@delta-infra/cli 1.1.19 → 1.1.23

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

@@ -1,66 +1,66 @@
-# Mutant Solubility Prediction (`huada_protein_tools` / `protein_sol_predict_mutation`)
-
-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
-
-Predict the solubility of mutant proteins.
-- Input: `protein_sequence`/`sequence_file`/`structure_file` + `mutant_list`/`mutant_list_file`
-- Optional: `chain` (A), `min_sol` (-1.0)
-- Output: solubility prediction results per mutant `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint protein_sol_predict_mutation --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `protein_sequence` / `sequence_file` / `structure_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `structure_file` | PDB/CIF | - |
-| `chain` | Protein chain identifier, default A | A |
-| `mutant_list` | Mutation list | [] |
-| `mutant_list_file` | CSV/XLSX mutation list file | - |
-| `min_sol` | Minimum solubility threshold, default -1.0 | -1.0 |
-
-## 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: Solubility score per mutant and change trend; flag mutations likely to affect solubility
-- Presentation form: Text/table
-- Downstream reuse: -
-## Output Template
-
-- Title: **Mutant solubility prediction result**
-- Lead with the conclusion: solubility score/change trend, flagging mutations likely to affect solubility
-- Add details 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.
+# Mutant Solubility Prediction (`huada_protein_tools` / `protein_sol_predict_mutation`)
+
+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
+
+Predict the solubility of mutant proteins.
+- Input: `protein_sequence`/`sequence_file`/`structure_file` + `mutant_list`/`mutant_list_file`
+- Optional: `chain` (A), `min_sol` (-1.0)
+- Output: solubility prediction results per mutant `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint protein_sol_predict_mutation --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `protein_sequence` / `sequence_file` / `structure_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `structure_file` | PDB/CIF | - |
+| `chain` | Protein chain identifier, default A | A |
+| `mutant_list` | Mutation list | [] |
+| `mutant_list_file` | CSV/XLSX mutation list file | - |
+| `min_sol` | Minimum solubility threshold, default -1.0 | -1.0 |
+
+## 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: Solubility score per mutant and change trend; flag mutations likely to affect solubility
+- Presentation form: Text/table
+- Downstream reuse: -
+## Output Template
+
+- Title: **Mutant solubility prediction result**
+- Lead with the conclusion: solubility score/change trend, flagging mutations likely to affect solubility
+- Add details 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/protein_sol_predict_protein.md

@@ -1,61 +1,61 @@
-# Protein Solubility Prediction (`huada_protein_tools` / `protein_sol_predict_protein`)
-
-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
-
-Predict protein solubility and isoelectric point (pI).
-- Input: `protein_list` / `protein_list_file` (choose one)
-- Important: `protein_list_file` must be a `.fasta/.fa/.csv/.xlsx` URL; never pass structure files
-- Output: solubility and pI results `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint protein_sol_predict_protein --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `protein_list` / `protein_list_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `protein_list` | List of single or multiple one-letter amino-acid sequences | [] |
-| `protein_list_file` | FASTA/FA/CSV/XLSX sequence file | - |
-
-## 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 solubility and isoelectric point pI (download_url)
-- Presentation form: Text
-- Downstream reuse: -
-## Output Template
-
-- Title: **Protein solubility prediction result**
-- Lead with the conclusion: predicted solubility trend and pI
-- Add details 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.
+# Protein Solubility Prediction (`huada_protein_tools` / `protein_sol_predict_protein`)
+
+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
+
+Predict protein solubility and isoelectric point (pI).
+- Input: `protein_list` / `protein_list_file` (choose one)
+- Important: `protein_list_file` must be a `.fasta/.fa/.csv/.xlsx` URL; never pass structure files
+- Output: solubility and pI results `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint protein_sol_predict_protein --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `protein_list` / `protein_list_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `protein_list` | List of single or multiple one-letter amino-acid sequences | [] |
+| `protein_list_file` | FASTA/FA/CSV/XLSX sequence file | - |
+
+## 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 solubility and isoelectric point pI (download_url)
+- Presentation form: Text
+- Downstream reuse: -
+## Output Template
+
+- Title: **Protein solubility prediction result**
+- Lead with the conclusion: predicted solubility trend and pI
+- Add details 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/protenix.md

