@delta-infra/cli 1.1.19 → 1.1.21

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

@@ -1,70 +1,70 @@
-# Vina Single-pose Scoring (`huada_protein_tools` / `dock_score`)
-
-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
-
-Single-pose scoring (score_only) of a protein-ligand complex with AutoDock Vina.
-- Input: `structure_file` (PDB/CIF complex file URL) + `dock_ligand` (ligand residue name in the complex, e.g. BTA)
-- Optional: `chain_id` (chain ID of the ligand, default A); `box_center`/`box_size` (manual box, format x,y,z or w,h,d) — when not provided, computed automatically from the ligand bounding box
-- Optional defaults: padding=8.0, min_box_size=20.0, ph=7.4, cpu=8, seed=42
-- Output: `resultjson` contains `best_score` (total binding energy, kcal/mol) and `scores` (energy breakdown dict)
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint dock_score --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `structure_file` **and** `dock_ligand`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `structure_file` | PDB/CIF complex | - |
-| `dock_ligand` | Ligand residue name in the complex to be scored, e.g. BTA | - |
-| `chain_id` | Chain ID of the ligand, default A | A |
-| `box_center` | Manually specified scoring box center, format x,y,z | - |
-| `box_size` | Manually specified scoring box size, a single number or w,h,d | - |
-| `padding` | Padding around the bounding box (Å) when the box is auto-computed | 8.0 |
-| `min_box_size` | Minimum length per side (Å) when the box is auto-computed | 20.0 |
-| `ph` | Protonation pH | 7.4 |
-| `cpu` | Number of CPU cores | 8 |
-| `seed` | Random seed | 42 |
-
-## 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: best_score (total binding energy kcal/mol), per-term energy breakdown, box_size/center, mode=score_only
-- Presentation form: Text (total binding energy + energy breakdown)
-- Downstream reuse: -
-## Output Template
-
-- Title: **Vina single-pose scoring result**
-- Lead with the conclusion: best_score (kcal/mol) and the box used (center/box_size)
-- Give the energy breakdown (gauss/hydrophobic/hbond etc., restated per returned keys)
-
-## 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.
+# Vina Single-pose Scoring (`huada_protein_tools` / `dock_score`)
+
+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
+
+Single-pose scoring (score_only) of a protein-ligand complex with AutoDock Vina.
+- Input: `structure_file` (PDB/CIF complex file URL) + `dock_ligand` (ligand residue name in the complex, e.g. BTA)
+- Optional: `chain_id` (chain ID of the ligand, default A); `box_center`/`box_size` (manual box, format x,y,z or w,h,d) — when not provided, computed automatically from the ligand bounding box
+- Optional defaults: padding=8.0, min_box_size=20.0, ph=7.4, cpu=8, seed=42
+- Output: `resultjson` contains `best_score` (total binding energy, kcal/mol) and `scores` (energy breakdown dict)
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint dock_score --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `structure_file` **and** `dock_ligand`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `structure_file` | PDB/CIF complex | - |
+| `dock_ligand` | Ligand residue name in the complex to be scored, e.g. BTA | - |
+| `chain_id` | Chain ID of the ligand, default A | A |
+| `box_center` | Manually specified scoring box center, format x,y,z | - |
+| `box_size` | Manually specified scoring box size, a single number or w,h,d | - |
+| `padding` | Padding around the bounding box (Å) when the box is auto-computed | 8.0 |
+| `min_box_size` | Minimum length per side (Å) when the box is auto-computed | 20.0 |
+| `ph` | Protonation pH | 7.4 |
+| `cpu` | Number of CPU cores | 8 |
+| `seed` | Random seed | 42 |
+
+## 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: best_score (total binding energy kcal/mol), per-term energy breakdown, box_size/center, mode=score_only
+- Presentation form: Text (total binding energy + energy breakdown)
+- Downstream reuse: -
+## Output Template
+
+- Title: **Vina single-pose scoring result**
+- Lead with the conclusion: best_score (kcal/mol) and the box used (center/box_size)
+- Give the energy breakdown (gauss/hydrophobic/hbond etc., restated per returned keys)
+
+## 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/easifa_predict_active_site.md

