Tool reference

alphafold-sovereign-mcp exposes 29 MCP tools organised into four modules.

At a glance

Module	Tools	What it does
Disease	lookup_disease, search_diseases, get_disease_targets, …	Ontology lookups (MONDO, HPO), disease-target evidence from Open Targets.
Precision medicine	generate_variant_clinical_report, classify_variant_acmg, assess_target_druggability, …	Variant triage (Ensembl VEP + ClinVar + gnomAD + AlphaMissense + AlphaFold), druggability heuristic.
Structure intelligence	analyze_structural_confidence, compute_topology_fingerprint, compare_proteins_topologically, …	AlphaFold model retrieval, pLDDT, PAE matrices, persistent-homology fingerprints.
Knowledge graph	query_variant_database, find_drug_gene_network, export_research_dataset, …	Traversal and export of the local SQLite knowledge graph.

Tool annotations

Every tool decorates @mcp.tool() with MCP-spec annotations:

• readOnlyHint=True — none of the tools mutate state outside the local cache.
• idempotentHint=True — re-running with the same args gives the same result (modulo upstream data drift).
• openWorldHint=True — most tools call live upstream APIs.

Provenance

Every tool result carries a provenance footer listing the server version, a UTC timestamp, and the upstream data sources that contributed to the response (the disease-layer tools additionally return a sources_queried field). The SQLite knowledge graph can record tool invocations via KnowledgeGraph.log_tool_invocation, but this writer is not yet hooked into tool dispatch, so the audit trail is populated only when a caller logs explicitly.

Limitations

The scientific outputs of the precision-medicine tools (the ACMG draft and the druggability tier) are not validated by independent domain experts. See Limitations L1 + L2 for details and Status — Roadmap (validation, post-1.2.0) for the validation plan.