSNPSearch method) (tooluniverse.gwas_tool.GWASSNPsForGene method) (tooluniverse.gwas_tool.GWASStudiesForTrait method) (tooluniverse.gwas_tool.GWASStudyByID method) (tooluniverse.gwas_tool.GWASStudySearch method) (tooluniverse.gwas_tool.GWASVariantsForTrait method) (tooluniverse.GWASAssociationByID method) (tooluniverse.GWASAssociationSearch method) (tooluniverse.GWASAssociationsForSNP method) (tooluniverse.GWASAssociationsForStudy method) (tooluniverse.GWASAssociationsForTrait method) (tooluniverse.GWASSNPByID method) (tooluniverse.GWASSNPSearch method) (tooluniverse.GWASSNPsForGene method) (tooluniverse.GWASStudiesForTrait method) (tooluniverse.GWASStudyByID method) (tooluniverse.GWASStudySearch method) (tooluniverse.GWASVariantsForTrait method) (tooluniverse.hpa_tool.BaseTool method) (tooluniverse.hpa_tool.HPAGetBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetComparativeExpressionTool method) (tooluniverse.hpa_tool.HPAGetContextualBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetDiseaseExpressionTool method) (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.hpa_tool.HPAGetRnaExpressionBySourceTool method) (tooluniverse.hpa_tool.HPAJsonApiTool method) (tooluniverse.hpa_tool.HPASearchApiTool method) (tooluniverse.hpa_tool.HPAXmlApiTool method) (tooluniverse.humanbase_tool.BaseTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.GeminiClient method) (tooluniverse.logging_config.ToolUniverseLogger method) (tooluniverse.mcp_client_tool.BaseMCPClient method) (tooluniverse.mcp_client_tool.BaseTool method) (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.mcp_client_tool.MCPProxyTool method) (tooluniverse.MCPAutoLoaderTool method) (tooluniverse.MCPClientTool method) (tooluniverse.medlineplus_tool.BaseTool method) (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.MonarchTool method) (tooluniverse.odphp_tool.BaseTool method) (tooluniverse.odphp_tool.BeautifulSoup method) (tooluniverse.odphp_tool.ODPHPOutlinkFetch method) (tooluniverse.odphp_tool.ODPHPRESTTool method) (tooluniverse.ODPHPOutlinkFetch method) (tooluniverse.openalex_tool.BaseTool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.openfda_adv_tool.BaseTool method) (tooluniverse.openfda_adv_tool.FDACountAdditiveReactionsTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_tool.BaseTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchIDTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchTool method) (tooluniverse.openfda_tool.FDADrugLabelTool method) (tooluniverse.openfda_tool.FDATool method) (tooluniverse.OpentargetGeneticsTool method) (tooluniverse.OpentargetTool method) (tooluniverse.OpentargetToolDrugNameMatch method) (tooluniverse.output_hook.FileSaveHook method) (tooluniverse.output_hook.HookManager method) (tooluniverse.output_hook.HookRule method) (tooluniverse.output_hook.OutputHook method) (tooluniverse.output_hook.SummarizationHook method) (tooluniverse.package_tool.BaseTool method) (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) (tooluniverse.pubchem_tool.BaseTool method) (tooluniverse.pubchem_tool.PubChemRESTTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.pubtator_tool.BaseTool method) (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) (tooluniverse.rcsb_pdb_tool.BaseTool method) (tooluniverse.rcsb_pdb_tool.DataQuery method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) (tooluniverse.reactome_tool.BaseTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.remote_tool.BaseTool method) (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.restful_tool.GraphQLTool method) (tooluniverse.restful_tool.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.restful_tool.MonarchTool method) (tooluniverse.restful_tool.RESTfulTool method) (tooluniverse.SearchSPLTool method) (tooluniverse.semantic_scholar_tool.BaseTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.SMCP method) (tooluniverse.smcp.FastMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.smcp.ThreadPoolExecutor method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.smcp_server.SMCP method) (tooluniverse.tool_finder_embedding.BaseTool method) (tooluniverse.tool_finder_embedding.SentenceTransformer method) (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.tool_finder_keyword.BaseTool method) (tooluniverse.tool_finder_keyword.Counter method) (tooluniverse.tool_finder_keyword.defaultdict method) (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.tool_finder_llm.AgenticTool method) (tooluniverse.tool_finder_llm.BaseTool method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.tool_graph_web_ui.Flask method) (tooluniverse.tool_graph_web_ui.ToolGraphWebUI method) (tooluniverse.ToolFinderEmbedding method) (tooluniverse.ToolFinderKeyword method) (tooluniverse.ToolFinderLLM method) (tooluniverse.ToolUniverse method) (tooluniverse.uniprot_tool.BaseTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.url_tool.BaseTool method) (tooluniverse.url_tool.URLHTMLTagTool method) (tooluniverse.url_tool.URLToPDFTextTool method) (tooluniverse.URLHTMLTagTool method) (tooluniverse.URLToPDFTextTool method) (tooluniverse.uspto_tool.BaseTool method) (tooluniverse.uspto_tool.HTTPAdapter method) (tooluniverse.uspto_tool.Retry method) (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) (tooluniverse.xml_tool.BaseTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) __instancecheck__() (tooluniverse.utils.ModelMetaclass method) __ior__() (tooluniverse.tool_finder_keyword.Counter method) __isub__() (tooluniverse.tool_finder_keyword.Counter method) __le__() (tooluniverse.tool_finder_keyword.Counter method) __lt__() (tooluniverse.tool_finder_keyword.Counter method) __missing__() (tooluniverse.tool_finder_keyword.Counter method) __ne__() (tooluniverse.tool_finder_keyword.Counter method) __neg__() (tooluniverse.tool_finder_keyword.Counter method) __new__() (tooluniverse.utils.ModelMetaclass static method) __or__() (tooluniverse.tool_finder_keyword.Counter method) __pos__() (tooluniverse.tool_finder_keyword.Counter method) __repr__() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.smcp.FastMCP method) (tooluniverse.tool_finder_keyword.Counter method) (tooluniverse.tool_finder_keyword.defaultdict method) (tooluniverse.tool_finder_llm.datetime method) (tooluniverse.uspto_tool.Retry method) __str__() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) __sub__() (tooluniverse.tool_finder_keyword.Counter method) __subclasscheck__() (tooluniverse.utils.ModelMetaclass method) A ABS (tooluniverse.chem_tool.Indigo attribute) absolute() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) accept_access_request() (tooluniverse.embedding_sync.HfApi method) add_collection_item() (tooluniverse.embedding_sync.HfApi method) add_custom_tool() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.smcp_server.SMCP method) add_headers() (tooluniverse.uspto_tool.HTTPAdapter method) add_middleware() (tooluniverse.smcp.FastMCP method) add_prompt() (tooluniverse.smcp.FastMCP method) add_resource() (tooluniverse.smcp.FastMCP method) add_resource_fn() (tooluniverse.smcp.FastMCP method) add_space_secret() (tooluniverse.embedding_sync.HfApi method) add_space_variable() (tooluniverse.embedding_sync.HfApi method) add_template() (tooluniverse.smcp.FastMCP method) add_tool() (tooluniverse.smcp.FastMCP method) add_tool_transformation() (tooluniverse.smcp.FastMCP method) ADMETAITool (class in tooluniverse) (class in tooluniverse.admetai_tool) ADMETModel (class in tooluniverse.admetai_tool) AgenticTool (class in tooluniverse) (class in tooluniverse.agentic_tool) (class in tooluniverse.tool_finder_llm) all_tool_dict (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.smcp.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) all_tools (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.smcp.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) ALLENE (tooluniverse.chem_tool.Indigo attribute) AlphaFoldRESTTool (class in tooluniverse) (class in tooluniverse.alphafold_tool) AND (tooluniverse.chem_tool.Indigo attribute) api_key (tooluniverse.embedding_database.OpenAI attribute) app_context() (tooluniverse.tool_graph_web_ui.Flask method) append_to_message() (tooluniverse.embedding_sync.HfHubHTTPError method) apply_hooks() (tooluniverse.execute_function.HookManager method) (tooluniverse.output_hook.HookManager method) as_proxy() (tooluniverse.smcp.FastMCP class method) ASCII_SPACES (tooluniverse.odphp_tool.BeautifulSoup attribute) assign_by_path() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) astimezone() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) async_to_sync() (tooluniverse.tool_graph_web_ui.Flask method) atc_code (tooluniverse.admetai_tool.ADMETModel property) audio (tooluniverse.embedding_database.OpenAI property) auth_check() (tooluniverse.embedding_sync.HfApi method) auth_headers (tooluniverse.embedding_database.OpenAI property) AuthenticationError auto_discover_tools() (in module tooluniverse.execute_function) (in module tooluniverse.tool_registry) auto_load_and_register() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) AzureOpenAI (class in tooluniverse.embedding_database) AzureOpenAIClient (class in tooluniverse.agentic_tool) (class in tooluniverse.llm_clients) B BaseLLMClient (class in tooluniverse.llm_clients) BaseMCPClient (class in tooluniverse.mcp_client_tool) BaseTool (class in tooluniverse) (class in tooluniverse.admetai_tool) (class in tooluniverse.agentic_tool) (class in tooluniverse.alphafold_tool) (class in tooluniverse.base_tool) (class in tooluniverse.boltz_tool) (class in tooluniverse.chem_tool) (class in tooluniverse.compose_tool) (class in tooluniverse.custom_tool) (class in tooluniverse.dailymed_tool) (class in tooluniverse.dataset_tool) (class in tooluniverse.efo_tool) (class in tooluniverse.embedding_database) (class in tooluniverse.embedding_sync) (class in tooluniverse.enrichr_tool) (class in tooluniverse.europe_pmc_tool) (class in tooluniverse.gene_ontology_tool) (class in tooluniverse.graphql_tool) (class in tooluniverse.gwas_tool) (class in tooluniverse.hpa_tool) (class in tooluniverse.humanbase_tool) (class in tooluniverse.mcp_client_tool) (class in tooluniverse.medlineplus_tool) (class in tooluniverse.odphp_tool) (class in tooluniverse.openalex_tool) (class in tooluniverse.openfda_adv_tool) (class in tooluniverse.openfda_tool) (class in tooluniverse.package_tool) (class in tooluniverse.pubchem_tool) (class in tooluniverse.pubtator_tool) (class in tooluniverse.rcsb_pdb_tool) (class in tooluniverse.reactome_tool) (class in tooluniverse.remote_tool) (class in tooluniverse.semantic_scholar_tool) (class in tooluniverse.tool_finder_embedding) (class in tooluniverse.tool_finder_keyword) (class in tooluniverse.tool_finder_llm) (class in tooluniverse.uniprot_tool) (class in tooluniverse.url_tool) (class in tooluniverse.uspto_tool) (class in tooluniverse.xml_tool) batches (tooluniverse.embedding_database.OpenAI property) BeautifulSoup (class in tooluniverse.odphp_tool) beta (tooluniverse.embedding_database.OpenAI property) Boltz2DockingTool (class in tooluniverse.boltz_tool) build_connection_pool_key_attributes() (tooluniverse.uspto_tool.HTTPAdapter method) build_graph() (tooluniverse.enrichr_tool.EnrichrTool method) build_lazy_registry() (in module tooluniverse.tool_registry) build_response() (tooluniverse.uspto_tool.HTTPAdapter method) build_schema() (in module tooluniverse.graphql_tool) buildPkaModel() (tooluniverse.chem_tool.Indigo method) C call_id_gen() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) call_tool() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPAutoLoaderTool method) (tooluniverse.MCPClientTool method) callable_functions (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.smcp.