docs/API.md

BioNexus API (automatically generated)

Generated by scripts/generate_docs.py — do not edit by hand.

• POST /api/admet/descriptors — Compute molecular descriptors from SMILES / chemical name / PubChem CID.
• POST /api/admet/protox — ProTox 3.0 ML-based toxicity prediction (Charité).
• GET /api/admet/search — PubChem autocomplete for chemical name search.
• GET /api/admin/cache-stats —
• POST /api/admin/cache-stats/reset —
• POST /api/ai/interpret —
• POST /api/ai/interpret/stream —
• POST /api/ai/tool-interpret — Generate a plain-language AI interpretation of a single tool result on demand.
• POST /api/alignment/pairwise —
• POST /api/alignment/run —
• POST /api/audit/event —
• GET /api/audit/insights —
• GET /api/benchmarks — Benchmark catalog (BBS-1 expansion), optionally filtered by category.
• POST /api/benchmarks/seed — Upsert the JSON benchmark catalog (app/data/benchmarks) into the DB.
• GET /api/benchmarks/summary — Per-category pass/fail statistics across recorded benchmark runs.
• GET /api/benchmarks/{benchmark_id} —
• POST /api/benchmarks/{benchmark_id}/run — Execute a benchmark against the stored context of an existing job.
• POST /api/castp/analyze —
• GET /api/dashboard/datasets —
• GET /api/dashboard/engines —
• GET /api/dashboard/runs —
• GET /api/dashboard/summary —
• POST /api/dashboard/upload_data — Ingest a scientist's own dataset file into the dashboard library.
• GET /api/datasets — Summaries of every dataset in the library.
• GET /api/datasets/{name} — One full dataset (records included).
• POST /api/datasets/{name}/snapshot — Copy a dataset (records + manifest) into an engine workspace folder.
• GET /api/docking —
• GET /api/docking/result/{job_id}/complex.pdb — Receptor + docked ligand merged into a single PDB (techspec §2).
• GET /api/docking/result/{job_id}/ligand.sdf — Ligand-only SDF of the docked poses (techspec §2).
• GET /api/docking/result/{job_id}/pdb —
• POST /api/docking/run —
• GET /api/docking/status/{job_id} —
• POST /api/domains/scan — Scan a raw protein sequence against PROSITE signatures (best-effort).
• GET /api/domains/{accession} — Fetch InterPro domain architecture (Pfam, SMART, PROSITE, CDD, PANTHER, PRINTS).
• GET /api/domains/{accession}/all — Combined analysis: domains, sites, PTMs, topology, motifs, variants, GO, pathways.
• GET /api/domains/{accession}/composition — Compositionally biased regions and low-complexity sequences.
• GET /api/domains/{accession}/disulfide — Disulfide bond connectivity.
• GET /api/domains/{accession}/features — Full UniProt feature table categorized by type.
• GET /api/domains/{accession}/go — Gene Ontology annotations (molecular function, biological process, cellular component).
• GET /api/domains/{accession}/motifs — Structural motifs: zinc fingers, coiled coils, repeats, domain families.
• GET /api/domains/{accession}/pathways — Pathway annotations from KEGG, Reactome, and WikiPathways.
• GET /api/domains/{accession}/ptm — Post-translational modifications (phosphorylation, glycosylation, etc.).
• GET /api/domains/{accession}/sites — Active sites, binding sites, and catalytic residues.
• GET /api/domains/{accession}/topology — Signal peptides, transmembrane regions, chains, and propeptides.
• GET /api/domains/{accession}/variants — Mutagenesis sites and natural variants.
• GET /api/engines — Every registered engine: name, tool, databases, benchmark coverage.
• GET /api/engines/{name} —
• POST /api/engines/{name}/export — Export an engine result to JSON or CSV.
• POST /api/engines/{name}/figure — Render a publication-style SVG figure for the result.
• POST /api/engines/{name}/validate — Validate a canonical engine output; returns PASS/FAIL checks,
• GET /api/experiments — Recent experiments (provenance metadata for reproducibility).
• GET /api/experiments/debug/fingerprint — Return the reproducibility fingerprint for an input (used by tests).
• POST /api/experiments/debug/new — Create an experiment record on demand (used by tests).
• POST /api/experiments/debug/trace — Record a provenance node on demand (used by tests).
• GET /api/experiments/{job_id} — The immutable experiment record for a job, including its provenance DAG.
• GET /api/experiments/{job_id}/evidence — Evidence graph linking every AI claim to its supporting computation.
• GET /api/experiments/{job_id}/evidence/validate — Validation report over the evidence graph (honesty invariant).
• POST /api/experiments/{job_id}/finalize — Manually finalize an experiment (used by tests / admin).
• GET /api/experiments/{job_id}/ledger —
• POST /api/experiments/{job_id}/ledger —
• GET /api/experiments/{job_id}/ledger/validate —
• GET /api/experiments/{job_id}/paper — Manuscript draft generated from the recorded experiment. Zero external calls.
• GET /api/experiments/{job_id}/paper/latest —
• POST /api/experiments/{job_id}/paper/regenerate —
• GET /api/experiments/{job_id}/paper/versions —
