@delta-infra/cli 1.1.19 → 1.1.21

package/skills/delta-protein/agents/openai.yaml

@@ -1,4 +1,4 @@
-interface:
-  display_name: "Delta Protein"
-  short_description: "Unified access to Huada protein analysis tools through the Delta CLI"
+interface:
+  display_name: "Delta Protein"
+  short_description: "Unified access to Huada protein analysis tools through the Delta CLI"
   default_prompt: "Use $delta-protein to analyze protein research goals: pick the right endpoint and complete the task by calling huada_protein_tools through the Delta CLI."

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

@@ -1,64 +1,64 @@
-# Protein Flexibility Analysis (`huada_protein_tools` / `bfitter`)
-
-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 flexible sites of a protein structure and identify candidate sites suitable
-for site-directed mutagenesis/directed evolution based on the B-factor.
-- Required: `structure_file` (PDB/CIF)
-- Optional: `chain` (default A), `b_parameter` (default B)
-- Output: flexibility results `resultjson`, `download_url`
-- Use case: identify flexible regions, select mutation sites
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint bfitter --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 |
-| `b_parameter` | B-factor parameter, B or B+, default B | B |
-
-## 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: Distribution of high/low B-factor positions and engineering implications
-- Presentation form: Residue list + text
-- Downstream reuse: flexible positions can be annotated as site-directed mutagenesis/directed-evolution candidates
-## Output Template
-
-- Title: **Protein flexibility analysis result (B-FITTER)**
-- Lead with the conclusion: distribution of high (flexible) / low (rigid) B-factor positions
-- Explain what flexible regions imply for site-directed mutagenesis / directed evolution
-
-## 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 Flexibility Analysis (`huada_protein_tools` / `bfitter`)
+
+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 flexible sites of a protein structure and identify candidate sites suitable
+for site-directed mutagenesis/directed evolution based on the B-factor.
+- Required: `structure_file` (PDB/CIF)
+- Optional: `chain` (default A), `b_parameter` (default B)
+- Output: flexibility results `resultjson`, `download_url`
+- Use case: identify flexible regions, select mutation sites
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint bfitter --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 |
+| `b_parameter` | B-factor parameter, B or B+, default B | B |
+
+## 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: Distribution of high/low B-factor positions and engineering implications
+- Presentation form: Residue list + text
+- Downstream reuse: flexible positions can be annotated as site-directed mutagenesis/directed-evolution candidates
+## Output Template
+
+- Title: **Protein flexibility analysis result (B-FITTER)**
+- Lead with the conclusion: distribution of high (flexible) / low (rigid) B-factor positions
+- Explain what flexible regions imply for site-directed mutagenesis / directed evolution
+
+## 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/catapro_predict.md

@@ -1,63 +1,63 @@
-# Enzyme Kinetic Parameter Prediction (`huada_protein_tools` / `catapro_predict`)
-
-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 enzyme kinetic parameters (kcat, Km, kcat/Km) with CataPro.
-- Required: `smiles` (substrate SMILES)
-- Optional: `protein_sequence`/`sequence_file`/`structure_file`, `chain` (A)
-- Output: prediction results `resultjson`, `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint catapro_predict --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `smiles`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `smiles` | Substrate SMILES string | - |
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `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: Enzyme kinetic parameters kcat, Km, kcat/Km predictions
-- Presentation form: Text
-- Downstream reuse: -
-## Output Template
-
-- Title: **Enzyme kinetic parameter prediction result (CataPro)**
-- Lead with the conclusion: predicted kcat, Km, kcat/Km (may include trends)
-
-## 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.
+# Enzyme Kinetic Parameter Prediction (`huada_protein_tools` / `catapro_predict`)
+
+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 enzyme kinetic parameters (kcat, Km, kcat/Km) with CataPro.
+- Required: `smiles` (substrate SMILES)
+- Optional: `protein_sequence`/`sequence_file`/`structure_file`, `chain` (A)
+- Output: prediction results `resultjson`, `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint catapro_predict --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `smiles`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `smiles` | Substrate SMILES string | - |
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `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: Enzyme kinetic parameters kcat, Km, kcat/Km predictions
+- Presentation form: Text
+- Downstream reuse: -
+## Output Template
+
+- Title: **Enzyme kinetic parameter prediction result (CataPro)**
+- Lead with the conclusion: predicted kcat, Km, kcat/Km (may include trends)
+
+## 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/catpred_predict.md