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) cancel_access_request() (tooluniverse.embedding_sync.HfApi method) cancel_job() (tooluniverse.embedding_sync.HfApi method) cert_verify() (tooluniverse.uspto_tool.HTTPAdapter method) CHAIN (tooluniverse.chem_tool.Indigo attribute) change_discussion_status() (tooluniverse.embedding_sync.HfApi method) chat (tooluniverse.embedding_database.OpenAI property) check() (tooluniverse.chem_tool.Indigo method) check_function_call() (tooluniverse.admetai_tool.BaseTool method) (tooluniverse.agentic_tool.BaseTool method) (tooluniverse.alphafold_tool.BaseTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.boltz_tool.BaseTool method) (tooluniverse.chem_tool.BaseTool method) (tooluniverse.compose_tool.BaseTool method) (tooluniverse.custom_tool.BaseTool method) (tooluniverse.dailymed_tool.BaseTool method) (tooluniverse.dataset_tool.BaseTool method) (tooluniverse.efo_tool.BaseTool method) (tooluniverse.embedding_database.BaseTool method) (tooluniverse.embedding_sync.BaseTool method) (tooluniverse.enrichr_tool.BaseTool method) (tooluniverse.europe_pmc_tool.BaseTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.gene_ontology_tool.BaseTool method) (tooluniverse.graphql_tool.BaseTool method) (tooluniverse.gwas_tool.BaseTool method) (tooluniverse.hpa_tool.BaseTool method) (tooluniverse.humanbase_tool.BaseTool method) (tooluniverse.mcp_client_tool.BaseTool method) (tooluniverse.medlineplus_tool.BaseTool method) (tooluniverse.odphp_tool.BaseTool method) (tooluniverse.openalex_tool.BaseTool method) (tooluniverse.openfda_adv_tool.BaseTool method) (tooluniverse.openfda_tool.BaseTool method) (tooluniverse.package_tool.BaseTool method) (tooluniverse.pubchem_tool.BaseTool method) (tooluniverse.pubtator_tool.BaseTool method) (tooluniverse.rcsb_pdb_tool.BaseTool method) (tooluniverse.reactome_tool.BaseTool method) (tooluniverse.remote_tool.BaseTool method) (tooluniverse.semantic_scholar_tool.BaseTool method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.tool_finder_embedding.BaseTool method) (tooluniverse.tool_finder_keyword.BaseTool method) (tooluniverse.tool_finder_llm.BaseTool method) (tooluniverse.ToolUniverse method) (tooluniverse.uniprot_tool.BaseTool method) (tooluniverse.url_tool.BaseTool method) (tooluniverse.uspto_tool.BaseTool method) (tooluniverse.xml_tool.BaseTool method) check_keys_present() (in module tooluniverse.openfda_tool) checkStructure() (tooluniverse.chem_tool.Indigo method) ChEMBLTool (class in tooluniverse) (class in tooluniverse.chem_tool) chmod() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) chunk_size (tooluniverse.output_hook.SummarizationHook attribute) CIS (tooluniverse.chem_tool.Indigo attribute) clear_cache() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) clearTautomerRules() (tooluniverse.chem_tool.Indigo method) cli (tooluniverse.tool_graph_web_ui.Flask attribute) ClinicalTrialsDetailsTool (class in tooluniverse) (class in tooluniverse.ctg_tool) ClinicalTrialsSearchTool (class in tooluniverse) (class in tooluniverse.ctg_tool) ClinicalTrialsTool (class in tooluniverse.ctg_tool) close() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.smcp_server.SMCP method) (tooluniverse.uspto_tool.HTTPAdapter method) COLORS (tooluniverse.logging_config.ToolUniverseFormatter attribute) combine() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) comment_discussion() (tooluniverse.embedding_sync.HfApi method) commonBits() (tooluniverse.chem_tool.Indigo method) compare_function_calls() (in module tooluniverse.utils) completions (tooluniverse.embedding_database.OpenAI property) compose() (in module tooluniverse.compose_scripts.biomarker_discovery) (in module tooluniverse.compose_scripts.comprehensive_drug_discovery) (in module tooluniverse.compose_scripts.drug_safety_analyzer) (in module tooluniverse.compose_scripts.literature_tool) (in module tooluniverse.compose_scripts.output_summarizer) (in module tooluniverse.compose_scripts.tool_description_optimizer) (in module tooluniverse.compose_scripts.tool_discover) (in module tooluniverse.compose_scripts.tool_graph_composer) (in module tooluniverse.compose_scripts.tool_graph_generation) (in module tooluniverse.compose_scripts.tool_metadata_generator) composer_tool_name (tooluniverse.output_hook.SummarizationHook attribute) ComposeTool (class in tooluniverse) (class in tooluniverse.compose_tool) conditions (tooluniverse.output_hook.HookRule attribute) config (tooluniverse.execute_function.HookManager attribute) (tooluniverse.extended_hooks.OutputHook attribute) (tooluniverse.output_hook.HookManager attribute) (tooluniverse.output_hook.OutputHook attribute) config_path (tooluniverse.execute_function.HookManager attribute) (tooluniverse.output_hook.HookManager attribute) connect_lookup_by_code() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) containers (tooluniverse.embedding_database.OpenAI property) contains_replacement_characters (tooluniverse.odphp_tool.BeautifulSoup attribute) conversations (tooluniverse.embedding_database.OpenAI property) convertToArray() (tooluniverse.chem_tool.Indigo method) copy() (tooluniverse.embedding_database.AzureOpenAI method) (tooluniverse.embedding_database.OpenAI method) (tooluniverse.tool_finder_keyword.Counter method) (tooluniverse.tool_finder_keyword.defaultdict method) copy_self() (tooluniverse.odphp_tool.BeautifulSoup method) Counter (class in tooluniverse.tool_finder_keyword) countReferences() (tooluniverse.chem_tool.Indigo method) create_branch() (tooluniverse.embedding_sync.HfApi method) create_collection() (tooluniverse.embedding_sync.HfApi method) create_commit() (tooluniverse.embedding_sync.HfApi method) create_discussion() (tooluniverse.embedding_sync.HfApi method) create_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) create_inference_endpoint_from_catalog() (tooluniverse.embedding_sync.HfApi method) create_jinja_environment() (tooluniverse.tool_graph_web_ui.Flask method) create_mcp_tools_config() (tooluniverse.mcp_client_tool.MCPServerDiscovery static method) create_pull_request() (tooluniverse.embedding_sync.HfApi method) create_repo() (tooluniverse.embedding_sync.HfApi method) create_scheduled_job() (tooluniverse.embedding_sync.HfApi method) create_scheduled_uv_job() (tooluniverse.embedding_sync.HfApi method) create_smcp_server() (in module tooluniverse) (in module tooluniverse.smcp) create_tag() (tooluniverse.embedding_sync.HfApi method) create_url_adapter() (tooluniverse.tool_graph_web_ui.Flask method) create_web_ui_files() (in module tooluniverse.tool_graph_web_ui) create_webhook() (tooluniverse.embedding_sync.HfApi method) createArray() (tooluniverse.chem_tool.Indigo method) createDecomposer() (tooluniverse.chem_tool.Indigo method) createFileSaver() (tooluniverse.chem_tool.Indigo method) createMolecule() (tooluniverse.chem_tool.Indigo method) createQueryMolecule() (tooluniverse.chem_tool.Indigo method) createQueryReaction() (tooluniverse.chem_tool.Indigo method) createReaction() (tooluniverse.chem_tool.Indigo method) createSaver() (tooluniverse.chem_tool.Indigo method) critical() (in module tooluniverse.logging_config) ctime() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) custom_route() (tooluniverse.smcp.FastMCP method) CustomTool (class in tooluniverse.custom_tool) cwd() (tooluniverse.base_tool.Path class method) (tooluniverse.embedding_database.Path class method) (tooluniverse.embedding_sync.Path class method) (tooluniverse.output_hook.Path class method) (tooluniverse.pubtator_tool.Path class method) D DataQuery (class in tooluniverse.rcsb_pdb_tool) dataset_info() (tooluniverse.embedding_sync.HfApi method) DatasetTool (class in tooluniverse) (class in tooluniverse.dataset_tool) date() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) datetime (class in tooluniverse.agentic_tool) (class in tooluniverse.compose_scripts.tool_graph_composer) (class in tooluniverse.embedding_sync) (class in tooluniverse.tool_finder_llm) dbgBreakpoint() (tooluniverse.chem_tool.Indigo method) debug() (in module tooluniverse.execute_function) (in module tooluniverse.logging_config) declared_html_encoding (tooluniverse.odphp_tool.BeautifulSoup attribute) decode() (tooluniverse.odphp_tool.BeautifulSoup method) decomposeMolecules() (tooluniverse.chem_tool.Indigo method) deepcopy() (in module tooluniverse.ctg_tool) (in module tooluniverse.dataset_tool) DEFAULT (tooluniverse.uspto_tool.Retry attribute) DEFAULT_ALLOWED_METHODS (tooluniverse.uspto_tool.Retry attribute) DEFAULT_BACKOFF_MAX (tooluniverse.uspto_tool.Retry attribute) DEFAULT_BUILDER_FEATURES (tooluniverse.odphp_tool.BeautifulSoup attribute) default_config (tooluniverse.tool_graph_web_ui.Flask attribute) default_factory (tooluniverse.tool_finder_keyword.defaultdict attribute) default_headers (tooluniverse.embedding_database.OpenAI property) DEFAULT_MODEL_LIMITS (tooluniverse.agentic_tool.AzureOpenAIClient attribute) (tooluniverse.llm_clients.AzureOpenAIClient attribute) DEFAULT_REMOVE_HEADERS_ON_REDIRECT (tooluniverse.uspto_tool.Retry attribute) defaultdict (class in tooluniverse.tool_finder_keyword) delete_branch() (tooluniverse.embedding_sync.HfApi method) delete_collection() (tooluniverse.embedding_sync.HfApi method) delete_collection_item() (tooluniverse.embedding_sync.HfApi method) delete_file() (tooluniverse.embedding_sync.HfApi method) delete_files() (tooluniverse.embedding_sync.HfApi method) delete_folder() (tooluniverse.embedding_sync.HfApi method) delete_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) delete_repo() (tooluniverse.embedding_sync.HfApi method) delete_scheduled_job() (tooluniverse.embedding_sync.HfApi method) delete_space_secret() (tooluniverse.embedding_sync.HfApi method) delete_space_storage() (tooluniverse.embedding_sync.HfApi method) delete_space_variable() (tooluniverse.embedding_sync.HfApi method) delete_tag() (tooluniverse.embedding_sync.HfApi method) delete_webhook() (tooluniverse.embedding_sync.HfApi method) deserialize() (tooluniverse.chem_tool.Indigo method) device (tooluniverse.tool_finder_embedding.SentenceTransformer property) disable_hook() (tooluniverse.execute_function.HookManager method) (tooluniverse.output_hook.HookManager method) disable_webhook() (tooluniverse.embedding_sync.HfApi method) discover_mcp_tools() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) discover_server_tools() (tooluniverse.mcp_client_tool.MCPServerDiscovery static method) discover_tools() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) DiseaseTargetScoreTool (class in tooluniverse) (class in tooluniverse.graphql_tool) dispatch_request() (tooluniverse.tool_graph_web_ui.Flask method) do_teardown_appcontext() (tooluniverse.tool_graph_web_ui.Flask method) do_teardown_request() (tooluniverse.tool_graph_web_ui.Flask method) DOUBLET (tooluniverse.chem_tool.Indigo attribute) DOWN (tooluniverse.chem_tool.Indigo attribute) download_from_hf() (in module tooluniverse.dataset_tool) (in module tooluniverse.utils) (in module tooluniverse.xml_tool) dst() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) dtype (tooluniverse.tool_finder_embedding.SentenceTransformer property) duplicate_space() (tooluniverse.embedding_sync.HfApi method) E edit_discussion_comment() (tooluniverse.embedding_sync.HfApi method) EFOTool (class in tooluniverse) (class in tooluniverse.efo_tool) EITHER (tooluniverse.chem_tool.Indigo attribute) elements() (tooluniverse.tool_finder_keyword.Counter method) EmbeddingDatabase (class in tooluniverse) (class in tooluniverse.embedding_database) embeddings (tooluniverse.embedding_database.OpenAI property) EmbeddingSync (class in tooluniverse) (class in tooluniverse.embedding_sync) EMOJI_PREFIX (tooluniverse.logging_config.ToolUniverseFormatter attribute) enable_hook() (tooluniverse.execute_function.HookManager method) (tooluniverse.output_hook.HookManager method) enable_webhook() (tooluniverse.embedding_sync.HfApi method) enabled (tooluniverse.execute_function.HookManager attribute) (tooluniverse.extended_hooks.OutputHook attribute) (tooluniverse.output_hook.HookManager attribute) (tooluniverse.output_hook.OutputHook attribute) encode() (tooluniverse.tool_finder_embedding.SentenceTransformer method) encode_document() (tooluniverse.tool_finder_embedding.SentenceTransformer method) encode_multi_process() (tooluniverse.tool_finder_embedding.SentenceTransformer method) encode_query() (tooluniverse.tool_finder_embedding.SentenceTransformer method) enrichr_api() (tooluniverse.enrichr_tool.EnrichrTool method) EnrichrTool (class in tooluniverse.enrichr_tool) ensure_sync() (tooluniverse.tool_graph_web_ui.Flask method) error() (in module tooluniverse.execute_function) (in module tooluniverse.logging_config) estimate_token_usage() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) EuropePMCTool (class in tooluniverse) (class in tooluniverse.europe_pmc_tool) evals (tooluniverse.embedding_database.OpenAI property) evaluate() (tooluniverse.output_hook.HookRule method) (tooluniverse.tool_finder_embedding.SentenceTransformer method) evaluate_function_call() (in module tooluniverse.base_tool) (in module tooluniverse.execute_function) (in module tooluniverse.utils) evaluate_function_call_from_toolbox() (in module tooluniverse.utils) exactMatch() (tooluniverse.chem_tool.Indigo method) exec() (tooluniverse.rcsb_pdb_tool.DataQuery method) execute_query() (in module tooluniverse.graphql_tool) execute_RESTful_query() (in module tooluniverse.ctg_tool) (in module tooluniverse.restful_tool) exists() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) expanduser() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) export_tool_names() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) extract_function_call_json() (in module tooluniverse.base_tool) (in module tooluniverse.execute_function) (in module tooluniverse.utils) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) extract_nested_fields() (in module tooluniverse.openfda_tool) extract_sentences_with_keywords() (in module tooluniverse.openfda_tool) extractCommonScaffold() (tooluniverse.chem_tool.Indigo method) F FastMCP (class in tooluniverse.smcp) FDACountAdditiveReactionsTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugAdverseEventTool (class in tooluniverse) (class in tooluniverse.openfda_adv_tool) FDADrugLabelGetDrugGenericNameTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelSearchIDTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelSearchTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDADrugLabelTool (class in tooluniverse) (class in tooluniverse.openfda_tool) FDATool (class in tooluniverse.openfda_tool) fetch_job_logs() (tooluniverse.embedding_sync.HfApi method) file_exists() (tooluniverse.embedding_sync.HfApi method) files (tooluniverse.embedding_database.OpenAI property) FileSaveHook (class in tooluniverse.output_hook) filter_tool_lists() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) FilteringHook (class in tooluniverse.extended_hooks) finalize_request() (tooluniverse.tool_graph_web_ui.Flask method) find_dotenv() (in module tooluniverse.uspto_tool) find_tools() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderEmbedding method) (tooluniverse.ToolFinderKeyword method) (tooluniverse.ToolFinderLLM method) find_tools_by_pattern() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) find_tools_legacy() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) find_tools_llm() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) fine_tuning (tooluniverse.embedding_database.OpenAI property) Flask (class in tooluniverse.tool_graph_web_ui) focus_areas (tooluniverse.output_hook.SummarizationHook attribute) fold (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) force_full_discovery() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) format() (tooluniverse.logging_config.ToolUniverseFormatter method) format_api_response() (in module tooluniverse.utils) FormattingHook (class in tooluniverse.extended_hooks) forward() (tooluniverse.tool_finder_embedding.SentenceTransformer method) from_client() (tooluniverse.smcp.FastMCP class method) from_fastapi() (tooluniverse.smcp.FastMCP class method) from_int() (tooluniverse.uspto_tool.Retry class method) from_openapi() (tooluniverse.smcp.FastMCP class method) fromisoformat() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) fromkeys() (tooluniverse.tool_finder_keyword.Counter class method) fromtimestamp() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) full_dispatch_request() (tooluniverse.tool_graph_web_ui.Flask method) G GeminiClient (class in tooluniverse.agentic_tool) (class in tooluniverse.llm_clients) GeneOntologyTool (class in tooluniverse.gene_ontology_tool) generate_env_template() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) generate_name() (tooluniverse.smcp.FastMCP class method) generate_proxy_tool_configs() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) get_availability_status() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) get_available_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_backend() (tooluniverse.tool_finder_embedding.SentenceTransformer method) get_backoff_time() (tooluniverse.uspto_tool.Retry method) get_by_path() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) get_chembl_id_by_name() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_chembl_smiles_pref_name_id_by_name() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_collection() (tooluniverse.embedding_sync.HfApi method) get_config_registry() (in module tooluniverse.tool_registry) get_connection() (tooluniverse.uspto_tool.HTTPAdapter method) get_connection_with_tls_context() (tooluniverse.uspto_tool.HTTPAdapter method) get_dataset_info() (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) get_dataset_tags() (tooluniverse.embedding_sync.HfApi method) get_default_config_file() (tooluniverse.admetai_tool.BaseTool class method) (tooluniverse.agentic_tool.BaseTool class method) (tooluniverse.alphafold_tool.BaseTool class method) (tooluniverse.base_tool.BaseTool class method) (tooluniverse.BaseTool class method) (tooluniverse.boltz_tool.BaseTool class method) (tooluniverse.chem_tool.BaseTool class method) (tooluniverse.compose_tool.BaseTool class method) (tooluniverse.custom_tool.BaseTool class method) (tooluniverse.dailymed_tool.BaseTool class method) (tooluniverse.dataset_tool.BaseTool class method) (tooluniverse.efo_tool.BaseTool class method) (tooluniverse.embedding_database.BaseTool class method) (tooluniverse.embedding_sync.BaseTool class method) (tooluniverse.enrichr_tool.BaseTool class method) (tooluniverse.europe_pmc_tool.BaseTool class method) (tooluniverse.gene_ontology_tool.BaseTool class method) (tooluniverse.graphql_tool.BaseTool class method) (tooluniverse.gwas_tool.BaseTool class method) (tooluniverse.hpa_tool.BaseTool class method) (tooluniverse.humanbase_tool.BaseTool class method) (tooluniverse.mcp_client_tool.BaseTool class method) (tooluniverse.medlineplus_tool.BaseTool class method) (tooluniverse.odphp_tool.BaseTool class method) (tooluniverse.openalex_tool.BaseTool class method) (tooluniverse.openfda_adv_tool.BaseTool class method) (tooluniverse.openfda_tool.BaseTool class method) (tooluniverse.package_tool.BaseTool class method) (tooluniverse.pubchem_tool.BaseTool class method) (tooluniverse.pubtator_tool.BaseTool class method) (tooluniverse.rcsb_pdb_tool.BaseTool class method) (tooluniverse.reactome_tool.BaseTool class method) (tooluniverse.remote_tool.BaseTool class method) (tooluniverse.semantic_scholar_tool.BaseTool class method) (tooluniverse.tool_finder_embedding.BaseTool class method) (tooluniverse.tool_finder_keyword.BaseTool class method) (tooluniverse.tool_finder_llm.BaseTool class method) (tooluniverse.uniprot_tool.BaseTool class method) (tooluniverse.url_tool.BaseTool class method) (tooluniverse.uspto_tool.BaseTool class method) (tooluniverse.xml_tool.BaseTool class method) get_default_hook_config() (in module tooluniverse.default_config) (in module tooluniverse.execute_function) get_discussion_details() (tooluniverse.embedding_sync.HfApi method) get_disease_variants_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_editor_link() (tooluniverse.rcsb_pdb_tool.DataQuery method) get_enrichment_results() (tooluniverse.enrichr_tool.EnrichrTool method) get_entrez_ids() (tooluniverse.humanbase_tool.HumanBaseTool method) get_entry_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_full_repo_name() (tooluniverse.embedding_sync.HfApi method) get_function_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_genes_for_term() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_genetics_condition_by_name() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) get_genetics_gene_by_name() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) get_genetics_index() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) get_hf_file_metadata() (tooluniverse.embedding_sync.HfApi method) get_hook() (tooluniverse.execute_function.HookManager method) (tooluniverse.output_hook.HookManager method) get_hook_logger() (in module tooluniverse.logging_config) get_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) get_input_arguments() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) get_input_ids() (tooluniverse.rcsb_pdb_tool.DataQuery method) get_input_type() (tooluniverse.rcsb_pdb_tool.DataQuery method) get_lazy_loading_status() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_logger() (in module tooluniverse.agentic_tool) (in module tooluniverse.embedding_database) (in module tooluniverse.embedding_sync) (in module tooluniverse.execute_function) (in module tooluniverse.logging_config) (in module tooluniverse.smcp) (tooluniverse.logging_config.ToolUniverseLogger method) get_max_seq_length() (tooluniverse.tool_finder_embedding.SentenceTransformer method) get_mcp_server_configs() (in module tooluniverse.mcp_tool_registry) get_mcp_tool_registry() (in module tooluniverse.mcp_tool_registry) get_mcp_tool_urls() (in module tooluniverse.mcp_tool_registry) get_md5() (in module tooluniverse.tool_finder_embedding) (in module tooluniverse.utils) get_model_info() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) get_model_kwargs() (tooluniverse.tool_finder_embedding.SentenceTransformer method) get_model_tags() (tooluniverse.embedding_sync.HfApi method) get_names_taxonomy_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_official_gene_name() (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) get_one_tool_by_one_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_paper_by_doi() (tooluniverse.openalex_tool.OpenAlexTool method) get_papers_by_author() (tooluniverse.openalex_tool.OpenAlexTool method) get_paths_info() (tooluniverse.embedding_sync.HfApi method) get_prompt() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) (tooluniverse.smcp.FastMCP method) get_prompt_preview() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) get_prompt_template() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) get_prompts() (tooluniverse.smcp.FastMCP method) get_ptm_processing_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_query() (tooluniverse.rcsb_pdb_tool.DataQuery