@delta-infra/cli 1.1.19 → 1.1.21

package/skills/delta-protein/references/structure_to_sequence.md

@@ -1,61 +1,61 @@
-# PDB Sequence Extraction (`huada_protein_tools` / `structure_to_sequence`)
-
-This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
-called via `delta-cli science invoke`; the business response described below lives
-under the CLI top-level `data` — read fields as documented in this file, do not
-recursively search. This file only documents the endpoint schema; it does not
-authorize direct HTTP. Endpoint names are authoritative as returned by
-`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
-guess, truncate, or alias.
-
-## Overview
-
-Extract the protein sequence from a PDB/CIF structure file.
-- Required: `structure_file`
-- Optional: `chain` (A)
-- Output: extracted protein sequence `resultjson`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint structure_to_sequence --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `structure_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `structure_file` | PDB/CIF | - |
-| `chain` | Protein chain identifier, default A | A |
-
-## Response
-
-- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
-- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
-- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
-  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
-  do not treat file contents as ordinary JSON results.
-
-## Output Projection
-
-> Verification status: derived from ToolSpec/agent templates; pending live calibration
-
-- Projection content: Protein sequence extracted from PDB/CIF
-- Presentation form: Sequence shown as inline code
-- Downstream reuse: sequence can be used as protein_sequence for downstream mutation/design/annotation endpoints (e.g. consensus_mutation, interpro_analyze)
-## Output Template
-
-- Title: **Structure-to-sequence extraction result**
-- Lead with the conclusion: extracted protein sequence for chain=<chain> (length N aa)
-- Show the sequence as inline code; no download needed
-
-## Boundaries & Failure Modes
-
-- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
-- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
-- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
+# PDB Sequence Extraction (`huada_protein_tools` / `structure_to_sequence`)
+
+This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
+called via `delta-cli science invoke`; the business response described below lives
+under the CLI top-level `data` — read fields as documented in this file, do not
+recursively search. This file only documents the endpoint schema; it does not
+authorize direct HTTP. Endpoint names are authoritative as returned by
+`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
+guess, truncate, or alias.
+
+## Overview
+
+Extract the protein sequence from a PDB/CIF structure file.
+- Required: `structure_file`
+- Optional: `chain` (A)
+- Output: extracted protein sequence `resultjson`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint structure_to_sequence --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `structure_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `structure_file` | PDB/CIF | - |
+| `chain` | Protein chain identifier, default A | A |
+
+## Response
+
+- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
+- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
+- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
+  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
+  do not treat file contents as ordinary JSON results.
+
+## Output Projection
+
+> Verification status: derived from ToolSpec/agent templates; pending live calibration
+
+- Projection content: Protein sequence extracted from PDB/CIF
+- Presentation form: Sequence shown as inline code
+- Downstream reuse: sequence can be used as protein_sequence for downstream mutation/design/annotation endpoints (e.g. consensus_mutation, interpro_analyze)
+## Output Template
+
+- Title: **Structure-to-sequence extraction result**
+- Lead with the conclusion: extracted protein sequence for chain=<chain> (length N aa)
+- Show the sequence as inline code; no download needed
+
+## Boundaries & Failure Modes
+
+- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
+- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
+- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
 - On failure, report a short summary of the CLI's raw error; do not blindly retry after remote computation timeouts (the outcome may be unknown because the task may already have happened).

package/skills/delta-protein/references/summarize_result.md

@@ -1,68 +1,68 @@
-# Multi-model Result Summary (`huada_protein_tools` / `summarize_result`)
-
-This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
-called via `delta-cli science invoke`; the business response described below lives
-under the CLI top-level `data` — read fields as documented in this file, do not
-recursively search. This file only documents the endpoint schema; it does not
-authorize direct HTTP. Endpoint names are authoritative as returned by
-`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
-guess, truncate, or alias.
-
-## Overview
-
-Summarize multi-model zero-shot prediction results as the final step of the
-mutation-prediction flow.
