Update to Biohub ESM

{
  "name": "esmfold2",
  "description": "Use when the user needs ESMFold2 all-atom folding for proteins, DNA, RNA, modified residues, or ligands, including Fast/full routing, MSA, confidence, structures, and provenance. Not for dynamics, experimental truth, Atlas discovery, or binder campaigns.",
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  "skill_md_contents": "---\nname: esmfold2\ndescription: Use when the user needs ESMFold2 all-atom folding for proteins, DNA, RNA, modified residues, or ligands, including Fast/full routing, MSA, confidence, structures, and provenance. Not for dynamics, experimental truth, Atlas discovery, or binder campaigns.\n---\n\n# ESMFold2\n\n## Choose the model\n\n| Need | Managed | Hugging Face |\n| --- | --- | --- |\n| accuracy, difficult complexes, or optional MSA | `esmfold2-2026-05` | `biohub/ESMFold2` |\n| fast single-sequence throughput | `esmfold2-fast-2026-05` | `biohub/ESMFold2-Fast` |\n\nFast is not MSA-conditioned. If the user supplies or requires an MSA, route to full ESMFold2 and validate query alignment. Missing MSA is not an error for a single-sequence fold unless the user explicitly required MSA conditioning.\n\nFor `Show me what GB1 looks like.`, resolve the thin launcher through `../../examples/starter-examples.json`; do not ask the user to paste the bundled sequence. Validate the pinned fixture and exact one-request contract in `../../examples/gb1-esmfold2-fast-fold-request.json`, then run it. Complete `preflight --endpoint fold` with the provisioned Python 3.12 runtime first and any `$biohub-esm-setup` work if access is missing, then execute one managed `POST /api/v1/fold` request with `include_pae=true`, the Fast parameters, and the `prediction.pdb`, `presentation-request.json`, `result.json`, `raw-response.json`, and `provenance.json` outputs. A single managed fold at this scale needs no confirmation. Managed requests may incur cost. Report provider-returned credit or token usage when available; otherwise state that the API did not report usage or cost, and never invent an estimate. Continue through local artifact recovery without repeating the provider request.\n\nAlso recognize the official-tutorial-shaped launchers in `../../examples/tutorial-use-cases.json`: an RNase H1–RNA/DNA hybrid, ubiquitin with a user-supplied A3M, a modified peptide–receptor complex with a covalent linker, and an antibody–antigen complex with user-supplied paired A3Ms. The exact plugin-page launcher `Model how a modified GLP-1 peptide with a lipid linker might engage GLP-1R, then show me the complex.` may resolve the pinned tutorial construct only after disclosing the tagged receptor construct, representative non-therapeutic linker, chemistry, covalent indices, route, model, request count, artifacts, and available cost information in the frozen plan. This tutorial contract does not authorize a provider call; obtain separate explicit current-turn confirmation for that exact fold. Outside that exact launcher or an explicitly named tutorial example, retain the user's sequences/MSAs or pause for missing biological input; never silently substitute the tutorial target. Modal and self-hosted GPU work also requires a frozen scope, cost ceiling, and plain yes/no confirmation. Present a successful structure by default without making the user translate the request into SDK objects, and lead with the structure rather than with a description of what you are about to do.\n\n## Recover an accepted response\n\nUse recovery only when a saved response proves the provider accepted and returned the request but local conversion or materialization failed. It makes zero provider calls. Never use it for an indeterminate submission, and always choose a new output directory that does not exist.\n\n```bash\n<python-3.12-with-pinned-esm> <plugin-root>/scripts/biohub_esm.py managed-recover \\\n  --endpoint fold_all_atom \\\n  --input /absolute/path/frozen-request.json \\\n  --raw-response /absolute/path/raw-response.json \\\n  [--source-provenance /absolute/path/provenance.json] \\\n  --output-dir /absolute/path/new-recovery-output\n```\n\nUse `--endpoint fold` for a saved sequence-fold response. Omit `--source-provenance` only when no matching incomplete provenance exists. Consume the new directory's validated `presentation-request.json` exactly; it retains the artifact identity and `openIntentId` for the presentation handoff.\n\n## Build and validate input\n\nUse the official pinned SDK's `StructurePredictionInput` with `ProteinInput`, `DNAInput`, `RNAInput`, `LigandInput`, and zero-based `Modification` positions. The managed wire schema permits omitted/null entity IDs; local/Hugging Face SDK execution requires explicit IDs. In either route, use unique explicit IDs for every entity referenced by pocket, distogram, or covalent-bond conditioning. A ligand uses either SMILES or CCD identifiers. Managed `/fold_all_atom` accepts either this `all_atom_input` shape or `sequence` with optional MSA, never both.