method) get_registered_tools() (in module tooluniverse.mcp_tool_registry) get_remote_info() (tooluniverse.remote_tool.RemoteTool method) get_repo_discussions() (tooluniverse.embedding_sync.HfApi method) get_required_parameters() (tooluniverse.admetai_tool.BaseTool method) (tooluniverse.agentic_tool.BaseTool method) (tooluniverse.alphafold_tool.BaseTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.boltz_tool.BaseTool method) (tooluniverse.chem_tool.BaseTool method) (tooluniverse.compose_tool.BaseTool method) (tooluniverse.custom_tool.BaseTool method) (tooluniverse.dailymed_tool.BaseTool method) (tooluniverse.dataset_tool.BaseTool method) (tooluniverse.efo_tool.BaseTool method) (tooluniverse.embedding_database.BaseTool method) (tooluniverse.embedding_sync.BaseTool method) (tooluniverse.enrichr_tool.BaseTool method) (tooluniverse.europe_pmc_tool.BaseTool method) (tooluniverse.gene_ontology_tool.BaseTool method) (tooluniverse.graphql_tool.BaseTool method) (tooluniverse.gwas_tool.BaseTool method) (tooluniverse.hpa_tool.BaseTool method) (tooluniverse.humanbase_tool.BaseTool method) (tooluniverse.mcp_client_tool.BaseTool method) (tooluniverse.medlineplus_tool.BaseTool method) (tooluniverse.odphp_tool.BaseTool method) (tooluniverse.openalex_tool.BaseTool method) (tooluniverse.openfda_adv_tool.BaseTool method) (tooluniverse.openfda_tool.BaseTool method) (tooluniverse.package_tool.BaseTool method) (tooluniverse.pubchem_tool.BaseTool method) (tooluniverse.pubtator_tool.BaseTool method) (tooluniverse.rcsb_pdb_tool.BaseTool method) (tooluniverse.reactome_tool.BaseTool method) (tooluniverse.remote_tool.BaseTool method) (tooluniverse.semantic_scholar_tool.BaseTool method) (tooluniverse.tool_finder_embedding.BaseTool method) (tooluniverse.tool_finder_keyword.BaseTool method) (tooluniverse.tool_finder_llm.BaseTool method) (tooluniverse.uniprot_tool.BaseTool method) (tooluniverse.url_tool.BaseTool method) (tooluniverse.uspto_tool.BaseTool method) (tooluniverse.xml_tool.BaseTool method) get_resource() (tooluniverse.smcp.FastMCP method) get_resource_template() (tooluniverse.smcp.FastMCP method) get_resource_templates() (tooluniverse.smcp.FastMCP method) get_resources() (tooluniverse.smcp.FastMCP method) get_response() (tooluniverse.rcsb_pdb_tool.DataQuery method) get_retry_after() (tooluniverse.uspto_tool.Retry method) get_return_data_list() (tooluniverse.rcsb_pdb_tool.DataQuery method) get_safetensors_metadata() (tooluniverse.embedding_sync.HfApi method) get_send_file_max_age() (tooluniverse.tool_graph_web_ui.Flask method) get_sentence_embedding_dimension() (tooluniverse.tool_finder_embedding.SentenceTransformer method) get_sentence_features() (tooluniverse.tool_finder_embedding.SentenceTransformer method) get_sequence_isoforms_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_server_info() (tooluniverse.remote_tool.RemoteTool method) get_smiles_pref_name_by_chembl_id() (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) get_space_runtime() (tooluniverse.embedding_sync.HfApi method) get_space_variables() (tooluniverse.embedding_sync.HfApi method) get_subcellular_location_by_accession() (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) get_term_details() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_terms_for_gene() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) get_token_permission() (tooluniverse.embedding_sync.HfApi method) get_tool() (tooluniverse.smcp.FastMCP method) get_tool_by_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_class_lazy() (in module tooluniverse.execute_function) (in module tooluniverse.tool_registry) get_tool_description() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_registry() (in module tooluniverse) (in module tooluniverse.execute_function) (in module tooluniverse.tool_registry) get_tool_specification_by_names() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_stats() (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.ToolFinderLLM method) get_tool_type_by_name() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tool_types() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) get_tools() (tooluniverse.smcp.FastMCP method) get_user_overview() (tooluniverse.embedding_sync.HfApi method) get_webhook() (tooluniverse.embedding_sync.HfApi method) getFragmentedMolecule() (tooluniverse.chem_tool.Indigo method) getOption() (tooluniverse.chem_tool.Indigo method) getOptionBool() (tooluniverse.chem_tool.Indigo method) getOptionFloat() (tooluniverse.chem_tool.Indigo method) getOptionInt() (tooluniverse.chem_tool.Indigo method) getOptionType() (tooluniverse.chem_tool.Indigo method) getSessionId() (tooluniverse.chem_tool.Indigo method) GetSPLBySetIDTool (class in tooluniverse) (class in tooluniverse.dailymed_tool) glob() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) gradient_checkpointing_enable() (tooluniverse.tool_finder_embedding.SentenceTransformer method) grant_access() (tooluniverse.embedding_sync.HfApi method) GraphQLTool (class in tooluniverse.graphql_tool) (class in tooluniverse.restful_tool) group() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) GWASAssociationByID (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationSearch (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationsForSNP (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationsForStudy (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASAssociationsForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASRESTTool (class in tooluniverse.gwas_tool) GWASSNPByID (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASSNPSearch (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASSNPsForGene (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASStudiesForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASStudyByID (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASStudySearch (class in tooluniverse) (class in tooluniverse.gwas_tool) GWASVariantsForTrait (class in tooluniverse) (class in tooluniverse.gwas_tool) H handle_exception() (tooluniverse.tool_graph_web_ui.Flask method) handle_http_exception() (tooluniverse.tool_graph_web_ui.Flask method) handle_user_exception() (tooluniverse.tool_graph_web_ui.Flask method) hardlink_to() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) has_any_api_keys() (tooluniverse.agentic_tool.AgenticTool static method) (tooluniverse.AgenticTool static method) (tooluniverse.tool_finder_llm.AgenticTool static method) hf_hub_download() (in module tooluniverse.utils) (tooluniverse.embedding_sync.HfApi method) HfApi (class in tooluniverse.embedding_sync) HfHubHTTPError hide_discussion_comment() (tooluniverse.embedding_sync.HfApi method) home() (tooluniverse.base_tool.Path class method) (tooluniverse.embedding_database.Path class method) (tooluniverse.embedding_sync.Path class method) (tooluniverse.output_hook.Path class method) (tooluniverse.pubtator_tool.Path class method) HookManager (class in tooluniverse.execute_function) (class in tooluniverse.output_hook) HookRule (class in tooluniverse.output_hook) hooks (tooluniverse.execute_function.HookManager attribute) (tooluniverse.output_hook.HookManager attribute) hour (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) HPAGetBiologicalProcessTool (class in tooluniverse.hpa_tool) HPAGetCancerPrognosticsTool (class in tooluniverse.hpa_tool) HPAGetComparativeExpressionTool (class in tooluniverse.hpa_tool) HPAGetContextualBiologicalProcessTool (class in tooluniverse.hpa_tool) HPAGetDiseaseExpressionTool (class in tooluniverse.hpa_tool) HPAGetGeneJSONTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetGenePageDetailsTool (class in tooluniverse.hpa_tool) HPAGetGeneXMLTool (class in tooluniverse) (class in tooluniverse.hpa_tool) HPAGetProteinInteractionsTool (class in tooluniverse.hpa_tool) HPAGetRnaExpressionBySourceTool (class in tooluniverse.hpa_tool) HPAGetRnaExpressionByTissueTool (class in tooluniverse.hpa_tool) HPAGetSubcellularLocationTool (class in tooluniverse.hpa_tool) HPAJsonApiTool (class in tooluniverse.hpa_tool) HPASearchApiTool (class in tooluniverse.hpa_tool) HPASearchGenesTool (class in tooluniverse.hpa_tool) HPAXmlApiTool (class in tooluniverse.hpa_tool) http_app() (tooluniverse.smcp.FastMCP method) HTTPAdapter (class in tooluniverse.uspto_tool) humanbase_ppi_retrieve() (tooluniverse.humanbase_tool.HumanBaseTool method) HumanBaseTool (class in tooluniverse.humanbase_tool) I images (tooluniverse.embedding_database.OpenAI property) import_server() (tooluniverse.smcp.FastMCP method) increment() (tooluniverse.uspto_tool.Retry method) Indigo (class in tooluniverse.chem_tool) infer() (tooluniverse.agentic_tool.AzureOpenAIClient method) (tooluniverse.agentic_tool.GeminiClient method) (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.BaseLLMClient method) (tooluniverse.llm_clients.GeminiClient method) info() (in module tooluniverse.execute_function) (in module tooluniverse.logging_config) init_poolmanager() (tooluniverse.uspto_tool.HTTPAdapter method) init_tool() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) insert_after() (tooluniverse.odphp_tool.BeautifulSoup method) insert_before() (tooluniverse.odphp_tool.BeautifulSoup method) inspect_job() (tooluniverse.embedding_sync.HfApi method) inspect_scheduled_job() (tooluniverse.embedding_sync.HfApi method) instructions (tooluniverse.smcp.FastMCP property) is_available() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) is_available_locally() (tooluniverse.remote_tool.RemoteTool method) is_block_device() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_char_device() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_dir() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_exhausted() (tooluniverse.uspto_tool.Retry method) is_fifo() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_file() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_mount() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_retry() (tooluniverse.uspto_tool.Retry method) is_socket() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_symlink() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) is_xml (tooluniverse.odphp_tool.BeautifulSoup attribute) isoformat() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) iterateCDX() (tooluniverse.chem_tool.Indigo method) iterateCDXFile() (tooluniverse.chem_tool.Indigo method) iterateCML() (tooluniverse.chem_tool.Indigo method) iterateCMLFile() (tooluniverse.chem_tool.Indigo method) iterateRDF() (tooluniverse.chem_tool.Indigo method) iterateRDFile() (tooluniverse.chem_tool.Indigo method) iterateSDF() (tooluniverse.chem_tool.Indigo method) iterateSDFile() (tooluniverse.chem_tool.Indigo method) iterateSmiles() (tooluniverse.chem_tool.Indigo method) iterateSmilesFile() (tooluniverse.chem_tool.Indigo method) iterateTautomers() (tooluniverse.chem_tool.Indigo method) iterative_code_improvement() (in module tooluniverse.compose_scripts.tool_discover) iterdir() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) J jsonify() (in module tooluniverse.tool_graph_web_ui) L lazy_import_tool() (in module tooluniverse.tool_registry) lchmod() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) link_to() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) list_accepted_access_requests() (tooluniverse.embedding_sync.HfApi method) list_built_in_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) list_collections() (tooluniverse.embedding_sync.HfApi method) list_datasets() (tooluniverse.embedding_sync.HfApi method) list_inference_catalog() (tooluniverse.embedding_sync.HfApi method) list_inference_endpoints() (tooluniverse.embedding_sync.HfApi method) list_jobs() (tooluniverse.embedding_sync.HfApi