@delta-infra/cli 1.1.19 → 1.1.23

package/skills/delta-protein/references/esmfold2_predict.md

@@ -1,67 +1,67 @@
-# Protein Structure Prediction (ESMFold2) (`huada_protein_tools` / `esmfold2_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 the three-dimensional structure of protein/DNA/RNA/ligand complexes with
-ESMFold2; supports combined prediction.
-- Protein input: `protein_sequence` (sequence) / `sequence_file` (FASTA) — choose one
-- Optional: `msa_file` (A3M), `dna_sequence` (DNA sequence), `rna_sequence` (RNA sequence), `ligand` (ligand CCD code or SMILES)
-- Distinguish from Protenix: use ESMFold2 when DNA/RNA/ligand are involved; use Protenix for pure protein structure prediction
-- Output: predicted structure CIF file `download_url`, confidence metrics `resultjson`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint esmfold2_predict --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `protein_sequence` / `sequence_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `protein_sequence` |  | - |
-| `sequence_file` | FASTA/FA | - |
-| `msa_file` | A3M MSA | - |
-| `dna_sequence` | DNA sequence, single str or list[str] | - |
-| `rna_sequence` | RNA sequence, single str or list[str] | - |
-| `ligand` | Small-molecule ligand: CCD code (e.g. ATP, MG) or SMILES string | - |
-
-## 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: Complex structure download_url (.cif, composition when protein+DNA/RNA/ligand) with confidence: plddt_mean, ptm, iptm, sequence_length
-- Presentation form: Structure file link + confidence text
-- Downstream reuse: structure can serve as downstream structure_file
-## Output Template
-
-- Title: **ESMFold2 structure prediction result**
-- Lead with the conclusion: prediction done (complex composition, e.g. protein(47aa)+dna(12nt)) and confidence (plddt_mean/ptm/iptm), sequence_length
-- Add the structure CIF link 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 Structure Prediction (ESMFold2) (`huada_protein_tools` / `esmfold2_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 the three-dimensional structure of protein/DNA/RNA/ligand complexes with
+ESMFold2; supports combined prediction.
+- Protein input: `protein_sequence` (sequence) / `sequence_file` (FASTA) — choose one
+- Optional: `msa_file` (A3M), `dna_sequence` (DNA sequence), `rna_sequence` (RNA sequence), `ligand` (ligand CCD code or SMILES)
+- Distinguish from Protenix: use ESMFold2 when DNA/RNA/ligand are involved; use Protenix for pure protein structure prediction
+- Output: predicted structure CIF file `download_url`, confidence metrics `resultjson`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint esmfold2_predict --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `protein_sequence` / `sequence_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `protein_sequence` |  | - |
+| `sequence_file` | FASTA/FA | - |
+| `msa_file` | A3M MSA | - |
+| `dna_sequence` | DNA sequence, single str or list[str] | - |
+| `rna_sequence` | RNA sequence, single str or list[str] | - |
+| `ligand` | Small-molecule ligand: CCD code (e.g. ATP, MG) or SMILES string | - |
+
+## 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: Complex structure download_url (.cif, composition when protein+DNA/RNA/ligand) with confidence: plddt_mean, ptm, iptm, sequence_length
+- Presentation form: Structure file link + confidence text
+- Downstream reuse: structure can serve as downstream structure_file
+## Output Template
+
+- Title: **ESMFold2 structure prediction result**
+- Lead with the conclusion: prediction done (complex composition, e.g. protein(47aa)+dna(12nt)) and confidence (plddt_mean/ptm/iptm), sequence_length
+- Add the structure CIF link 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/evcouplings_mutation.md

@@ -1,64 +1,64 @@
-# EVcouplings Coevolution & Mutation Analysis (`huada_protein_tools` / `evcouplings_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
-
-Infer a coevolutionary coupling model from an equal-length aligned MSA with plmc and
-output single-site mutation statistical energy scores plus coupling parameters.
-- Input: `msa_file` (equal-length aligned MSA file URL, FASTA/Clustal/Stockholm)
-- Optional: `query_id` (focus sequence ID in the MSA, default first), `model_file` (existing plmc .model file), `mutant_list_file` (Excel/CSV with a mutant column)
-- Output: single-site mutation score Excel `download_url`, `zip_download_url` (contains .model, coupling parameters, etc.)
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint evcouplings_mutation --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `msa_file` / `model_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `msa_file` | Equal-length aligned MSA file URL (FASTA/Clustal/Stockholm) | - |
-| `query_id` | Focus sequence ID in the MSA, default first | - |
-| `model_file` | Existing plmc .model file URL or path | - |
-| `mutant_list_file` | Excel/CSV URL or path with a mutant column | - |
-
-## 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: Single-site mutation statistical energy scores (Excel download_url) + zip_download_url (.model and coupling parameters)
-- Presentation form: Energy score summary + Excel/ZIP links
-- Downstream reuse: -
-## Output Template
-
-- Title: **EVcouplings coevolutionary mutation analysis result**
-- Lead with the conclusion: TOP positions by single-site statistical energy score
-- Add the Excel and ZIP (with .model/coupling parameters) 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.
+# EVcouplings Coevolution & Mutation Analysis (`huada_protein_tools` / `evcouplings_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
+
+Infer a coevolutionary coupling model from an equal-length aligned MSA with plmc and
+output single-site mutation statistical energy scores plus coupling parameters.
+- Input: `msa_file` (equal-length aligned MSA file URL, FASTA/Clustal/Stockholm)
+- Optional: `query_id` (focus sequence ID in the MSA, default first), `model_file` (existing plmc .model file), `mutant_list_file` (Excel/CSV with a mutant column)
+- Output: single-site mutation score Excel `download_url`, `zip_download_url` (contains .model, coupling parameters, etc.)
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint evcouplings_mutation --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `msa_file` / `model_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `msa_file` | Equal-length aligned MSA file URL (FASTA/Clustal/Stockholm) | - |
+| `query_id` | Focus sequence ID in the MSA, default first | - |
+| `model_file` | Existing plmc .model file URL or path | - |
+| `mutant_list_file` | Excel/CSV URL or path with a mutant column | - |
+
+## 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: Single-site mutation statistical energy scores (Excel download_url) + zip_download_url (.model and coupling parameters)
+- Presentation form: Energy score summary + Excel/ZIP links
+- Downstream reuse: -
+## Output Template
+
+- Title: **EVcouplings coevolutionary mutation analysis result**
+- Lead with the conclusion: TOP positions by single-site statistical energy score
+- Add the Excel and ZIP (with .model/coupling parameters) 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/fasta_to_sequence.md

