@delta-infra/cli 1.1.19 → 1.1.21

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

@@ -1,68 +1,68 @@
-# PubChem Compound Search (`huada_protein_tools` / `pubchem_search`)
-
-This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
-called via `delta-cli science invoke`; the business response described below lives
-under the CLI top-level `data` — read fields as documented in this file, do not
-recursively search. This file only documents the endpoint schema; it does not
-authorize direct HTTP. Endpoint names are authoritative as returned by
-`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
-guess, truncate, or alias.
-
-## Overview
-
-Call PubChem (NCBI) to search basic chemical molecule information.
-- Supports querying compounds by name, SMILES, InChI, InChIKey, PubChem CID.
-- `input_type` options: name (default) | smiles | inchi | inchikey | cid.
-- `query` passes the corresponding identifier per input_type: name like "aspirin",
-  SMILES like "CC(=O)OC1=CC=CC=C1C(=O)O", CID like "2244".
-- Optional: `max_results` (default 10, max 100)
-- Output: compound results `resultjson`, containing
-  cid/name/molecular_formula/molecular_weight/canonical_smiles/inchi/inchikey/
-  iupac_name/synonyms/pubchem_url
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint pubchem_search --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `query`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `query` | Query string: name, SMILES, InChI, InChIKey, or CID | - |
-| `input_type` | Query type: name \| smiles \| inchi \| inchikey \| cid, default name | name |
-| `max_results` | Maximum number of compounds to return, default 10, max 100 | 10 |
-
-## Response
-
-- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
-- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
-- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
-  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
-  do not treat file contents as ordinary JSON results.
-
-## Output Projection
-
-> Verification status: verified by a real `delta-cli` invocation
-
-- Projection content: Compound entries: name, synonyms, molecular_formula, molecular_weight, canonical_smiles, inchi, inchikey, cid, pubchem_url
-- Presentation form: Text (formula/weight/name/SMILES) + entry URL
-- Downstream reuse: canonical_smiles -> smiles / primary_smiles for catpred_predict / catapro_predict
-## Output Template
-
-- Title: **PubChem compound search**
-- Lead with the conclusion: compound name, molecular formula, molecular weight
-- Also give: canonical_smiles / InChIKey, cid, `[PubChem entry](pubchem_url)` (URL in a safe form)
-- Avoid listing every JSON key
-
-## 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.
+# PubChem Compound Search (`huada_protein_tools` / `pubchem_search`)
+
+This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
+called via `delta-cli science invoke`; the business response described below lives
+under the CLI top-level `data` — read fields as documented in this file, do not
+recursively search. This file only documents the endpoint schema; it does not
+authorize direct HTTP. Endpoint names are authoritative as returned by
+`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
+guess, truncate, or alias.
+
+## Overview
+
+Call PubChem (NCBI) to search basic chemical molecule information.
+- Supports querying compounds by name, SMILES, InChI, InChIKey, PubChem CID.
+- `input_type` options: name (default) | smiles | inchi | inchikey | cid.
+- `query` passes the corresponding identifier per input_type: name like "aspirin",
+  SMILES like "CC(=O)OC1=CC=CC=C1C(=O)O", CID like "2244".
+- Optional: `max_results` (default 10, max 100)
+- Output: compound results `resultjson`, containing
+  cid/name/molecular_formula/molecular_weight/canonical_smiles/inchi/inchikey/
+  iupac_name/synonyms/pubchem_url
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint pubchem_search --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `query`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `query` | Query string: name, SMILES, InChI, InChIKey, or CID | - |
+| `input_type` | Query type: name \| smiles \| inchi \| inchikey \| cid, default name | name |
+| `max_results` | Maximum number of compounds to return, default 10, max 100 | 10 |
+
+## Response
+
+- CLI top-level envelope: a call succeeds only when the exit code is 0 AND `ok` is `true`; the service response lives under `data`.
+- Server-side contract: `status` (success/error/partial), `message`, `tool_type`, `resultjson`, `download_url`; some endpoints also return `total_count`. `resultjson` may be a single object or an array — read only the keys documented in this file, do not recursively search.