method) list_lfs_files() (tooluniverse.embedding_sync.HfApi method) list_liked_repos() (tooluniverse.embedding_sync.HfApi method) list_mcp_connections() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) list_mcp_tools() (in module tooluniverse.mcp_tool_registry) list_models() (tooluniverse.embedding_sync.HfApi method) list_organization_members() (tooluniverse.embedding_sync.HfApi method) list_papers() (tooluniverse.embedding_sync.HfApi method) list_pending_access_requests() (tooluniverse.embedding_sync.HfApi method) list_prompts() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) list_rejected_access_requests() (tooluniverse.embedding_sync.HfApi method) list_repo_commits() (tooluniverse.embedding_sync.HfApi method) list_repo_files() (tooluniverse.embedding_sync.HfApi method) list_repo_likers() (tooluniverse.embedding_sync.HfApi method) list_repo_refs() (tooluniverse.embedding_sync.HfApi method) list_repo_tree() (tooluniverse.embedding_sync.HfApi method) list_resources() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) list_scheduled_jobs() (tooluniverse.embedding_sync.HfApi method) list_spaces() (tooluniverse.embedding_sync.HfApi method) list_tools() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) list_user_followers() (tooluniverse.embedding_sync.HfApi method) list_user_following() (tooluniverse.embedding_sync.HfApi method) list_webhooks() (tooluniverse.embedding_sync.HfApi method) load() (tooluniverse.tool_finder_embedding.SentenceTransformer static method) load_defaults_from_file() (tooluniverse.admetai_tool.BaseTool class method) (tooluniverse.agentic_tool.BaseTool class method) (tooluniverse.alphafold_tool.BaseTool class method) (tooluniverse.base_tool.BaseTool class method) (tooluniverse.BaseTool class method) (tooluniverse.boltz_tool.BaseTool class method) (tooluniverse.chem_tool.BaseTool class method) (tooluniverse.compose_tool.BaseTool class method) (tooluniverse.custom_tool.BaseTool class method) (tooluniverse.dailymed_tool.BaseTool class method) (tooluniverse.dataset_tool.BaseTool class method) (tooluniverse.efo_tool.BaseTool class method) (tooluniverse.embedding_database.BaseTool class method) (tooluniverse.embedding_sync.BaseTool class method) (tooluniverse.enrichr_tool.BaseTool class method) (tooluniverse.europe_pmc_tool.BaseTool class method) (tooluniverse.gene_ontology_tool.BaseTool class method) (tooluniverse.graphql_tool.BaseTool class method) (tooluniverse.gwas_tool.BaseTool class method) (tooluniverse.hpa_tool.BaseTool class method) (tooluniverse.humanbase_tool.BaseTool class method) (tooluniverse.mcp_client_tool.BaseTool class method) (tooluniverse.medlineplus_tool.BaseTool class method) (tooluniverse.odphp_tool.BaseTool class method) (tooluniverse.openalex_tool.BaseTool class method) (tooluniverse.openfda_adv_tool.BaseTool class method) (tooluniverse.openfda_tool.BaseTool class method) (tooluniverse.package_tool.BaseTool class method) (tooluniverse.pubchem_tool.BaseTool class method) (tooluniverse.pubtator_tool.BaseTool class method) (tooluniverse.rcsb_pdb_tool.BaseTool class method) (tooluniverse.reactome_tool.BaseTool class method) (tooluniverse.remote_tool.BaseTool class method) (tooluniverse.semantic_scholar_tool.BaseTool class method) (tooluniverse.tool_finder_embedding.BaseTool class method) (tooluniverse.tool_finder_keyword.BaseTool class method) (tooluniverse.tool_finder_llm.BaseTool class method) (tooluniverse.uniprot_tool.BaseTool class method) (tooluniverse.url_tool.BaseTool class method) (tooluniverse.uspto_tool.BaseTool class method) (tooluniverse.xml_tool.BaseTool class method) load_dotenv() (in module tooluniverse.uspto_tool) load_mcp_tools() (in module tooluniverse.mcp_integration) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) load_mcp_tools_to_tooluniverse() (in module tooluniverse.mcp_tool_registry) load_rag_model() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) load_tool_desc_embedding() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) load_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) load_tools_from_names_list() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) loadBuffer() (tooluniverse.chem_tool.Indigo method) loadFasta() (tooluniverse.chem_tool.Indigo method) loadFastaFromFile() (tooluniverse.chem_tool.Indigo method) loadFingerprintFromBuffer() (tooluniverse.chem_tool.Indigo method) loadFingerprintFromDescriptors() (tooluniverse.chem_tool.Indigo method) loadHelm() (tooluniverse.chem_tool.Indigo method) loadHelmFromFile() (tooluniverse.chem_tool.Indigo method) loadIdt() (tooluniverse.chem_tool.Indigo method) loadIdtFromFile() (tooluniverse.chem_tool.Indigo method) loadKetDocument() (tooluniverse.chem_tool.Indigo method) loadKetDocumentFromFile() (tooluniverse.chem_tool.Indigo method) loadMolecule() (tooluniverse.chem_tool.Indigo method) loadMoleculeFromBuffer() (tooluniverse.chem_tool.Indigo method) loadMoleculeFromFile() (tooluniverse.chem_tool.Indigo method) loadMoleculeWithLib() (tooluniverse.chem_tool.Indigo method) loadMoleculeWithLibFromBuffer() (tooluniverse.chem_tool.Indigo method) loadMoleculeWithLibFromFile() (tooluniverse.chem_tool.Indigo method) loadMonomerLibrary() (tooluniverse.chem_tool.Indigo method) loadMonomerLibraryFromFile() (tooluniverse.chem_tool.Indigo method) loadQueryMolecule() (tooluniverse.chem_tool.Indigo method) loadQueryMoleculeFromFile() (tooluniverse.chem_tool.Indigo method) loadQueryMoleculeWithLib() (tooluniverse.chem_tool.Indigo method) loadQueryMoleculeWithLibFromFile() (tooluniverse.chem_tool.Indigo method) loadQueryReaction() (tooluniverse.chem_tool.Indigo method) loadQueryReactionFromFile() (tooluniverse.chem_tool.Indigo method) loadQueryReactionFromFileWithLib() (tooluniverse.chem_tool.Indigo method) loadQueryReactionWithLib() (tooluniverse.chem_tool.Indigo method) loadReaction() (tooluniverse.chem_tool.Indigo method) loadReactionFromFile() (tooluniverse.chem_tool.Indigo method) loadReactionFromFileWithLib() (tooluniverse.chem_tool.Indigo method) loadReactionSmarts() (tooluniverse.chem_tool.Indigo method) loadReactionSmartsFromFile() (tooluniverse.chem_tool.Indigo method) loadReactionWithLib() (tooluniverse.chem_tool.Indigo method) loadSequence() (tooluniverse.chem_tool.Indigo method) loadSequenceFromFile() (tooluniverse.chem_tool.Indigo method) loadSmarts() (tooluniverse.chem_tool.Indigo method) loadSmartsFromFile() (tooluniverse.chem_tool.Indigo method) loadString() (tooluniverse.chem_tool.Indigo method) loadStructure() (tooluniverse.chem_tool.Indigo method) loadStructureFromBuffer() (tooluniverse.chem_tool.Indigo method) loadStructureFromFile() (tooluniverse.chem_tool.Indigo method) log_exception() (tooluniverse.tool_graph_web_ui.Flask method) log_hook_execution() (in module tooluniverse.logging_config) LoggingHook (class in tooluniverse.extended_hooks) lstat() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) M make_default_options_response() (tooluniverse.tool_graph_web_ui.Flask method) make_response() (tooluniverse.tool_graph_web_ui.Flask method) make_shell_context() (tooluniverse.tool_graph_web_ui.Flask method) map_properties_to_openfda_fields() (in module tooluniverse.openfda_tool) max (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) max_seq_length (tooluniverse.tool_finder_embedding.SentenceTransformer property) max_summary_length (tooluniverse.output_hook.SummarizationHook attribute) MCPAutoLoaderTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPClientTool (class in tooluniverse) (class in tooluniverse.mcp_client_tool) MCPProxyTool (class in tooluniverse.mcp_client_tool) MCPServerDiscovery (class in tooluniverse.mcp_client_tool) MedlinePlusRESTTool (class in tooluniverse) (class in tooluniverse.medlineplus_tool) merge_pull_request() (tooluniverse.embedding_sync.HfApi method) microsecond (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) min (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) minimal() (in module tooluniverse.logging_config) minute (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) mkdir() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) model_card_data_class (tooluniverse.tool_finder_embedding.SentenceTransformer attribute) model_info() (tooluniverse.embedding_sync.HfApi method) ModelMetaclass (class in tooluniverse.utils) models (tooluniverse.embedding_database.OpenAI property) moderations (tooluniverse.embedding_database.OpenAI property) module tooluniverse tooluniverse.admetai_tool tooluniverse.agentic_tool tooluniverse.alphafold_tool tooluniverse.base_tool tooluniverse.boltz_tool tooluniverse.chem_tool tooluniverse.compose_scripts tooluniverse.compose_scripts.biomarker_discovery tooluniverse.compose_scripts.comprehensive_drug_discovery tooluniverse.compose_scripts.drug_safety_analyzer tooluniverse.compose_scripts.literature_tool tooluniverse.compose_scripts.output_summarizer tooluniverse.compose_scripts.tool_description_optimizer tooluniverse.compose_scripts.tool_discover tooluniverse.compose_scripts.tool_graph_composer tooluniverse.compose_scripts.tool_graph_generation tooluniverse.compose_scripts.tool_metadata_generator tooluniverse.compose_tool tooluniverse.ctg_tool tooluniverse.custom_tool tooluniverse.dailymed_tool tooluniverse.data tooluniverse.data.fda_drugs_with_brand_generic_names_for_tool tooluniverse.dataset_tool tooluniverse.default_config tooluniverse.efo_tool tooluniverse.embedding_database tooluniverse.embedding_sync tooluniverse.enrichr_tool tooluniverse.europe_pmc_tool tooluniverse.execute_function tooluniverse.extended_hooks tooluniverse.gene_ontology_tool tooluniverse.graphql_tool tooluniverse.gwas_tool tooluniverse.hpa_tool tooluniverse.humanbase_tool tooluniverse.llm_clients tooluniverse.logging_config tooluniverse.mcp_client_tool tooluniverse.mcp_integration tooluniverse.mcp_tool_registry tooluniverse.medlineplus_tool tooluniverse.odphp_tool tooluniverse.openalex_tool tooluniverse.openfda_adv_tool tooluniverse.openfda_tool tooluniverse.output_hook tooluniverse.package_tool tooluniverse.pubchem_tool tooluniverse.pubtator_tool tooluniverse.rcsb_pdb_tool tooluniverse.reactome_tool tooluniverse.remote_tool tooluniverse.restful_tool tooluniverse.semantic_scholar_tool tooluniverse.smcp tooluniverse.smcp_server tooluniverse.tool_finder_embedding tooluniverse.tool_finder_keyword tooluniverse.tool_finder_llm tooluniverse.tool_graph_web_ui tooluniverse.tool_registry tooluniverse.uniprot_tool tooluniverse.url_tool tooluniverse.uspto_tool tooluniverse.utils tooluniverse.xml_tool MonarchDiseasesForMultiplePhenoTool (class in tooluniverse) (class in tooluniverse.restful_tool) MonarchTool (class in tooluniverse) (class in tooluniverse.restful_tool) most_common() (tooluniverse.tool_finder_keyword.Counter method) mount() (tooluniverse.smcp.FastMCP method) move_repo() (tooluniverse.embedding_sync.HfApi method) N name (tooluniverse.extended_hooks.OutputHook attribute) (tooluniverse.output_hook.OutputHook attribute) (tooluniverse.smcp.FastMCP property) nameToStructure() (tooluniverse.chem_tool.Indigo method) new() (tooluniverse.uspto_tool.Retry method) new_string() (tooluniverse.odphp_tool.BeautifulSoup method) new_tag() (tooluniverse.odphp_tool.BeautifulSoup method) no_type_check() (in module tooluniverse.base_tool) normalize_gene_symbol() (in module tooluniverse.utils) now() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) num_ensembles (tooluniverse.admetai_tool.ADMETModel property) O ODPHPItemList (class in tooluniverse) (class in tooluniverse.odphp_tool) ODPHPMyHealthfinder (class in tooluniverse) (class in tooluniverse.odphp_tool) ODPHPOutlinkFetch (class in tooluniverse) (class