@@ -1,65 +1,65 @@
-# Enzyme Kinetic Parameter Prediction (`huada_protein_tools` / `catpred_predict`)
-
-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 enzyme kinetic parameters (kcat, Km, kcat/Km).
-- Required: `primary_smiles` (substrate SMILES)
-- Optional: `protein_sequence`/`sequence_file`/`structure_file`, `chain` (A), `additional_smiles`
-- Output: kinetic parameter predictions `resultjson`, `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint catpred_predict --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `primary_smiles`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `primary_smiles` | Substrate SMILES string | - |
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `structure_file` | PDB/CIF | - |
-| `chain` | Protein chain identifier, default A | A |
-| `additional_smiles` | List of additional substrate SMILES | [] |
-
-## 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: kcat, Km, kcat/Km predictions (restate resultjson per the actual keys returned)
-- Presentation form: Text
-- Downstream reuse: -
-## Output Template
-
-- Title: **Enzyme kinetic parameter prediction result (CatPred)**
-- Lead with the conclusion: predicted kcat, Km, kcat/Km and trends
-- Restate key parameters in natural language or a small table
-
-## 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.
+# Enzyme Kinetic Parameter Prediction (`huada_protein_tools` / `catpred_predict`)
+
+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 enzyme kinetic parameters (kcat, Km, kcat/Km).
+- Required: `primary_smiles` (substrate SMILES)
+- Optional: `protein_sequence`/`sequence_file`/`structure_file`, `chain` (A), `additional_smiles`
+- Output: kinetic parameter predictions `resultjson`, `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint catpred_predict --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `primary_smiles`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `primary_smiles` | Substrate SMILES string | - |
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `structure_file` | PDB/CIF | - |
+| `chain` | Protein chain identifier, default A | A |
+| `additional_smiles` | List of additional substrate SMILES | [] |
+
+## 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: kcat, Km, kcat/Km predictions (restate resultjson per the actual keys returned)
+- Presentation form: Text
+- Downstream reuse: -
+## Output Template
+
+- Title: **Enzyme kinetic parameter prediction result (CatPred)**
+- Lead with the conclusion: predicted kcat, Km, kcat/Km and trends
+- Restate key parameters in natural language or a small table
+
+## 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/caver_tunnel_analyze.md

@@ -1,63 +1,63 @@
-# Protein Tunnel/Channel Analysis (`huada_protein_tools` / `caver_tunnel_analyze`)
-
-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 internal tunnels and channels with CAVER 3.x.
-- Required: `structure_file` (PDB/CIF URL, local path, or 4-character PDB ID; never pass FASTA/raw sequences)
-- Optional: `probe_radius` (probe radius Å; when omitted, the server-side default is used)
-- The tunnel start is auto-predicted by PrankWeb (center of the top-ranked pocket); no manual specification needed
-- Output: tunnel analysis results, visualization/download links
-- Use case: structural analysis such as enzyme active-site channels, ligand entry/exit pathways
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint caver_tunnel_analyze --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `structure_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `structure_file` | 3D protein structure: PDB/CIF URL, local path, or 4-character PDB ID; never pass FASTA/raw sequences | - |
-| `probe_radius` | Probe radius (Å); when omitted the server-side config.yaml default is used | - |
-
-## 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: Tunnel/channel location, length, bottleneck residues + visualization/download links
-- Presentation form: Text/table + links
-- Downstream reuse: -
-## Output Template
-
-- Title: **Protein tunnel/channel analysis result (CAVER)**
-- Lead with the conclusion: tunnel/channel location, length, bottleneck residues
-- Add visualization outputs 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 Tunnel/Channel Analysis (`huada_protein_tools` / `caver_tunnel_analyze`)
+
+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 internal tunnels and channels with CAVER 3.x.
+- Required: `structure_file` (PDB/CIF URL, local path, or 4-character PDB ID; never pass FASTA/raw sequences)
+- Optional: `probe_radius` (probe radius Å; when omitted, the server-side default is used)
+- The tunnel start is auto-predicted by PrankWeb (center of the top-ranked pocket); no manual specification needed
+- Output: tunnel analysis results, visualization/download links
+- Use case: structural analysis such as enzyme active-site channels, ligand entry/exit pathways
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint caver_tunnel_analyze --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `structure_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `structure_file` | 3D protein structure: PDB/CIF URL, local path, or 4-character PDB ID; never pass FASTA/raw sequences | - |
+| `probe_radius` | Probe radius (Å); when omitted the server-side config.yaml default is used | - |
+
+## 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: Tunnel/channel location, length, bottleneck residues + visualization/download links
+- Presentation form: Text/table + links
+- Downstream reuse: -
+## Output Template
+
+- Title: **Protein tunnel/channel analysis result (CAVER)**
+- Lead with the conclusion: tunnel/channel location, length, bottleneck residues
+- Add visualization outputs 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).