@@ -1,70 +1,70 @@
-# Enzyme Active-site Prediction (`huada_protein_tools` / `easifa_predict_active_site`)
-
-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 active sites with EasIFA.
-- Required: `input_mode` (structure/sequence/uniprot)
-- structure mode requires `structure_file`; sequence mode requires `protein_sequence` or `sequence_file`
-- Optional: `rxn_smiles` (reaction SMILES), `chain`
-- Output: active-site predictions `resultjson`, `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint easifa_predict_active_site --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `input_mode`
-
-Server-side default parameters:
-
-- `input_mode` = `structure`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `input_mode` | Input mode: structure/sequence/uniprot | structure |
-| `structure_file` | PDB/CIF | - |
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `rxn_smiles` | Reaction SMILES (substrate>>product) | - |
-| `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 active-site/binding-site residues, positions and confidence; positions overlapping zero-shot mutant results are marked as not recommended for engineering
-- Presentation form: Text/table
-- Downstream reuse: site information cross-annotated with zero_shot_mutant_candidates overlap
-## Output Template
-
-- Title: **Enzyme active-site/binding-site prediction result (EasIFA)**
-- Lead with the conclusion: active-site residues, positions, confidence
-- When zero-shot mutant results exist, mark overlapping positions (overlaps not recommended for engineering)
-
-## 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 Active-site Prediction (`huada_protein_tools` / `easifa_predict_active_site`)
+
+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 active sites with EasIFA.
+- Required: `input_mode` (structure/sequence/uniprot)
+- structure mode requires `structure_file`; sequence mode requires `protein_sequence` or `sequence_file`
+- Optional: `rxn_smiles` (reaction SMILES), `chain`
+- Output: active-site predictions `resultjson`, `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint easifa_predict_active_site --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `input_mode`
+
+Server-side default parameters:
+
+- `input_mode` = `structure`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `input_mode` | Input mode: structure/sequence/uniprot | structure |
+| `structure_file` | PDB/CIF | - |
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `rxn_smiles` | Reaction SMILES (substrate>>product) | - |
+| `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 active-site/binding-site residues, positions and confidence; positions overlapping zero-shot mutant results are marked as not recommended for engineering
+- Presentation form: Text/table
+- Downstream reuse: site information cross-annotated with zero_shot_mutant_candidates overlap
+## Output Template
+
+- Title: **Enzyme active-site/binding-site prediction result (EasIFA)**
+- Lead with the conclusion: active-site residues, positions, confidence
+- When zero-shot mutant results exist, mark overlapping positions (overlaps not recommended for engineering)
+
+## 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/ephod_predict_mutation.md

@@ -1,66 +1,66 @@
-# Mutant Optimal pH Prediction (`huada_protein_tools` / `ephod_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 optimal pH of mutant proteins.
-- Input: `protein_sequence`/`sequence_file`/`structure_file` + `mutant_list`/`mutant_list_file`
-- Optional: `chain` (A), `target_pH` (-1.0 returns all)
-- Output: mutant optimal pH results `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint ephod_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, e.g. ["A1V", "K2M"] | [] |
-| `mutant_list_file` | CSV/XLSX mutation list file | - |
-| `target_pH` | Target pH, 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: Optimal pH per mutant and its change (download_url)
-- Presentation form: Text/table
-- Downstream reuse: -
-## Output Template
-
-- Title: **Mutant optimal pH prediction result**
-- Lead with the conclusion: optimal pH per mutant and differences vs wild type
-- 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 Optimal pH Prediction (`huada_protein_tools` / `ephod_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 optimal pH of mutant proteins.
+- Input: `protein_sequence`/`sequence_file`/`structure_file` + `mutant_list`/`mutant_list_file`
+- Optional: `chain` (A), `target_pH` (-1.0 returns all)
+- Output: mutant optimal pH results `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint ephod_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, e.g. ["A1V", "K2M"] | [] |
+| `mutant_list_file` | CSV/XLSX mutation list file | - |
+| `target_pH` | Target pH, 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: Optimal pH per mutant and its change (download_url)
+- Presentation form: Text/table
+- Downstream reuse: -
+## Output Template
+
+- Title: **Mutant optimal pH prediction result**
+- Lead with the conclusion: optimal pH per mutant and differences vs wild type
+- 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/ephod_predict_protein.md

@@ -1,61 +1,61 @@
-# Protein Optimal pH Prediction (`huada_protein_tools` / `ephod_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 the optimal pH of proteins.
-- Input: `protein_list` (list of one-letter sequences) / `protein_list_file` (sequence file URL) — choose one
-- Important: `protein_list_file` must be a `.fasta/.fa/.csv/.xlsx` sequence-file URL; never pass `.pdb/.cif` structure files
-- Output: optimal pH prediction results `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint ephod_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: Optimal pH for each protein (download_url)
-- Presentation form: Text/table
-- Downstream reuse: -
-## Output Template
-
-- Title: **Protein optimal pH prediction result**
-- Lead with the conclusion: optimal pH range per protein
-- 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 Optimal pH Prediction (`huada_protein_tools` / `ephod_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 the optimal pH of proteins.
+- Input: `protein_list` (list of one-letter sequences) / `protein_list_file` (sequence file URL) — choose one
+- Important: `protein_list_file` must be a `.fasta/.fa/.csv/.xlsx` sequence-file URL; never pass `.pdb/.cif` structure files
+- Output: optimal pH prediction results `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint ephod_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: Optimal pH for each protein (download_url)
+- Presentation form: Text/table
+- Downstream reuse: -
+## Output Template
+
+- Title: **Protein optimal pH prediction result**
+- Lead with the conclusion: optimal pH range per protein
+- 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).