in tooluniverse.odphp_tool) ODPHPRESTTool (class in tooluniverse.odphp_tool) ODPHPTopicSearch (class in tooluniverse) (class in tooluniverse.odphp_tool) open() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) open_instance_resource() (tooluniverse.tool_graph_web_ui.Flask method) open_resource() (tooluniverse.tool_graph_web_ui.Flask method) OpenAI (class in tooluniverse.embedding_database) OpenAlexTool (class in tooluniverse.openalex_tool) OpentargetGeneticsTool (class in tooluniverse) (class in tooluniverse.graphql_tool) OpentargetTool (class in tooluniverse) (class in tooluniverse.graphql_tool) OpentargetToolDrugNameMatch (class in tooluniverse) (class in tooluniverse.graphql_tool) OR (tooluniverse.chem_tool.Indigo attribute) organization (tooluniverse.embedding_database.OpenAI attribute) original_encoding (tooluniverse.odphp_tool.BeautifulSoup attribute) OutputHook (class in tooluniverse.extended_hooks) (class in tooluniverse.output_hook) owner() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) P PackageTool (class in tooluniverse) (class in tooluniverse.package_tool) paper_info() (tooluniverse.embedding_sync.HfApi method) parse() (in module tooluniverse.graphql_tool) parse_retry_after() (tooluniverse.uspto_tool.Retry method) parse_safetensors_file_metadata() (tooluniverse.embedding_sync.HfApi method) Path (class in tooluniverse.base_tool) (class in tooluniverse.embedding_database) (class in tooluniverse.embedding_sync) (class in tooluniverse.output_hook) (class in tooluniverse.pubtator_tool) pause_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) pause_space() (tooluniverse.embedding_sync.HfApi method) permanently_delete_lfs_files() (tooluniverse.embedding_sync.HfApi method) predict() (tooluniverse.admetai_tool.ADMETModel method) prepare_input_ids() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) prepare_one_tool_prompt() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) prepare_tool_examples() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) prepare_tool_prompts() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) preprocess_request() (tooluniverse.tool_graph_web_ui.Flask method) preupload_lfs_files() (tooluniverse.embedding_sync.HfApi method) priority (tooluniverse.extended_hooks.OutputHook attribute) (tooluniverse.output_hook.OutputHook attribute) process() (tooluniverse.extended_hooks.FilteringHook method) (tooluniverse.extended_hooks.FormattingHook method) (tooluniverse.extended_hooks.LoggingHook method) (tooluniverse.extended_hooks.OutputHook method) (tooluniverse.extended_hooks.ValidationHook method) (tooluniverse.output_hook.FileSaveHook method) (tooluniverse.output_hook.OutputHook method) (tooluniverse.output_hook.SummarizationHook method) process_response() (tooluniverse.tool_graph_web_ui.Flask method) progress() (in module tooluniverse.logging_config) progress_log() (in module tooluniverse.logging_config) project (tooluniverse.embedding_database.OpenAI attribute) prompt() (tooluniverse.smcp.FastMCP method) proxy_headers() (tooluniverse.uspto_tool.HTTPAdapter method) proxy_manager_for() (tooluniverse.uspto_tool.HTTPAdapter method) prune_item() (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) PubChemRESTTool (class in tooluniverse) (class in tooluniverse.pubchem_tool) PubTatorTool (class in tooluniverse) (class in tooluniverse.pubtator_tool) push_to_hub() (tooluniverse.tool_finder_embedding.SentenceTransformer method) Q qs (tooluniverse.embedding_database.OpenAI property) quote() (in module tooluniverse.chem_tool) (in module tooluniverse.gene_ontology_tool) R rag_infer() (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.ToolFinderEmbedding method) rag_model (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) rag_model_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) rank_paths_by_weight() (tooluniverse.enrichr_tool.EnrichrTool method) rank_paths_to_term() (tooluniverse.enrichr_tool.EnrichrTool method) RateLimitError RC_CENTER (tooluniverse.chem_tool.Indigo attribute) RC_MADE_OR_BROKEN (tooluniverse.chem_tool.Indigo attribute) RC_NOT_CENTER (tooluniverse.chem_tool.Indigo attribute) RC_ORDER_CHANGED (tooluniverse.chem_tool.Indigo attribute) RC_UNCHANGED (tooluniverse.chem_tool.Indigo attribute) RC_UNMARKED (tooluniverse.chem_tool.Indigo attribute) RCSBTool (class in tooluniverse) (class in tooluniverse.rcsb_pdb_tool) reactionProductEnumerate() (tooluniverse.chem_tool.Indigo method) ReactomeRESTTool (class in tooluniverse) (class in tooluniverse.reactome_tool) read_bytes() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) read_json_list() (in module tooluniverse.execute_function) (in module tooluniverse.utils) read_resource() (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.MCPClientTool method) read_text() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) readlink() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) realtime (tooluniverse.embedding_database.OpenAI property) refresh_tool_name_desc() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) register_config() (in module tooluniverse.tool_registry) register_custom_tool() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) register_external_tool() (in module tooluniverse.execute_function) (in module tooluniverse.tool_registry) register_mcp_tool() (in module tooluniverse.mcp_tool_registry) register_mcp_tool_from_config() (in module tooluniverse.mcp_tool_registry) register_tool() (in module tooluniverse) (in module tooluniverse.admetai_tool) (in module tooluniverse.agentic_tool) (in module tooluniverse.alphafold_tool) (in module tooluniverse.boltz_tool) (in module tooluniverse.chem_tool) (in module tooluniverse.compose_tool) (in module tooluniverse.ctg_tool) (in module tooluniverse.custom_tool) (in module tooluniverse.dailymed_tool) (in module tooluniverse.dataset_tool) (in module tooluniverse.efo_tool) (in module tooluniverse.embedding_database) (in module tooluniverse.embedding_sync) (in module tooluniverse.enrichr_tool) (in module tooluniverse.europe_pmc_tool) (in module tooluniverse.gene_ontology_tool) (in module tooluniverse.graphql_tool) (in module tooluniverse.gwas_tool) (in module tooluniverse.hpa_tool) (in module tooluniverse.humanbase_tool) (in module tooluniverse.mcp_client_tool) (in module tooluniverse.medlineplus_tool) (in module tooluniverse.odphp_tool) (in module tooluniverse.openalex_tool) (in module tooluniverse.openfda_adv_tool) (in module tooluniverse.openfda_tool) (in module tooluniverse.package_tool) (in module tooluniverse.pubchem_tool) (in module tooluniverse.pubtator_tool) (in module tooluniverse.rcsb_pdb_tool) (in module tooluniverse.reactome_tool) (in module tooluniverse.remote_tool) (in module tooluniverse.restful_tool) (in module tooluniverse.semantic_scholar_tool) (in module tooluniverse.tool_finder_embedding) (in module tooluniverse.tool_finder_keyword) (in module tooluniverse.tool_finder_llm) (in module tooluniverse.tool_registry) (in module tooluniverse.uniprot_tool) (in module tooluniverse.url_tool) (in module tooluniverse.uspto_tool) (in module tooluniverse.xml_tool) register_tools_in_engine() (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.MCPAutoLoaderTool method) reject_access_request() (tooluniverse.embedding_sync.HfApi method) reload_config() (tooluniverse.execute_function.HookManager method) (tooluniverse.output_hook.HookManager method) remote_info (tooluniverse.remote_tool.RemoteTool attribute) RemoteTool (class in tooluniverse.remote_tool) remove_keys() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) remove_none_and_empty_values() (in module tooluniverse.graphql_tool) remove_tool() (tooluniverse.smcp.FastMCP method) remove_tool_transformation() (tooluniverse.smcp.FastMCP method) removeTautomerRule() (tooluniverse.chem_tool.Indigo method) rename() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) rename_discussion() (tooluniverse.embedding_sync.HfApi method) render_template() (in module tooluniverse.tool_graph_web_ui) replace() (tooluniverse.agentic_tool.datetime method) (tooluniverse.base_tool.Path method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) (tooluniverse.tool_finder_llm.datetime method) repo_exists() (tooluniverse.embedding_sync.HfApi method) repo_info() (tooluniverse.embedding_sync.HfApi method) request_class (tooluniverse.tool_graph_web_ui.Flask attribute) request_context() (tooluniverse.tool_graph_web_ui.Flask method) request_space_hardware() (tooluniverse.embedding_sync.HfApi method) request_space_storage() (tooluniverse.embedding_sync.HfApi method) request_url() (tooluniverse.uspto_tool.HTTPAdapter method) reset() (tooluniverse.odphp_tool.BeautifulSoup method) resetOptions() (tooluniverse.chem_tool.Indigo method) resolution (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) resolve() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) resource() (tooluniverse.smcp.FastMCP method) response_class (tooluniverse.tool_graph_web_ui.Flask attribute) responses (tooluniverse.embedding_database.OpenAI property) restart_space() (tooluniverse.embedding_sync.HfApi method) RESTfulTool (class in tooluniverse.ctg_tool) (class in tooluniverse.restful_tool) resume_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) resume_scheduled_job() (tooluniverse.embedding_sync.HfApi method) Retry (class in tooluniverse.uspto_tool) RETRY_AFTER_STATUS_CODES (tooluniverse.uspto_tool.Retry attribute) retry_initialization() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) return_all_loaded_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) revision_exists() (tooluniverse.embedding_sync.HfApi method) rglob() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) rgroupComposition() (tooluniverse.chem_tool.Indigo method) RING (tooluniverse.chem_tool.Indigo attribute) rmdir() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) ROOT_TAG_NAME (tooluniverse.odphp_tool.BeautifulSoup attribute) rule (tooluniverse.extended_hooks.OutputHook attribute) (tooluniverse.output_hook.OutputHook attribute) run() (tooluniverse.admetai_tool.ADMETAITool method) (tooluniverse.admetai_tool.BaseTool method) (tooluniverse.ADMETAITool method) (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.agentic_tool.BaseTool method) (tooluniverse.AgenticTool method) (tooluniverse.alphafold_tool.AlphaFoldRESTTool method) (tooluniverse.alphafold_tool.BaseTool method) (tooluniverse.AlphaFoldRESTTool method) (tooluniverse.base_tool.BaseTool method) (tooluniverse.BaseTool method) (tooluniverse.boltz_tool.BaseTool method) (tooluniverse.boltz_tool.Boltz2DockingTool method) (tooluniverse.chem_tool.BaseTool method) (tooluniverse.chem_tool.ChEMBLTool method) (tooluniverse.ChEMBLTool method) (tooluniverse.ClinicalTrialsDetailsTool method) (tooluniverse.ClinicalTrialsSearchTool method) (tooluniverse.compose_tool.BaseTool method) (tooluniverse.compose_tool.ComposeTool method) (tooluniverse.ComposeTool method) (tooluniverse.ctg_tool.ClinicalTrialsDetailsTool method) (tooluniverse.ctg_tool.ClinicalTrialsSearchTool method) (tooluniverse.ctg_tool.ClinicalTrialsTool method) (tooluniverse.ctg_tool.RESTfulTool method) (tooluniverse.custom_tool.BaseTool method) (tooluniverse.custom_tool.CustomTool method) (tooluniverse.dailymed_tool.BaseTool method) (tooluniverse.dailymed_tool.GetSPLBySetIDTool method) (tooluniverse.dailymed_tool.SearchSPLTool method) (tooluniverse.dataset_tool.BaseTool method) (tooluniverse.dataset_tool.DatasetTool method) (tooluniverse.DatasetTool method) (tooluniverse.DiseaseTargetScoreTool method) (tooluniverse.efo_tool.BaseTool method) (tooluniverse.efo_tool.EFOTool method) (tooluniverse.EFOTool method) (tooluniverse.embedding_database.BaseTool