@@ -1,66 +1,66 @@
-# Protein Structure Prediction (Protenix) (`huada_protein_tools` / `protenix`)
-
-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
-
-Predict the three-dimensional structure of a protein with the Protenix model.
-- Input: `protein_sequence` / `sequence_file` (choose one)
-- Optional: `use_msa` (false)
-- Output: predicted structure file (PDB) `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint protenix --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `protein_sequence` / `sequence_file`
-
-Server-side default parameters:
-
-- `use_msa` = `false`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `use_msa` | Whether to use multiple sequence alignment | false |
-
-## 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: Predicted structure download_url (.cif/.pdb) with confidence: plddt, ptm, gpde, num_recycles, has_clash
-- Presentation form: Structure file link + confidence text
-- Downstream reuse: structure can serve as downstream structure_file, or extract the sequence first via structure_to_sequence and use as protein_sequence
-## Output Template
-
-- Title: **Protenix structure prediction result**
-- Lead with the conclusion: prediction done + confidence (plddt/ptm/gpde), num_recycles, clash status
-- Add the structure file link to the "Result files & downloads" section: `[Protenix structure prediction result file](download_url)`
-
-## 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.
+# Protein Structure Prediction (Protenix) (`huada_protein_tools` / `protenix`)
+
+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
+
+Predict the three-dimensional structure of a protein with the Protenix model.
+- Input: `protein_sequence` / `sequence_file` (choose one)
+- Optional: `use_msa` (false)
+- Output: predicted structure file (PDB) `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint protenix --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `protein_sequence` / `sequence_file`
+
+Server-side default parameters:
+
+- `use_msa` = `false`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `use_msa` | Whether to use multiple sequence alignment | false |
+
+## 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: Predicted structure download_url (.cif/.pdb) with confidence: plddt, ptm, gpde, num_recycles, has_clash
+- Presentation form: Structure file link + confidence text
+- Downstream reuse: structure can serve as downstream structure_file, or extract the sequence first via structure_to_sequence and use as protein_sequence
+## Output Template
+
+- Title: **Protenix structure prediction result**
+- Lead with the conclusion: prediction done + confidence (plddt/ptm/gpde), num_recycles, clash status
+- Add the structure file link to the "Result files & downloads" section: `[Protenix structure prediction result file](download_url)`
+
+## 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/protrek_search.md