+- Binary/file artifacts (such as the PDB/XLSX/FASTA/ZIP files that `download_url` points to) are downloaded and verified with
+  `delta-cli science file download --tool huada_protein_tools --endpoint ... --output <path>`;
+  do not treat file contents as ordinary JSON results.
+
+## Output Projection
+
+> Verification status: verified by a real `delta-cli` invocation
+
+- Projection content: Compound entries: name, synonyms, molecular_formula, molecular_weight, canonical_smiles, inchi, inchikey, cid, pubchem_url
+- Presentation form: Text (formula/weight/name/SMILES) + entry URL
+- Downstream reuse: canonical_smiles -> smiles / primary_smiles for catpred_predict / catapro_predict
+## Output Template
+
+- Title: **PubChem compound search**
+- Lead with the conclusion: compound name, molecular formula, molecular weight
+- Also give: canonical_smiles / InChIKey, cid, `[PubChem entry](pubchem_url)` (URL in a safe form)
+- Avoid listing every JSON key
+
+## 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/pubmed_search.md

@@ -1,79 +1,79 @@
-# PubMed Literature Search (`huada_protein_tools` / `pubmed_search`)
-
-This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
-called via `delta-cli science invoke`; the business response described below lives
-under the CLI top-level `data` — read fields as documented in this file, do not
-recursively search. This file only documents the endpoint schema; it does not
-authorize direct HTTP. Endpoint names are authoritative as returned by
-`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
-guess, truncate, or alias.
-
-## Overview
-
-Call PubMed (NCBI) to search academic literature, supporting cascaded retrieval of
-PMC/Europe PMC/OA PDF full texts. Various tasks may attempt to obtain relevant
-information through literature search.
-- `query` must be an English PubMed boolean search expression. If the user inputs
-  Chinese, first translate the core concepts into English academic terms, then
-  assemble them into a boolean expression. Recommended format:
-  ("concept A" OR "synonym A2") AND ("concept B" OR "synonym B2") AND ... Split
-  into 2-4 core concept groups, each with 2-4 English synonyms/related terms/MeSH
-  terms; phrases wrapped in double quotes.
-- Correct example: ("human enterokinase" OR "human enteropeptidase" OR
-  "enterokinase catalytic subunit") AND (solubility OR "soluble expression") AND
-  (mutation OR mutagenesis); when the user asks about "溶菌酶 活性位点" (lysozyme
-  active site), the query should be ("lysozyme" OR "muramidase") AND ("active site"
-  OR "catalytic site") AND (mutation OR mutagenesis).
-- Forbidden: UniProt IDs, full English questions, meaningless words (analysis of /
-  study of / improvement / optimization / design of / engineering of).
-- Optional: `max_results` (default 10, max 10), `min_year` (default 2000),
-  `max_year` (default 2026)
-- Output: literature results `resultjson`
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint pubmed_search --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `query`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `query` | PubMed English boolean search expression; when the user inputs Chinese, provide the translated & expanded English boolean expression here, never pass Chinese | - |
-| `max_results` | Maximum number of papers to return, default 10, max 10 | 10 |
-| `min_year` | Start year, default 2000 | 2000 |
-| `max_year` | End year, default 2026 | 2026 |
-
-## 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_papers and summary; table grouped by PMID (protein name, mutation (original notation), key finding, source reference)
-- Presentation form: Markdown table; keep original mutation notation (e.g. Y126A/Y206F); site-level comparison only when zero-shot mutant results exist and the literature contains those mutations
-- Downstream reuse: literature evidence can be cross-checked with zero_shot_mutant_candidates positions (note the PMID, distinguish reported hotspots/new targets)
-## Output Template
-
-- Title: **PubMed literature search result**
-- Lead with a review summary: 4-6 bullet points depending on focus (mutation/engineering vs application/mechanism)
-- Table grouped by PMID with the source reference in the last column (`PMID: XXXXXXXX`, fall back to the title when missing); keep original mutation notation
-- Papers with empty mutations do not show mutation-related columns; site-level comparison only when zero-shot mutant results exist and the literature contains those mutations
-
-## 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.
