Tool reference¶
alphafold-sovereign-mcp exposes 25 MCP tools organised into four
modules.
At a glance¶
| Module | Tools | What it does |
|---|---|---|
| Disease | query_disease_ontology, explore_disease_target_landscape, … |
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 | fetch_alphafold_structure, compute_structure_fingerprint, compare_structures, … |
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 accumulated 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 includes a sources_cited array listing the
upstream APIs that contributed to the response. The local cache
records every tool invocation in the SQLite knowledge graph for
later query via the knowledge-graph tools.
⚠ 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 to v1.2.0 for the validation plan.