• GET /api/experiments/{job_id}/provenance — Clickable provenance trace: nodes + edges for a job's experiment.
• GET /api/figure/formats — Publication formats the Figure Engine can emit (SVG only by design:
• GET /api/figures/{job_id} — One publication figure for a recorded experiment (paneled, captioned).
• POST /api/function/predict — Submit a function prediction job (queued through the durable worker).
• GET /api/function/status/{job_id} —
• POST /api/history/branch — Create a new pipeline job branched from an existing job's results.
• GET /api/history/children/{job_id} — Return direct children of a job (for the 'branch from here' list).
• GET /api/history/graph/{job_id} — Return the full ancestry + descendants of a job as a DAG.
• GET /api/interactions/{gene_name} —
• GET /api/jobs —
• GET /api/jobs/count —
• DELETE /api/jobs/{job_id} —
• GET /api/jobs/{job_id} —
• GET /api/keys —
• POST /api/keys —
• DELETE /api/keys/{key_id} —
• GET /api/md/forcefields — Return the force field / solvent menu (verified combos only).
• POST /api/md/run — Submit an MD simulation job (queued through the durable worker).
• GET /api/md/status/{job_id} —
• POST /api/md/v2/analyze — Run the full in-process staged MD DAG over a structure and return the audit report.
• GET /api/md/v2/engine — Report MD engine availability + versions (OpenMM primary, GROMACS gated).
• GET /api/md/v2/stages — Return the ordered stage contracts (names + human explanations) for the MD v2 DAG.
• GET /api/ngs/references —
• POST /api/ngs/run —
• GET /api/ngs/status/{job_id} —
• POST /api/ngs/v2/analyze —
• GET /api/ngs/v2/benchmarks/portable —
• POST /api/ngs/v2/clinical/evaluate —
• GET /api/ngs/v2/demos —
• POST /api/ngs/v2/detect —
• GET /api/ngs/v2/production/capabilities —
• POST /api/ngs/v2/production/plan —
• GET /api/ngs/v2/production/runs/{run_id} —
• GET /api/ngs/v2/production/runs/{run_id}/artifacts —
• POST /api/ngs/v2/production/submit —
• GET /api/ngs/v2/stages —
• POST /api/paper/continuous —
• GET /api/paper/continuous/subscriptions —
• POST /api/paper/continuous/tick —
• GET /api/paper/journal-formats — Journal templates the Publication Engine can emit.
• POST /api/pathways/detail —
• POST /api/pathways/enrichment —
• POST /api/pathways/enrichment/cross-validate — Run both Reactome and g:Profiler enrichment, returning concordant pathways.
• POST /api/pathways/kegg/search —
• POST /api/pathways/search —
• POST /api/pipeline/v2/run —
• GET /api/pipeline/v2/status/{job_id} —
• GET /api/pipelines/definitions —
• POST /api/pipelines/run —
• GET /api/pipelines/{pipeline_type}/definition —
• GET /api/plugins —
• POST /api/plugins/event —
• POST /api/plugins/reload —
• POST /api/plugins/{name}/disable —
• POST /api/plugins/{name}/enable —
• POST /api/primers/analyze — Run oligo QC (hairpin, self-/hetero-dimer, Tm, GC) and in-silico PCR.
• POST /api/primers/design —
• POST /api/primers/search — Search NCBI Nucleotide for a gene/sequence to design primers against.
• GET /api/profile —
• PUT /api/profile —
• POST /api/seq-tools/analyze —
• POST /api/seq-tools/dotplot —
• POST /api/seq-tools/motif-library —
• GET /api/seq-tools/motif-library/categories — Return the ordered list of motif categories for UI filters.
• GET /api/seq-tools/motif-library/patterns — Return the curated motif library so the UI can offer presets.
• POST /api/seq-tools/motif-scan —
• POST /api/sequences/fetch —
• POST /api/sequences/search —
• POST /api/sequences/validate —
• GET /api/sequencing/references —
• POST /api/sequencing/run —
• GET /api/sequencing/status/{job_id} —
• POST /api/share —
• GET /api/share/{token} —
• GET /api/structure-export/structure/{identifier} — Download a structure as PDB, mmCIF, or a styled PyMOL session (.pse).
• POST /api/structure-predict/predict —
• GET /api/structure-predict/status/{job_id} —
• POST /api/structure-prep/run —
• GET /api/structure-prep/status/{job_id} —
• GET /api/structure_analysis/compare/{pdb_id} —
• GET /api/structure_analysis/ramachandran/{pdb_id} —
• GET /api/structure_analysis/secondary_structure/{identifier} —
• POST /api/structures/fetch —
• POST /api/structures/inventory — Return lightweight chain and non-polymer inventory for workbench controls.
• POST /api/structures/search —
• GET /api/swissmodel/coordinates/{accession} —
• POST /api/swissmodel/repository —
• GET /api/templates —
• POST /api/templates —
• GET /api/templates/shared/{token} —
• DELETE /api/templates/{template_id} —
• GET /api/templates/{template_id} —
• PUT /api/templates/{template_id} —
• POST /api/templates/{template_id}/share —
• GET /api/tools —
• GET /api/tools/{tool_id} —
• POST /api/uniprot/cds — Fetch the CDS nucleotide sequence for a UniProt entry given an EMBL/GenBank accession.
• POST /api/uniprot/detail —
• POST /api/uniprot/search —
• GET /docs —
• GET /docs/oauth2-redirect —
• GET /openapi.json —
• GET /phylo/models —
• POST /phylo/run —
• GET /phylo/status/{job_id} —
• GET /redoc —