+# PubMed Literature Search (`huada_protein_tools` / `pubmed_search`)
+
+This endpoint is a real endpoint of the `huada_protein_tools` tool. It can only be
+called via `delta-cli science invoke`; the business response described below lives
+under the CLI top-level `data` — read fields as documented in this file, do not
+recursively search. This file only documents the endpoint schema; it does not
+authorize direct HTTP. Endpoint names are authoritative as returned by
+`delta-cli science endpoints list huada_protein_tools`; use them verbatim — never
+guess, truncate, or alias.
+
+## Overview
+
+Call PubMed (NCBI) to search academic literature, supporting cascaded retrieval of
+PMC/Europe PMC/OA PDF full texts. Various tasks may attempt to obtain relevant
+information through literature search.
+- `query` must be an English PubMed boolean search expression. If the user inputs
+  Chinese, first translate the core concepts into English academic terms, then
+  assemble them into a boolean expression. Recommended format:
+  ("concept A" OR "synonym A2") AND ("concept B" OR "synonym B2") AND ... Split
+  into 2-4 core concept groups, each with 2-4 English synonyms/related terms/MeSH
+  terms; phrases wrapped in double quotes.
+- Correct example: ("human enterokinase" OR "human enteropeptidase" OR
+  "enterokinase catalytic subunit") AND (solubility OR "soluble expression") AND
+  (mutation OR mutagenesis); when the user asks about "溶菌酶 活性位点" (lysozyme
+  active site), the query should be ("lysozyme" OR "muramidase") AND ("active site"
+  OR "catalytic site") AND (mutation OR mutagenesis).
+- Forbidden: UniProt IDs, full English questions, meaningless words (analysis of /
+  study of / improvement / optimization / design of / engineering of).
+- Optional: `max_results` (default 10, max 10), `min_year` (default 2000),
+  `max_year` (default 2026)
+- Output: literature results `resultjson`
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint pubmed_search --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `query`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `query` | PubMed English boolean search expression; when the user inputs Chinese, provide the translated & expanded English boolean expression here, never pass Chinese | - |
+| `max_results` | Maximum number of papers to return, default 10, max 10 | 10 |
+| `min_year` | Start year, default 2000 | 2000 |
+| `max_year` | End year, default 2026 | 2026 |
+
+## 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_papers and summary; table grouped by PMID (protein name, mutation (original notation), key finding, source reference)
+- Presentation form: Markdown table; keep original mutation notation (e.g. Y126A/Y206F); site-level comparison only when zero-shot mutant results exist and the literature contains those mutations
+- Downstream reuse: literature evidence can be cross-checked with zero_shot_mutant_candidates positions (note the PMID, distinguish reported hotspots/new targets)
+## Output Template
+
+- Title: **PubMed literature search result**
+- Lead with a review summary: 4-6 bullet points depending on focus (mutation/engineering vs application/mechanism)
+- Table grouped by PMID with the source reference in the last column (`PMID: XXXXXXXX`, fall back to the title when missing); keep original mutation notation
+- Papers with empty mutations do not show mutation-related columns; site-level comparison only when zero-shot mutant results exist and the literature contains those mutations
+
+## 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/reap_design_primer.md

@@ -1,69 +1,69 @@
-# Single-site Mutation Primer Design (`huada_protein_tools` / `reap_design_primer`)
-
-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
-
-REAP Step 7: design overlapping PCR site-directed mutagenesis primers for single-site
-mutations.