@@ -1,90 +1,90 @@
-# ProTrek API Search (`huada_protein_tools` / `protrek_search`)
-
-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
-
-Open-ended protein retrieval (text/sequence/structure) across multiple databases
-with the ProTrek protein search API.
-- Typical scenarios:
-- Search related proteins by functional/reaction/family descriptions in protein
-  databases (`input_type=text`).
-- Search similar proteins by sequence (`input_type=sequence`).
-- Search similar structures by structure (`input_type=structure`).
-- Not for: exact metadata queries of a known UniProt accession / UniParc ID / gene
-  name / protein name (use `uniprot_query` for those).
-- Optional parameters: `input_type` (text/sequence/structure), `query_type`
-  (sequence/structure), `topk` (10), `db` (Swiss-Prot), `protein_sequence`,
-  `sequence_file`, `structure_file`, `chain` (A), `text`
-- `query_type` defaults to `sequence`;
-- when the user mentions "structure search / structure / 3D structure", choose `structure`;
-- `input_type` is inferred from whether a sequence/structure file is provided; when
-  neither is provided, `input_type` is `text`;
-- the `text` parameter is specifically for functional/reaction/family
-  description-style text searches;
-- Supported databases: with `query_type=sequence`, Swiss-Prot/UniRef50/Uncharacterized/OMG_prot50/PDB/GOPC/NCBI/MGnify/OMG are supported; with `query_type=structure`, only PDB
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint protrek_search --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `protein_sequence` / `sequence_file` / `structure_file` / `text`
-
-Server-side default parameters:
-
-- `input_type` = `sequence`
-- `query_type` = `sequence`
-- `topk` = `10`
-- `db` = `Swiss-Prot`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `input_type` | Input type: text/sequence/structure; inferred from whether a sequence/structure file is provided, text when neither | sequence |
-| `query_type` | Query type: sequence/structure; default sequence; choose structure when "structure search" is mentioned | sequence |
-| `topk` | Number of results to return, default 10 | 10 |
-| `db` | Database name or list, default Swiss-Prot; with query_type=sequence supports ['Swiss-Prot', 'UniRef50', 'Uncharacterized', 'OMG_prot50', 'PDB', 'GOPC', 'NCBI', 'MGnify', 'OMG']; with query_type=structure only PDB | Swiss-Prot |
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `structure_file` | PDB/CIF | - |
-| `chain` | Protein chain identifier, default A | A |
-| `text` | Core search description when input_type=text, e.g. function/reaction/family; translate to English | - |
-
-## 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: Hit protein entries, similarity and functional information
-- Presentation form: Hit list text/table
-- Downstream reuse: for known targets with metadata use uniprot_query; this endpoint is for open-ended retrieval
-## Output Template
-
-- Title: **ProTrek database search result**
-- Lead with the conclusion: number of hit protein entries; list similarity per hit (score vs query) and functional information
-- For structure/sequence search, state the retrieval mode (query_type/input_type)
-
-## 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.
+# ProTrek API Search (`huada_protein_tools` / `protrek_search`)
+
+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
+
+Open-ended protein retrieval (text/sequence/structure) across multiple databases
+with the ProTrek protein search API.
+- Typical scenarios:
+- Search related proteins by functional/reaction/family descriptions in protein
+  databases (`input_type=text`).
+- Search similar proteins by sequence (`input_type=sequence`).
+- Search similar structures by structure (`input_type=structure`).
+- Not for: exact metadata queries of a known UniProt accession / UniParc ID / gene
+  name / protein name (use `uniprot_query` for those).
+- Optional parameters: `input_type` (text/sequence/structure), `query_type`
+  (sequence/structure), `topk` (10), `db` (Swiss-Prot), `protein_sequence`,
+  `sequence_file`, `structure_file`, `chain` (A), `text`
+- `query_type` defaults to `sequence`;
+- when the user mentions "structure search / structure / 3D structure", choose `structure`;
+- `input_type` is inferred from whether a sequence/structure file is provided; when
+  neither is provided, `input_type` is `text`;
+- the `text` parameter is specifically for functional/reaction/family
+  description-style text searches;
+- Supported databases: with `query_type=sequence`, Swiss-Prot/UniRef50/Uncharacterized/OMG_prot50/PDB/GOPC/NCBI/MGnify/OMG are supported; with `query_type=structure`, only PDB
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint protrek_search --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `protein_sequence` / `sequence_file` / `structure_file` / `text`
+
+Server-side default parameters:
+
+- `input_type` = `sequence`
+- `query_type` = `sequence`
+- `topk` = `10`
+- `db` = `Swiss-Prot`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `input_type` | Input type: text/sequence/structure; inferred from whether a sequence/structure file is provided, text when neither | sequence |
+| `query_type` | Query type: sequence/structure; default sequence; choose structure when "structure search" is mentioned | sequence |
+| `topk` | Number of results to return, default 10 | 10 |
+| `db` | Database name or list, default Swiss-Prot; with query_type=sequence supports ['Swiss-Prot', 'UniRef50', 'Uncharacterized', 'OMG_prot50', 'PDB', 'GOPC', 'NCBI', 'MGnify', 'OMG']; with query_type=structure only PDB | Swiss-Prot |
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `structure_file` | PDB/CIF | - |
+| `chain` | Protein chain identifier, default A | A |
+| `text` | Core search description when input_type=text, e.g. function/reaction/family; translate to English | - |
+
+## 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: Hit protein entries, similarity and functional information
+- Presentation form: Hit list text/table
+- Downstream reuse: for known targets with metadata use uniprot_query; this endpoint is for open-ended retrieval
+## Output Template
+
+- Title: **ProTrek database search result**
+- Lead with the conclusion: number of hit protein entries; list similarity per hit (score vs query) and functional information
+- For structure/sequence search, state the retrieval mode (query_type/input_type)
+
+## 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).