@@ -1,59 +1,59 @@
-# FASTA Sequence Extraction (`huada_protein_tools` / `fasta_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 FASTA file.
-- Required: `fasta_file`
-- Output: extracted protein sequence `resultjson`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint fasta_to_sequence --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `fasta_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `fasta_file` | FASTA/FA | - |
-
-## 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 FASTA
-- Presentation form: Sequence shown as inline code
-- Downstream reuse: sequence can be used as downstream protein_sequence input
-## Output Template
-
-- Title: **FASTA sequence parsing result**
-- Lead with the conclusion: parsed sequence id/length
-- Show the sequence as inline code
-
-## 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.
+# FASTA Sequence Extraction (`huada_protein_tools` / `fasta_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 FASTA file.
+- Required: `fasta_file`
+- Output: extracted protein sequence `resultjson`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint fasta_to_sequence --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `fasta_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `fasta_file` | FASTA/FA | - |
+
+## 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 FASTA
+- Presentation form: Sequence shown as inline code
+- Downstream reuse: sequence can be used as downstream protein_sequence input
+## Output Template
+
+- Title: **FASTA sequence parsing result**
+- Lead with the conclusion: parsed sequence id/length
+- Show the sequence as inline code
+
+## 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/foldseek.md

@@ -1,61 +1,61 @@
-# Foldseek Sequence Extraction (`huada_protein_tools` / `foldseek`)
-
-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 Foldseek/SaProt combined sequence from a protein structure file.
-- Required: `structure_file` (.pdb/.cif)
-- Optional: `chain` (A)
-- Output: extraction summary, `download_url` (FASTA)
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint foldseek --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: Extracted Foldseek/SaProt combined sequence, download_url (FASTA)
-- Presentation form: Sequence inline code + FASTA link
-- Downstream reuse: sequence can serve as downstream protein_sequence input
-## Output Template
-
-- Title: **Foldseek structure search result**
-- Lead with the conclusion: sequence extraction summary (length)
-- Add sequence inline code + FASTA link 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.
+# Foldseek Sequence Extraction (`huada_protein_tools` / `foldseek`)
+
+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 Foldseek/SaProt combined sequence from a protein structure file.
+- Required: `structure_file` (.pdb/.cif)
+- Optional: `chain` (A)
+- Output: extraction summary, `download_url` (FASTA)
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint foldseek --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: Extracted Foldseek/SaProt combined sequence, download_url (FASTA)
+- Presentation form: Sequence inline code + FASTA link
+- Downstream reuse: sequence can serve as downstream protein_sequence input
+## Output Template
+
+- Title: **Foldseek structure search result**
+- Lead with the conclusion: sequence extraction summary (length)
+- Add sequence inline code + FASTA link 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/generate_msa.md

@@ -1,61 +1,61 @@
-# Multiple Sequence Alignment Computation (`huada_protein_tools` / `generate_msa`)
-
-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
-
-Compute a homolog protein MSA (A3M format) with MMseqs2 against the uniref100
-database.
-- Input: `protein_sequence` / `fasta_file` (choose one)
-- Output: A3M MSA file `download_url`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint generate_msa --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `protein_sequence` / `fasta_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `protein_sequence` |  | - |
-| `fasta_file` | FASTA/FA | - |
-
-## 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: Homolog MSA (A3M), download_url
-- Presentation form: Download link; note MSA can be used for homology/conservation inference
-- Downstream reuse: download_url -> msa_file for consensus_mutation / evcouplings_mutation / zero_shot_mutant_candidates
-## Output Template
-
-- Title: **Multiple sequence alignment (MSA) result**
-- Lead with the conclusion: MSA computed, usable for homology and conservation inference
-- Add the MSA file link to the "Result files & downloads" section and note it can serve as downstream msa_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.
+# Multiple Sequence Alignment Computation (`huada_protein_tools` / `generate_msa`)
+
+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
+
+Compute a homolog protein MSA (A3M format) with MMseqs2 against the uniref100
+database.
+- Input: `protein_sequence` / `fasta_file` (choose one)
+- Output: A3M MSA file `download_url`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint generate_msa --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `protein_sequence` / `fasta_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `protein_sequence` |  | - |
+| `fasta_file` | FASTA/FA | - |
+
+## 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: Homolog MSA (A3M), download_url
+- Presentation form: Download link; note MSA can be used for homology/conservation inference
+- Downstream reuse: download_url -> msa_file for consensus_mutation / evcouplings_mutation / zero_shot_mutant_candidates
+## Output Template
+
+- Title: **Multiple sequence alignment (MSA) result**
+- Lead with the conclusion: MSA computed, usable for homology and conservation inference
+- Add the MSA file link to the "Result files & downloads" section and note it can serve as downstream msa_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).