method) (tooluniverse.embedding_database.EmbeddingDatabase method) (tooluniverse.embedding_sync.BaseTool method) (tooluniverse.embedding_sync.EmbeddingSync method) (tooluniverse.EmbeddingDatabase method) (tooluniverse.EmbeddingSync method) (tooluniverse.enrichr_tool.BaseTool method) (tooluniverse.enrichr_tool.EnrichrTool method) (tooluniverse.europe_pmc_tool.BaseTool method) (tooluniverse.europe_pmc_tool.EuropePMCTool method) (tooluniverse.EuropePMCTool method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.FDACountAdditiveReactionsTool method) (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.FDADrugLabelSearchIDTool method) (tooluniverse.FDADrugLabelSearchTool method) (tooluniverse.gene_ontology_tool.BaseTool method) (tooluniverse.gene_ontology_tool.GeneOntologyTool method) (tooluniverse.GetSPLBySetIDTool method) (tooluniverse.graphql_tool.BaseTool method) (tooluniverse.graphql_tool.DiseaseTargetScoreTool method) (tooluniverse.graphql_tool.GraphQLTool method) (tooluniverse.graphql_tool.OpentargetTool method) (tooluniverse.graphql_tool.OpentargetToolDrugNameMatch method) (tooluniverse.gwas_tool.BaseTool method) (tooluniverse.gwas_tool.GWASAssociationByID method) (tooluniverse.gwas_tool.GWASAssociationSearch method) (tooluniverse.gwas_tool.GWASAssociationsForSNP method) (tooluniverse.gwas_tool.GWASAssociationsForStudy method) (tooluniverse.gwas_tool.GWASAssociationsForTrait method) (tooluniverse.gwas_tool.GWASRESTTool method) (tooluniverse.gwas_tool.GWASSNPByID method) (tooluniverse.gwas_tool.GWASSNPSearch method) (tooluniverse.gwas_tool.GWASSNPsForGene method) (tooluniverse.gwas_tool.GWASStudiesForTrait method) (tooluniverse.gwas_tool.GWASStudyByID method) (tooluniverse.gwas_tool.GWASStudySearch method) (tooluniverse.gwas_tool.GWASVariantsForTrait method) (tooluniverse.GWASAssociationByID method) (tooluniverse.GWASAssociationSearch method) (tooluniverse.GWASAssociationsForSNP method) (tooluniverse.GWASAssociationsForStudy method) (tooluniverse.GWASAssociationsForTrait method) (tooluniverse.GWASSNPByID method) (tooluniverse.GWASSNPSearch method) (tooluniverse.GWASSNPsForGene method) (tooluniverse.GWASStudiesForTrait method) (tooluniverse.GWASStudyByID method) (tooluniverse.GWASStudySearch method) (tooluniverse.GWASVariantsForTrait method) (tooluniverse.hpa_tool.BaseTool method) (tooluniverse.hpa_tool.HPAGetBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetCancerPrognosticsTool method) (tooluniverse.hpa_tool.HPAGetComparativeExpressionTool method) (tooluniverse.hpa_tool.HPAGetContextualBiologicalProcessTool method) (tooluniverse.hpa_tool.HPAGetDiseaseExpressionTool method) (tooluniverse.hpa_tool.HPAGetGeneJSONTool method) (tooluniverse.hpa_tool.HPAGetGenePageDetailsTool method) (tooluniverse.hpa_tool.HPAGetGeneXMLTool method) (tooluniverse.hpa_tool.HPAGetProteinInteractionsTool method) (tooluniverse.hpa_tool.HPAGetRnaExpressionBySourceTool method) (tooluniverse.hpa_tool.HPAGetRnaExpressionByTissueTool method) (tooluniverse.hpa_tool.HPAGetSubcellularLocationTool method) (tooluniverse.hpa_tool.HPASearchGenesTool method) (tooluniverse.HPAGetGeneJSONTool method) (tooluniverse.HPAGetGeneXMLTool method) (tooluniverse.humanbase_tool.BaseTool method) (tooluniverse.humanbase_tool.HumanBaseTool method) (tooluniverse.mcp_client_tool.BaseTool method) (tooluniverse.mcp_client_tool.MCPAutoLoaderTool method) (tooluniverse.mcp_client_tool.MCPClientTool method) (tooluniverse.mcp_client_tool.MCPProxyTool method) (tooluniverse.MCPAutoLoaderTool method) (tooluniverse.MCPClientTool method) (tooluniverse.medlineplus_tool.BaseTool method) (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) (tooluniverse.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.MonarchTool method) (tooluniverse.odphp_tool.BaseTool method) (tooluniverse.odphp_tool.ODPHPItemList method) (tooluniverse.odphp_tool.ODPHPMyHealthfinder method) (tooluniverse.odphp_tool.ODPHPOutlinkFetch method) (tooluniverse.odphp_tool.ODPHPTopicSearch method) (tooluniverse.ODPHPItemList method) (tooluniverse.ODPHPMyHealthfinder method) (tooluniverse.ODPHPOutlinkFetch method) (tooluniverse.ODPHPTopicSearch method) (tooluniverse.openalex_tool.BaseTool method) (tooluniverse.openalex_tool.OpenAlexTool method) (tooluniverse.openfda_adv_tool.BaseTool method) (tooluniverse.openfda_adv_tool.FDACountAdditiveReactionsTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) (tooluniverse.openfda_tool.BaseTool method) (tooluniverse.openfda_tool.FDADrugLabelGetDrugGenericNameTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchIDTool method) (tooluniverse.openfda_tool.FDADrugLabelSearchTool method) (tooluniverse.openfda_tool.FDATool method) (tooluniverse.OpentargetTool method) (tooluniverse.OpentargetToolDrugNameMatch method) (tooluniverse.package_tool.BaseTool method) (tooluniverse.package_tool.PackageTool method) (tooluniverse.PackageTool method) (tooluniverse.pubchem_tool.BaseTool method) (tooluniverse.pubchem_tool.PubChemRESTTool method) (tooluniverse.PubChemRESTTool method) (tooluniverse.pubtator_tool.BaseTool method) (tooluniverse.pubtator_tool.PubTatorTool method) (tooluniverse.PubTatorTool method) (tooluniverse.rcsb_pdb_tool.BaseTool method) (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) (tooluniverse.reactome_tool.BaseTool method) (tooluniverse.reactome_tool.ReactomeRESTTool method) (tooluniverse.ReactomeRESTTool method) (tooluniverse.remote_tool.BaseTool method) (tooluniverse.remote_tool.RemoteTool method) (tooluniverse.restful_tool.GraphQLTool method) (tooluniverse.restful_tool.MonarchDiseasesForMultiplePhenoTool method) (tooluniverse.restful_tool.MonarchTool method) (tooluniverse.restful_tool.RESTfulTool method) (tooluniverse.SearchSPLTool method) (tooluniverse.semantic_scholar_tool.BaseTool method) (tooluniverse.semantic_scholar_tool.SemanticScholarTool method) (tooluniverse.SemanticScholarTool method) (tooluniverse.smcp.FastMCP method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.tool_finder_embedding.BaseTool method) (tooluniverse.tool_finder_embedding.ToolFinderEmbedding method) (tooluniverse.tool_finder_keyword.BaseTool method) (tooluniverse.tool_finder_keyword.ToolFinderKeyword method) (tooluniverse.tool_finder_llm.AgenticTool method) (tooluniverse.tool_finder_llm.BaseTool method) (tooluniverse.tool_finder_llm.ToolFinderLLM method) (tooluniverse.tool_graph_web_ui.Flask method) (tooluniverse.tool_graph_web_ui.ToolGraphWebUI method) (tooluniverse.ToolFinderEmbedding method) (tooluniverse.ToolFinderKeyword method) (tooluniverse.ToolFinderLLM method) (tooluniverse.ToolUniverse method) (tooluniverse.uniprot_tool.BaseTool method) (tooluniverse.uniprot_tool.UniProtRESTTool method) (tooluniverse.UniProtRESTTool method) (tooluniverse.url_tool.BaseTool method) (tooluniverse.url_tool.URLHTMLTagTool method) (tooluniverse.url_tool.URLToPDFTextTool method) (tooluniverse.URLHTMLTagTool method) (tooluniverse.URLToPDFTextTool method) (tooluniverse.uspto_tool.BaseTool method) (tooluniverse.uspto_tool.USPTOOpenDataPortalTool method) (tooluniverse.USPTOOpenDataPortalTool method) (tooluniverse.xml_tool.BaseTool method) (tooluniverse.xml_tool.XMLDatasetTool method) (tooluniverse.XMLDatasetTool method) run_as_future() (tooluniverse.embedding_sync.HfApi method) run_async() (tooluniverse.smcp.FastMCP method) run_http_async() (tooluniverse.smcp.FastMCP method) run_http_server() (in module tooluniverse.smcp_server) run_job() (tooluniverse.embedding_sync.HfApi method) run_one_function() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) run_simple() (tooluniverse.SMCP method) (tooluniverse.smcp.SMCP method) (tooluniverse.smcp_server.SMCP method) run_smcp_server() (in module tooluniverse.smcp_server) run_sse_async() (tooluniverse.smcp.FastMCP method) run_stdio_async() (tooluniverse.smcp.FastMCP method) run_stdio_server() (in module tooluniverse.smcp_server) run_streamable_http_async() (tooluniverse.smcp.FastMCP method) run_uv_job() (tooluniverse.embedding_sync.HfApi method) S samefile() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) save() (tooluniverse.tool_finder_embedding.SentenceTransformer method) save_pretrained() (tooluniverse.tool_finder_embedding.SentenceTransformer method) save_to_hub() (tooluniverse.tool_finder_embedding.SentenceTransformer method) scale_to_zero_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) search_literature() (tooluniverse.openalex_tool.OpenAlexTool method) search_openfda() (in module tooluniverse.openfda_tool) search_terms() (tooluniverse.gene_ontology_tool.GeneOntologyTool method) search_topics_by_keyword() (tooluniverse.medlineplus_tool.MedlinePlusRESTTool method) (tooluniverse.MedlinePlusRESTTool method) SearchSPLTool (class in tooluniverse) (class in tooluniverse.dailymed_tool) second (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) select_tools() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) SemanticScholarTool (class in tooluniverse) (class in tooluniverse.semantic_scholar_tool) send() (tooluniverse.uspto_tool.HTTPAdapter method) send_static_file() (tooluniverse.tool_graph_web_ui.Flask method) SentenceTransformer (class in tooluniverse.tool_finder_embedding) session_interface (tooluniverse.tool_graph_web_ui.Flask attribute) set_level() (tooluniverse.logging_config.ToolUniverseLogger method) set_log_level() (in module tooluniverse.execute_function) (in module tooluniverse.logging_config) set_pooling_include_prompt() (tooluniverse.tool_finder_embedding.SentenceTransformer method) set_space_sleep_time() (tooluniverse.embedding_sync.HfApi method) setOption() (tooluniverse.chem_tool.Indigo method) setTautomerRule() (tooluniverse.chem_tool.Indigo method) settings (tooluniverse.smcp.FastMCP property) setup_logging() (in module tooluniverse.logging_config) SG_TYPE_ANY (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_COM (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_COP (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_CRO (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_DAT (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_FOR (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_GEN (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_GRA (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_MER (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_MIX (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_MOD (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_MON (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_MUL (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_SRU (tooluniverse.chem_tool.Indigo attribute) SG_TYPE_SUP (tooluniverse.chem_tool.Indigo attribute) should_trigger() (tooluniverse.extended_hooks.OutputHook method) (tooluniverse.output_hook.OutputHook method) shutdown() (tooluniverse.smcp.ThreadPoolExecutor method) similarity (tooluniverse.tool_finder_embedding.SentenceTransformer property) similarity() (tooluniverse.chem_tool.Indigo method) similarity_fn_name (tooluniverse.tool_finder_embedding.SentenceTransformer property) similarity_pairwise (tooluniverse.tool_finder_embedding.SentenceTransformer property) SINGLET (tooluniverse.chem_tool.Indigo attribute) sleep() (tooluniverse.uspto_tool.Retry method) sleep_for_retry() (tooluniverse.uspto_tool.Retry method) SMCP (class in tooluniverse) (class in tooluniverse.smcp) (class in tooluniverse.smcp_server) snapshot_download() (in module tooluniverse.embedding_sync) (tooluniverse.embedding_sync.HfApi method) space_info() (tooluniverse.embedding_sync.HfApi method) special_tools_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) sse_app() (tooluniverse.smcp.FastMCP