-- Required: `result_files` (list of paths to multiple prediction result files)
-- Optional: `protein_sequence`, `topk` (10)
-- Output: summarized ranking `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint summarize_result --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `result_files`
-
-Server-side default parameters:
-
-- `topk` = `10`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `result_files` | URL list of result files from previous steps | [] |
-| `protein_sequence` |  | - |
-| `topk` | Return the top k results, default 10 | 10 |
-
-## Response
-
-- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
-- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
-- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
-  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
-  do not treat file contents as ordinary JSON results.
-
-## Output Projection
-
-> Verification status: derived from ToolSpec/agent templates; pending live calibration
-
-- Projection content: Multi-model summarized ranking (topk) with all rows retained; restated as a table with the tool's original fields, prompting download of the full file when too long
-- Presentation form: Full Markdown table (≤100 rows); better for filtering/sorting
-- Downstream reuse: final step of the mutation-prediction chain (terminal)
-## Output Template
-
-- Title: **Multi-model result summary**
-- Show the full summary table (≤100 rows, no truncation), column names restated in natural language
-- Lead with the conclusion: positions where models agree/disagree; base final recommendations on the summary rather than restating single-model raw tables
-- When more than 100 rows, prompt downloading the full file
-
-## Boundaries & Failure Modes
-
-- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
-- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
-- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
+# Multi-model Result Summary (`huada_protein_tools` / `summarize_result`)
+
+This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
+called via `delta-cli science invoke`; the business response described below lives
+under the CLI top-level `data` — read fields as documented in this file, do not
+recursively search. This file only documents the endpoint schema; it does not
+authorize direct HTTP. Endpoint names are authoritative as returned by
+`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
+guess, truncate, or alias.
+
+## Overview
+
+Summarize multi-model zero-shot prediction results as the final step of the
+mutation-prediction flow.
+- Required: `result_files` (list of paths to multiple prediction result files)
+- Optional: `protein_sequence`, `topk` (10)
+- Output: summarized ranking `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint summarize_result --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `result_files`
+
+Server-side default parameters:
+
+- `topk` = `10`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `result_files` | URL list of result files from previous steps | [] |
+| `protein_sequence` |  | - |
+| `topk` | Return the top k results, default 10 | 10 |
+
+## Response
+
+- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
+- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
+- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
+  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
+  do not treat file contents as ordinary JSON results.
+
+## Output Projection
+
+> Verification status: derived from ToolSpec/agent templates; pending live calibration
+
+- Projection content: Multi-model summarized ranking (topk) with all rows retained; restated as a table with the tool's original fields, prompting download of the full file when too long
+- Presentation form: Full Markdown table (≤100 rows); better for filtering/sorting
+- Downstream reuse: final step of the mutation-prediction chain (terminal)
+## Output Template
+
+- Title: **Multi-model result summary**
+- Show the full summary table (≤100 rows, no truncation), column names restated in natural language
+- Lead with the conclusion: positions where models agree/disagree; base final recommendations on the summary rather than restating single-model raw tables
+- When more than 100 rows, prompt downloading the full file
+
+## Boundaries & Failure Modes
+
+- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
+- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
+- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
 - On failure, report a short summary of the CLI's raw error; do not blindly retry after remote computation timeouts (the outcome may be unknown because the task may already have happened).

package/skills/delta-protein/references/surface_charge.md

@@ -1,84 +1,84 @@
-# Surface Residue Charge Analysis (`huada_protein_tools` / `surface_charge`)
-
-This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
-called via `delta-cli science invoke`; the business response described below lives
-under the CLI top-level `data` — read fields as documented in this file, do not
-recursively search. This file only documents the endpoint schema; it does not
-authorize direct HTTP. Endpoint names are authoritative as returned by
-`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
-guess, truncate, or alias.
-
-## Overview
-
-Analyze protein surface residue charges with ProCaliper + APBS.