-- Required: `mutant_list_file` (Excel/CSV with a mutant column)
-- Required: `plasmid_fasta` (user-uploaded DNA FASTA template)
-- Required: `cds_start` (0-based CDS start in `plasmid_fasta`; needs to be extracted from the user's question)
-- Optional: `mutation_format` (protein default A123C / dna → G367A), `codon_pref_file`, `sheet`
-- Output: primer Excel `download_url`, ZIP `zip_download_url`, `resultjson` (primer preview and Tm)
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint reap_design_primer --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `mutant_list_file` **and** `template_file` / `plasmid_fasta`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `mutant_list_file` | Excel/CSV/TXT mutation list | - |
-| `template_file` | Segmented template TXT (upstream/gene/downstream) | - |
-| `plasmid_fasta` | Plasmid/template DNA FASTA | - |
-| `cds_start` | 0-based CDS start position in plasmid_fasta mode | - |
-| `mutation_format` | Mutation format: protein or dna, default protein | protein |
-| `codon_pref_file` | AA:CODON codon preference file | - |
-| `sheet` | Excel sheet index or name, default 0 | 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: Primer design table (mutation id, forward/reverse primer sequences, Tm) + Excel download_url + ZIP zip_download_url
-- Presentation form: Markdown table + Excel/ZIP download links
-- Downstream reuse: -
-## Output Template
-
-- Title: **Single-site mutation primer design result (REAP Step 7)**
-- Markdown table: `| Mutation ID | Forward primer | Reverse primer | Tm |`
-- Add the Excel and ZIP 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.
+# Single-site Mutation Primer Design (`huada_protein_tools` / `reap_design_primer`)
+
+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
+
+REAP Step 7: design overlapping PCR site-directed mutagenesis primers for single-site
+mutations.
+- Required: `mutant_list_file` (Excel/CSV with a mutant column)
+- Required: `plasmid_fasta` (user-uploaded DNA FASTA template)
+- Required: `cds_start` (0-based CDS start in `plasmid_fasta`; needs to be extracted from the user's question)
+- Optional: `mutation_format` (protein default A123C / dna → G367A), `codon_pref_file`, `sheet`
+- Output: primer Excel `download_url`, ZIP `zip_download_url`, `resultjson` (primer preview and Tm)
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint reap_design_primer --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `mutant_list_file` **and** `template_file` / `plasmid_fasta`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `mutant_list_file` | Excel/CSV/TXT mutation list | - |
+| `template_file` | Segmented template TXT (upstream/gene/downstream) | - |
+| `plasmid_fasta` | Plasmid/template DNA FASTA | - |
+| `cds_start` | 0-based CDS start position in plasmid_fasta mode | - |
+| `mutation_format` | Mutation format: protein or dna, default protein | protein |
+| `codon_pref_file` | AA:CODON codon preference file | - |
+| `sheet` | Excel sheet index or name, default 0 | 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: Primer design table (mutation id, forward/reverse primer sequences, Tm) + Excel download_url + ZIP zip_download_url
+- Presentation form: Markdown table + Excel/ZIP download links
+- Downstream reuse: -
+## Output Template
+
+- Title: **Single-site mutation primer design result (REAP Step 7)**
+- Markdown table: `| Mutation ID | Forward primer | Reverse primer | Tm |`
+- Add the Excel and ZIP 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/rfd3_design.md

@@ -1,65 +1,65 @@
-# Protein Scaffold Design (RFdiffusion3) (`huada_protein_tools` / `rfd3_design`)
-
-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
-
-Protein scaffold design with RFdiffusion3 (without MPNN sequence design).