method) start_mcp_server() (in module tooluniverse.mcp_tool_registry) start_mcp_server_for_tool() (in module tooluniverse.mcp_tool_registry) start_multi_process_pool() (tooluniverse.tool_finder_embedding.SentenceTransformer method) stat() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) STEMMING_RULES (tooluniverse.tool_finder_keyword.ToolFinderKeyword attribute) (tooluniverse.ToolFinderKeyword attribute) stop_mcp_server() (in module tooluniverse.mcp_tool_registry) stop_multi_process_pool() (tooluniverse.tool_finder_embedding.SentenceTransformer static method) STOP_WORDS (tooluniverse.tool_finder_keyword.ToolFinderKeyword attribute) (tooluniverse.ToolFinderKeyword attribute) streamable_http_app() (tooluniverse.smcp.FastMCP method) string_container() (tooluniverse.odphp_tool.BeautifulSoup method) strptime() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) submit() (tooluniverse.smcp.ThreadPoolExecutor method) submit_gene_list() (tooluniverse.enrichr_tool.EnrichrTool method) substructureMatcher() (tooluniverse.chem_tool.Indigo method) subtract() (tooluniverse.tool_finder_keyword.Counter method) SummarizationHook (class in tooluniverse.output_hook) super_squash_history() (tooluniverse.embedding_sync.HfApi method) suspend_scheduled_job() (tooluniverse.embedding_sync.HfApi method) symlink_to() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) sync_playwright() (in module tooluniverse.url_tool) T test_api() (tooluniverse.agentic_tool.AzureOpenAIClient method) (tooluniverse.agentic_tool.GeminiClient method) (tooluniverse.llm_clients.AzureOpenAIClient method) (tooluniverse.llm_clients.BaseLLMClient method) (tooluniverse.llm_clients.GeminiClient method) test_cli_runner() (tooluniverse.tool_graph_web_ui.Flask method) test_client() (tooluniverse.tool_graph_web_ui.Flask method) test_request_context() (tooluniverse.tool_graph_web_ui.Flask method) ThreadPoolExecutor (class in tooluniverse.smcp) time() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) timestamp() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) timetuple() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) timetz() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) toggle_hooks() (tooluniverse.execute_function.HookManager method) (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.output_hook.HookManager method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) tokenize() (tooluniverse.tool_finder_embedding.SentenceTransformer method) tokenizer (tooluniverse.tool_finder_embedding.SentenceTransformer property) tool() (tooluniverse.smcp.FastMCP method) tool_category_dicts (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.smcp.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) tool_config (tooluniverse.remote_tool.RemoteTool attribute) tool_desc_embedding (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tool_embedding_path (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tool_files (tooluniverse.execute_function.ToolUniverse attribute) (tooluniverse.smcp.ToolUniverse attribute) (tooluniverse.ToolUniverse attribute) tool_name (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tool_specification() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) tool_to_str() (tooluniverse.execute_function.ToolUniverse method) (tooluniverse.smcp.ToolUniverse method) (tooluniverse.ToolUniverse method) ToolExecutionError ToolFinderEmbedding (class in tooluniverse) (class in tooluniverse.tool_finder_embedding) ToolFinderKeyword (class in tooluniverse) (class in tooluniverse.tool_finder_keyword) ToolFinderLLM (class in tooluniverse) (class in tooluniverse.tool_finder_llm) ToolGraphWebUI (class in tooluniverse.tool_graph_web_ui) tooluniverse module ToolUniverse (class in tooluniverse) (class in tooluniverse.execute_function) (class in tooluniverse.smcp) tooluniverse (tooluniverse.execute_function.HookManager attribute) (tooluniverse.output_hook.HookManager attribute) (tooluniverse.output_hook.SummarizationHook attribute) (tooluniverse.tool_finder_embedding.ToolFinderEmbedding attribute) (tooluniverse.ToolFinderEmbedding attribute) tooluniverse.admetai_tool module tooluniverse.agentic_tool module tooluniverse.alphafold_tool module tooluniverse.base_tool module tooluniverse.boltz_tool module tooluniverse.chem_tool module tooluniverse.compose_scripts module tooluniverse.compose_scripts.biomarker_discovery module tooluniverse.compose_scripts.comprehensive_drug_discovery module tooluniverse.compose_scripts.drug_safety_analyzer module tooluniverse.compose_scripts.literature_tool module tooluniverse.compose_scripts.output_summarizer module tooluniverse.compose_scripts.tool_description_optimizer module tooluniverse.compose_scripts.tool_discover module tooluniverse.compose_scripts.tool_graph_composer module tooluniverse.compose_scripts.tool_graph_generation module tooluniverse.compose_scripts.tool_metadata_generator module tooluniverse.compose_tool module tooluniverse.ctg_tool module tooluniverse.custom_tool module tooluniverse.dailymed_tool module tooluniverse.data module tooluniverse.data.fda_drugs_with_brand_generic_names_for_tool module tooluniverse.dataset_tool module tooluniverse.default_config module tooluniverse.efo_tool module tooluniverse.embedding_database module tooluniverse.embedding_sync module tooluniverse.enrichr_tool module tooluniverse.europe_pmc_tool module tooluniverse.execute_function module tooluniverse.extended_hooks module tooluniverse.gene_ontology_tool module tooluniverse.graphql_tool module tooluniverse.gwas_tool module tooluniverse.hpa_tool module tooluniverse.humanbase_tool module tooluniverse.llm_clients module tooluniverse.logging_config module tooluniverse.mcp_client_tool module tooluniverse.mcp_integration module tooluniverse.mcp_tool_registry module tooluniverse.medlineplus_tool module tooluniverse.odphp_tool module tooluniverse.openalex_tool module tooluniverse.openfda_adv_tool module tooluniverse.openfda_tool module tooluniverse.output_hook module tooluniverse.package_tool module tooluniverse.pubchem_tool module tooluniverse.pubtator_tool module tooluniverse.rcsb_pdb_tool module tooluniverse.reactome_tool module tooluniverse.remote_tool module tooluniverse.restful_tool module tooluniverse.semantic_scholar_tool module tooluniverse.smcp module tooluniverse.smcp_server module tooluniverse.tool_finder_embedding module tooluniverse.tool_finder_keyword module tooluniverse.tool_finder_llm module tooluniverse.tool_graph_web_ui module tooluniverse.tool_registry module tooluniverse.uniprot_tool module tooluniverse.url_tool module tooluniverse.uspto_tool module tooluniverse.utils module tooluniverse.xml_tool module ToolUniverseFormatter (class in tooluniverse.logging_config) ToolUniverseLogger (class in tooluniverse.logging_config) total() (tooluniverse.tool_finder_keyword.Counter method) touch() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) TRANS (tooluniverse.chem_tool.Indigo attribute) transform() (tooluniverse.chem_tool.Indigo method) transformers_model (tooluniverse.tool_finder_embedding.SentenceTransformer property) transformHELMtoSCSR() (tooluniverse.chem_tool.Indigo method) TRIPLET (tooluniverse.chem_tool.Indigo attribute) truncate_sentence_embeddings() (tooluniverse.tool_finder_embedding.SentenceTransformer method) tzinfo (tooluniverse.agentic_tool.datetime attribute) (tooluniverse.compose_scripts.tool_graph_composer.datetime attribute) (tooluniverse.embedding_sync.datetime attribute) (tooluniverse.tool_finder_llm.datetime attribute) tzname() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) U unescape() (in module tooluniverse.url_tool) UniProtRESTTool (class in tooluniverse) (class in tooluniverse.uniprot_tool) unlike() (tooluniverse.embedding_sync.HfApi method) unlink() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) unserialize() (tooluniverse.chem_tool.Indigo method) UP (tooluniverse.chem_tool.Indigo attribute) update() (tooluniverse.tool_finder_keyword.Counter method) update_collection_item() (tooluniverse.embedding_sync.HfApi method) update_collection_metadata() (tooluniverse.embedding_sync.HfApi method) update_inference_endpoint() (tooluniverse.embedding_sync.HfApi method) update_repo_settings() (tooluniverse.embedding_sync.HfApi method) update_repo_visibility() (tooluniverse.embedding_sync.HfApi method) update_template_context() (tooluniverse.tool_graph_web_ui.Flask method) update_webhook() (tooluniverse.embedding_sync.HfApi method) upload_file() (tooluniverse.embedding_sync.HfApi method) upload_folder() (in module tooluniverse.embedding_sync) (tooluniverse.embedding_sync.HfApi method) upload_large_folder() (tooluniverse.embedding_sync.HfApi method) uploads (tooluniverse.embedding_database.OpenAI property) url_for() (tooluniverse.tool_graph_web_ui.Flask method) URLHTMLTagTool (class in tooluniverse) (class in tooluniverse.url_tool) urljoin() (in module tooluniverse.ctg_tool) (in module tooluniverse.mcp_client_tool) URLToPDFTextTool (class in tooluniverse) (class in tooluniverse.url_tool) USPTOOpenDataPortalTool (class in tooluniverse) (class in tooluniverse.uspto_tool) utcfromtimestamp() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) utcnow() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) utcoffset() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) utctimetuple() (tooluniverse.agentic_tool.datetime method) (tooluniverse.compose_scripts.tool_graph_composer.datetime method) (tooluniverse.embedding_sync.datetime method) (tooluniverse.tool_finder_llm.datetime method) V validate() (in module tooluniverse.graphql_tool) validate_configuration() (tooluniverse.agentic_tool.AgenticTool method) (tooluniverse.AgenticTool method) (tooluniverse.tool_finder_llm.AgenticTool method) validate_enum_arguments() (tooluniverse.FDADrugAdverseEventTool method) (tooluniverse.openfda_adv_tool.FDADrugAdverseEventTool method) validate_hook_conditions() (in module tooluniverse.utils) validate_hook_config() (in module tooluniverse.utils) validate_params() (tooluniverse.rcsb_pdb_tool.RCSBTool method) (tooluniverse.RCSBTool method) validate_query() (in module tooluniverse.graphql_tool) (in module tooluniverse.utils) ValidationError ValidationHook (class in tooluniverse.extended_hooks) vector_stores (tooluniverse.embedding_database.OpenAI property) verbose() (in module tooluniverse.logging_config) version (tooluniverse.smcp.FastMCP property) version() (tooluniverse.chem_tool.Indigo method) versionInfo() (tooluniverse.chem_tool.Indigo method) W warning() (in module tooluniverse.execute_function) (in module tooluniverse.logging_config) webhook_secret (tooluniverse.embedding_database.OpenAI attribute) webhooks (tooluniverse.embedding_database.OpenAI property) websocket_base_url (tooluniverse.embedding_database.OpenAI attribute) whoami() (tooluniverse.embedding_sync.HfApi method) with_options() (tooluniverse.embedding_database.AzureOpenAI method) (tooluniverse.embedding_database.OpenAI method) with_raw_response (tooluniverse.embedding_database.OpenAI property) with_streaming_response (tooluniverse.embedding_database.OpenAI property) write_bytes() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) write_text() (tooluniverse.base_tool.Path method) (tooluniverse.embedding_database.Path method) (tooluniverse.embedding_sync.Path method) (tooluniverse.output_hook.Path method) (tooluniverse.pubtator_tool.Path method) writeBuffer() (tooluniverse.chem_tool.Indigo method) writeFile() (tooluniverse.chem_tool.Indigo method) wsgi_app() (tooluniverse.tool_graph_web_ui.Flask method) X XMLDatasetTool (class in tooluniverse) (class in tooluniverse.xml_tool) Y yaml_to_dict() (in module tooluniverse.utils)