-- Required: `structure_file` (.pdb/.cif/.ent)
-- Optional: `pH` (default 7.4), `forcefield` (default PARSE), `chain_ids` (e.g. 'A,B'),
-  `sasa_threshold` (default 20.0 Ų), `potential_threshold` (default 1.0 kT/e), `precision` (standard/high)
-- ProCaliper computes SASA + PROPKA pKa to determine surface/buried status and charge type; pH affects PDB2PQR protonation (APBS) and charge-type determination
-- APBS solves the electrostatic potential .dx grid → maps it back to surface residues, identifying charge patches
-- Use case: analyze protein surface electrostatic properties, identify charge patches, assist binding-interface analysis
-
-This endpoint's `resultjson` is a flat structure (tested, not an analysis/visualization wrapper):
-
-- `negative_surface` / `positive_surface` / `net_surface_charge`: negative/positive/net charge residue counts
-- `patch_count` / `patches[]`: charge patches (non-empty only when APBS is available)
-- `residues[]`: per residue `chain` / `res3` / `seq` / `sasa` / `pka` / `charge_type` /
-  `is_surface` / `protonation_state` / `potential` / `potential_type` / `in_patch` / `patch_id`
-- `sasa_threshold` / `surface_residues`: surface-determination threshold and surface residue count
-- `pdb2pqr{pka_df[]}`: PROPKA pKa details; `procaliper{sasa, titration}`: SASA and titration state
-- `apbs{status, message}`: electrostatic-potential solving status. When APBS is unavailable the overall
-  `status` is `partial`, `message` notes the reason (e.g. `APBS executable 'apbs' not found. Set APBS_BIN.`),
-  `potential` is null and `patch_count=0`; in that case report only the ProCaliper charge results and do
-  not misreport it as a call failure
-- `download_url`: the electrostatic potential `.dx` grid download link when APBS is available
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint surface_charge --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `structure_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `structure_file` | PDB/CIF | - |
-| `pH` | pH value; affects APBS protonation and residue charge-type determination | 7.4 |
-| `forcefield` | PDB2PQR forcefield | PARSE |
-| `chain_ids` | Select chains in multi-chain structures, e.g. A,B; default all chains | - |
-| `sasa_threshold` | Surface residue SASA threshold (Ų) | 20.0 |
-| `potential_threshold` | Potential polarity threshold (kT/e) | 1.0 |
-| `precision` | Grid precision: standard / high | standard |
-
-## Response
-
-- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
-- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
-- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
-  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
-  do not treat file contents as ordinary JSON results.
-
-## Output Projection
-
-> Verification status: verified by a real `delta-cli` invocation
-
-- Projection content: Charge summary: negative_surface / positive_surface / net_surface_charge / surface_residues / patch_count / patches; residues[] details (sasa/pka/charge_type/is_surface)
-- Presentation form: Text/table; when APBS is unavailable status=partial — report only ProCaliper results and explain why; download_url is the .dx grid (when APBS available)
-- Downstream reuse: -
-## Output Template
-
-- Title: **Surface residue charge analysis result (ProCaliper + APBS)**
-- Lead with the conclusion: net charge (positive/negative/net_surface_charge), surface residue count, charge patch count
-- List key surface positive/negative-charge residues (with pKa/sasa)
-- When APBS is unavailable (status=partial) state plainly that electrostatics were not solved and report only ProCaliper results; add the .dx grid (if any) to the "Result files & downloads" section
-
-## Boundaries & Failure Modes
-
-- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
-- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
-- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
+# Surface Residue Charge Analysis (`huada_protein_tools` / `surface_charge`)
+
+This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
+called via `delta-cli science invoke`; the business response described below lives
+under the CLI top-level `data` — read fields as documented in this file, do not
+recursively search. This file only documents the endpoint schema; it does not
+authorize direct HTTP. Endpoint names are authoritative as returned by
+`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
+guess, truncate, or alias.