-- Required: `structure_file` (cropped PDB/CIF structure URL or path, e.g. the `download_url` returned by pocket_prediction)
-- Optional: `chain_id` (design only this chain, default "A"; specifying a single chain on a multi-chain structure such as a tetramer avoids cross-chain cost-matrix conflicts), `length` (design length range, e.g. "100-200", default "100-200"), `rfd3_n` (RFdiffusion3 sample count, default 1)
-- The backend auto-infers `unindex` / `select_fixed_atoms` / `ori_token`
-- Output: generated PDB structure files and sequence FASTA files packaged as a ZIP `download_url`; `resultjson` contains `{structures: [...], structure_links: [...]}`, where each `structures` entry carries chain/length/sequence/sample_score/quality_metrics, and `quality_metrics` includes insertion RMSD, clashes, chain breaks, secondary structure, etc.; `structure_links` are the best ≤5 scaffold PDB links sorted by `sample_score` (highest score first)
-- Use case: scaffold design only, without MPNN sequence design
-
-## Invocation
-
-```text
-delta-cli science invoke --tool huada_protein_tools --endpoint rfd3_design --data JSON
-```
-
-Required input groups (at least one per group; all groups must be satisfied):
-
-- `structure_file`
-
-Request fields:
-
-| Field | Description | Default |
-|---|---|---|
-| `structure_file` | Cropped PDB/CIF | - |
-| `chain_id` | Design only this protein chain, default "A" | A |
-| `length` | Design length range, e.g. "100-200" | 100-200 |
-| `rfd3_n` | RFdiffusion3 sample count, default 1 | 1 |
-
-## 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: structure_links (best ≤5 scaffold PDBs sorted by sample_score) with structures overview (chain/length/sequence/sample_score/quality metrics)
-- Presentation form: Scaffold PDB link list; quality metrics include insertion RMSD, clashes, chain breaks, secondary structure
-- Downstream reuse: scaffolds can feed mpnn_design_sequence / protein_design for sequence design
-## Output Template
-
-- Title: **RFdiffusion3 protein scaffold design result**
-- Lead with the conclusion: number of scaffolds generated (best ≤5), sample_score range
-- Add scaffold PDB links to the "Result files & downloads" section; summarize quality metrics in text (insertion RMSD/clashes/chain breaks/secondary structure)
-
-## 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 Scaffold Design (RFdiffusion3) (`huada_protein_tools` / `rfd3_design`)
+
+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
+
+Protein scaffold design with RFdiffusion3 (without MPNN sequence design).
+- Required: `structure_file` (cropped PDB/CIF structure URL or path, e.g. the `download_url` returned by pocket_prediction)
+- Optional: `chain_id` (design only this chain, default "A"; specifying a single chain on a multi-chain structure such as a tetramer avoids cross-chain cost-matrix conflicts), `length` (design length range, e.g. "100-200", default "100-200"), `rfd3_n` (RFdiffusion3 sample count, default 1)
+- The backend auto-infers `unindex` / `select_fixed_atoms` / `ori_token`
+- Output: generated PDB structure files and sequence FASTA files packaged as a ZIP `download_url`; `resultjson` contains `{structures: [...], structure_links: [...]}`, where each `structures` entry carries chain/length/sequence/sample_score/quality_metrics, and `quality_metrics` includes insertion RMSD, clashes, chain breaks, secondary structure, etc.; `structure_links` are the best ≤5 scaffold PDB links sorted by `sample_score` (highest score first)
+- Use case: scaffold design only, without MPNN sequence design
+
+## Invocation
+
+```text
+delta-cli science invoke --tool huada_protein_tools --endpoint rfd3_design --data JSON
+```
+
+Required input groups (at least one per group; all groups must be satisfied):
+
+- `structure_file`
+
+Request fields:
+
+| Field | Description | Default |
+|---|---|---|
+| `structure_file` | Cropped PDB/CIF | - |
+| `chain_id` | Design only this protein chain, default "A" | A |
+| `length` | Design length range, e.g. "100-200" | 100-200 |
+| `rfd3_n` | RFdiffusion3 sample count, default 1 | 1 |
+
+## 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: structure_links (best ≤5 scaffold PDBs sorted by sample_score) with structures overview (chain/length/sequence/sample_score/quality metrics)
+- Presentation form: Scaffold PDB link list; quality metrics include insertion RMSD, clashes, chain breaks, secondary structure
+- Downstream reuse: scaffolds can feed mpnn_design_sequence / protein_design for sequence design
+## Output Template
+
+- Title: **RFdiffusion3 protein scaffold design result**
+- Lead with the conclusion: number of scaffolds generated (best ≤5), sample_score range
+- Add scaffold PDB links to the "Result files & downloads" section; summarize quality metrics in text (insertion RMSD/clashes/chain breaks/secondary structure)
+
+## 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).