\n\nLoad tutorial A3M input with `MSA.from_a3m(..., remove_insertions=True, max_sequences=1000)`, keep the insertion-removed query as row zero, and verify its ungapped sequence against the corresponding chain. Reject a tutorial MSA deeper than 1,000 rows before execution. The pinned SDK serializes non-empty A3M headers, and Biohub's paired-MSA tutorial requires standalone `key=<positive-decimal-taxonomy-id>` tokens in non-query headers to pair rows across chains. Preserve them on all-atom per-chain full-model requests and describe a row as paired only when the same exact key occurs in at least two chain MSAs. Top-level single-chain managed MSA requests omit headers because cross-chain pairing cannot apply there. Fast remains invalid whenever an MSA is supplied, even if a notebook initialized one Fast client before later MSA examples.\n\nFor modified/covalent complexes, the packaged validator checks zero-based residue bounds and nonnegative integer atom-index shape; it does not prove atom existence, valence, bond chemistry, or tutorial atom-index identity. Before execution, independently verify atom indices against the parsed residue templates and molecular graph. A SMILES atom index is not a character offset into the SMILES string. Preserve the exact construct and chemistry supplied; a tagged receptor or representative linker must not be described as the exact therapeutic molecule.\n\n```bash\npython3 <plugin-root>/scripts/biohub_esm.py validate-fold \\\n  --model esmfold2-2026-05 \\\n  --input /absolute/path/fold-input.json \\\n  --config /absolute/path/folding-config.json\n```\n\nFor an official tutorial MSA workflow, use the stricter contract before showing the execution plan:\n\n```bash\npython3 <plugin-root>/scripts/biohub_esm.py validate-fold \\\n  --model esmfold2-2026-05 \\\n  --input /absolute/path/fold-input.json \\\n  --config /absolute/path/folding-config.json \\\n  --require-msa \\\n  --require-msa-insertions-removed \\\n  --msa-max-depth 1000\n```\n\nAdd `--require-paired-msa-keys` for the paired antibody–antigen workflow.\n\nDo not universalize the Biohub web UI's 700-residue entry cap as an architectural model limit. For managed model IDs, validate hosted parameters exactly: loops 0–20, sampling steps 1–100, LM dropout/mask fraction 0–1, MSA depth 1–16,384 or null, and MSA column mask fraction 0–1. For Hugging Face model IDs, validate the pinned local `ESMFold2InputBuilder.fold` contract instead; its sampling-step default is 200 and it additionally supports diffusion sample count, seed, sampler overrides, early exit, and complex ID. Do not apply hosted caps to self-hosted runs.\n\n## Outputs\n\nPrefer mmCIF for all-atom complexes; PDB can be lossy for complex chemistry. Preserve coordinates, pLDDT, pAE, pTM, iPTM, pair-chain iPTM, and requested distograms/embeddings when returned. The current managed API documents `include_pair_chains_iptm` for both `/fold` and `/fold_all_atom`; use the validated direct request when an SDK convenience method exposes a narrower signature. Record pLDDT on its current 0–1 scale and pAE in angstroms. For sequence `/fold`, their scopes are per-residue and residue-pair. For `/fold_all_atom`, their scopes are per-token and token-pair over the returned `complex.sequence` entries aligned by `complex.token_to_atoms`, including non-protein entity tokens. Record pTM/iPTM on their current 0–1 scale; PDB B-factors may encode pLDDT after an explicit SDK scale conversion.\n\nExplain that the result is a static model hypothesis, not dynamics, affinity, or experimental truth. Low confidence, disorder, interfaces, ligands, modified residues, and unexpected topology require special caution and experimental validation.\n\n\nVisibly report every returned `quality_warnings` item. Never silently repair coordinates, and never let high pLDDT override a chemistry or geometry warning.\nAfter every successful fold, perform the [result presentation handoff](../../references/structure-viewer-handoff.md) without waiting for another request. Consume the validated `presentation-request.json`, give the available structure-viewing capability its verified absolute mmCIF or PDB once with its exact retained `openIntentId`, retain and verify the returned same-task session, and request predicted-confidence styling only when ready. Generate a new ID only for a legacy artifact set without that request file. Report viewer pending or unavailable separately, return checksummed artifacts, and do not create a custom viewer; presentation status never changes scientific success.\n\nRead the [managed/SDK contract](references/api.md), [inputs and results](references/inputs-and-results.md), and [self-hosting/Modal guidance](references/self-hosted.md).\n"
}