+
+## Overview
+
+Analyze protein surface residue charges with ProCaliper + APBS.
+- Required: `structure_file` (.pdb/.cif/.ent)
+- Optional: `pH` (default 7.4), `forcefield` (default PARSE), `chain_ids` (e.g. 'A,B'),
+  `sasa_threshold` (default 20.0 Ų), `potential_threshold` (default 1.0 kT/e), `precision` (standard/high)
+- ProCaliper computes SASA + PROPKA pKa to determine surface/buried status and charge type; pH affects PDB2PQR protonation (APBS) and charge-type determination
+- APBS solves the electrostatic potential .dx grid → maps it back to surface residues, identifying charge patches
+- Use case: analyze protein surface electrostatic properties, identify charge patches, assist binding-interface analysis
+
+This endpoint's `resultjson` is a flat structure (tested, not an analysis/visualization wrapper):
+
+- `negative_surface` / `positive_surface` / `net_surface_charge`: negative/positive/net charge residue counts
+- `patch_count` / `patches[]`: charge patches (non-empty only when APBS is available)
+- `residues[]`: per residue `chain` / `res3` / `seq` / `sasa` / `pka` / `charge_type` /
+  `is_surface` / `protonation_state` / `potential` / `potential_type` / `in_patch` / `patch_id`
+- `sasa_threshold` / `surface_residues`: surface-determination threshold and surface residue count
+- `pdb2pqr{pka_df[]}`: PROPKA pKa details; `procaliper{sasa, titration}`: SASA and titration state
+- `apbs{status, message}`: electrostatic-potential solving status. When APBS is unavailable the overall
+  `status` is `partial`, `message` notes the reason (e.g. `APBS executable 'apbs' not found. Set APBS_BIN.`),
+  `potential` is null and `patch_count=0`; in that case report only the ProCaliper charge results and do
+  not misreport it as a call failure
+- `download_url`: the electrostatic potential `.dx` grid download link when APBS is available
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint surface_charge --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `structure_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `structure_file` | PDB/CIF | - |
+| `pH` | pH value; affects APBS protonation and residue charge-type determination | 7.4 |
+| `forcefield` | PDB2PQR forcefield | PARSE |
+| `chain_ids` | Select chains in multi-chain structures, e.g. A,B; default all chains | - |
+| `sasa_threshold` | Surface residue SASA threshold (Ų) | 20.0 |
+| `potential_threshold` | Potential polarity threshold (kT/e) | 1.0 |
+| `precision` | Grid precision: standard / high | standard |
+
+## Response
+
+- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
+- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
+- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
+  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
+  do not treat file contents as ordinary JSON results.
+
+## Output Projection
+
+> Verification status: verified by a real `delta-cli` invocation
+
+- Projection content: Charge summary: negative_surface / positive_surface / net_surface_charge / surface_residues / patch_count / patches; residues[] details (sasa/pka/charge_type/is_surface)
+- Presentation form: Text/table; when APBS is unavailable status=partial — report only ProCaliper results and explain why; download_url is the .dx grid (when APBS available)
+- Downstream reuse: -
+## Output Template
+
+- Title: **Surface residue charge analysis result (ProCaliper + APBS)**
+- Lead with the conclusion: net charge (positive/negative/net_surface_charge), surface residue count, charge patch count
+- List key surface positive/negative-charge residues (with pKa/sasa)
+- When APBS is unavailable (status=partial) state plainly that electrostatics were not solved and report only ProCaliper results; add the .dx grid (if any) to the "Result files & downloads" section
+
+## Boundaries & Failure Modes
+
+- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
+- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
+- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
 - On failure, report a short summary of the CLI's raw error; do not blindly retry after remote computation timeouts (the outcome may be unknown because the task may already have happened).

package/skills/delta-protein/references/uniprot_batch_query.md

@@ -1,63 +1,63 @@
-# UniProt Batch Query (`huada_protein_tools` / `uniprot_batch_query`)
-
-This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
-called via `delta-cli science invoke`; the business response described below lives
-under the CLI top-level `data` — read fields as documented in this file, do not
-recursively search. This file only documents the endpoint schema; it does not
-authorize direct HTTP. Endpoint names are authoritative as returned by
-`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
-guess, truncate, or alias.
-
-## Overview
-
-Batch query UniProt. Supports UniProtKB accessions, UniParc IDs, or keyword
-searches. Does not support direct text retrieval.
-- Input: List[str]
-- Output:
-- source: uniprotkb | uniparc
-- resultjson: {query_str: {uniprotkb/uniparc: ..., structure_links: [...], ...}, ...}
-- Use case: query metadata for multiple proteins at once
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint uniprot_batch_query --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `query`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `query` | UniProt accession / UniParc ID list | - |
-
-## Response
-
-- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
-- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
-- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
-  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
-  do not treat file contents as ordinary JSON results.
-
-## Output Projection
-
-> Verification status: derived from ToolSpec/agent templates; pending live calibration
-
-- Projection content: Metadata per query id (uniprotkb/uniparc, name, species, sequence length, structure_links)
-- Presentation form: Entry list/table for easy selection
-- Downstream reuse: sequence of the selected entry can be used as downstream input
-## Output Template
-
-- Title: **UniProt candidate match result**
-- One row per candidate entry: Entry/protein name/species/sequence identity/sequence length (table or list)
-- Prompt the user to confirm the selection
-
-## Boundaries & Failure Modes
-
-- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
-- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
-- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
+# UniProt Batch Query (`huada_protein_tools` / `uniprot_batch_query`)
+
+This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
+called via `delta-cli science invoke`; the business response described below lives
+under the CLI top-level `data` — read fields as documented in this file, do not
+recursively search. This file only documents the endpoint schema; it does not
+authorize direct HTTP. Endpoint names are authoritative as returned by
+`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
+guess, truncate, or alias.
+
+## Overview
+
+Batch query UniProt. Supports UniProtKB accessions, UniParc IDs, or keyword
+searches. Does not support direct text retrieval.
+- Input: List[str]
+- Output:
+- source: uniprotkb | uniparc
+- resultjson: {query_str: {uniprotkb/uniparc: ..., structure_links: [...], ...}, ...}
+- Use case: query metadata for multiple proteins at once
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint uniprot_batch_query --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `query`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `query` | UniProt accession / UniParc ID list | - |
+
+## Response
+
+- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
+- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
+- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
+  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
+  do not treat file contents as ordinary JSON results.
+
+## Output Projection
+
+> Verification status: derived from ToolSpec/agent templates; pending live calibration
+
+- Projection content: Metadata per query id (uniprotkb/uniparc, name, species, sequence length, structure_links)
+- Presentation form: Entry list/table for easy selection
+- Downstream reuse: sequence of the selected entry can be used as downstream input
+## Output Template
+
+- Title: **UniProt candidate match result**
+- One row per candidate entry: Entry/protein name/species/sequence identity/sequence length (table or list)
+- Prompt the user to confirm the selection
+
+## Boundaries & Failure Modes
+
+- File-type parameters (`structure_file`/`sequence_file`/`msa_file` etc.) take server-accessible URL/path strings, not local upload paths; a `download_url` or `pdb_url` returned by an upstream endpoint can be backfilled directly as downstream input.
+- Make only the minimal calls needed to complete the task; `--data` carries only the fields declared by this endpoint. Do not invent enum values or branches beyond the required combinations.
+- Do not pass off local tool (RDKit/pymatgen/LAMMPS/self-attached MCP) results as this endpoint's results; do not connect directly to Huada or gateway URLs.
 - On failure, report a short summary of the CLI's raw error; do not blindly retry after remote computation timeouts (the outcome may be unknown because the task may already have happened).