@delta-infra/cli 1.0.80 → 1.0.81

package/skills/delta-science/references/pubchem.md

@@ -1,127 +1,127 @@
-# PubChem 详细规则
-
+# PubChem 详细规则
+
 只能通过当前 Skill 目录下的 `scripts/invoke.py` 调用。wrapper 已解包服务
-信封，因此以下文档所说的业务 `data` 在 wrapper 结果中就是 `result["native"]`
-顶层；禁止再读取 `result["native"]["data"]`。本文件中的 URL 只用于说明 endpoint
-schema，不授权直接 HTTP。普通名称基础查询只调用一次 `compound-summary`；多个名称
-只调用一次 `compound-batch-summary`，默认 body 仅包含 `identifiers` 和
-`namespace:"name"`，不得先调用 health/schema。
-
-结果直接从 `native` 投影。批量记录位于 `native.results[*]`，原始标签在 `input`，
-属性在嵌套 `properties`。SMILES 回退顺序固定为
-`CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES`。
-PubChem `XLogP` 与 RDKit `MolLogP` 不得互换；not_found 不得用本地计算补值。
-
-Namespaces: `cid`, `name`, `smiles`, `inchi`, `inchikey`, `formula`.
-
-## Health
-
-operation：`health`，无 body。
-
-## Resolve CIDs
-
-operation：`compound-resolve-cids`。
-
-```json
-{"identifier": "aspirin", "namespace": "name", "max_records": 20}
-```
-
-`max_records`: 1-100.
-
-## Properties
-
-operation：`compound-properties`。
-
-```json
-{
-  "identifier": "2244",
-  "namespace": "cid",
-  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IUPACName"]
-}
-```
-
-Allowed properties include `MolecularFormula`, `MolecularWeight`,
-`CanonicalSMILES`, `IsomericSMILES`, `SMILES`, `ConnectivitySMILES`,
-`IUPACName`, `InChI`, `InChIKey`, `XLogP`, `TPSA`, `HBondDonorCount`,
-`HBondAcceptorCount`, `RotatableBondCount`, `ExactMass`, `MonoisotopicMass`,
-`Charge`, `HeavyAtomCount`, `Complexity`, `CovalentUnitCount`,
-`DefinedAtomStereoCount`, `UndefinedAtomStereoCount`, `DefinedBondStereoCount`,
-`UndefinedBondStereoCount`, and `IsotopeAtomCount`.
-
-## Synonyms
-
-operation：`compound-synonyms`。
-
-```json
-{"identifier": "2244", "namespace": "cid", "max_synonyms": 50}
-```
-
-`max_synonyms`: 1-500.
-
-## Summary
-
-operation：`compound-summary`。
-
-```json
-{
-  "identifier": "aspirin",
-  "namespace": "name",
-  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IUPACName"],
-  "synonym_limit": 20
-}
-```
-
-`synonym_limit`: 0-100. Use this endpoint for general compound lookup because
-it resolves CID, selected properties, and synonyms in one call.
-
-Response fields include `valid`, `cid`, `properties`, `properties_raw`,
-`aliases`, `synonyms`, and `metadata`. Numeric properties are coerced to JSON
-numbers when possible. Requested SMILES aliases are filled when PubChem returns
-an equivalent key such as `ConnectivitySMILES`.
-
-## Batch Summary
-
-operation：`compound-batch-summary`。
-
-```json
-{
-  "identifiers": ["aspirin", "ibuprofen", "caffeine"],
-  "namespace": "name",
-  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "XLogP", "TPSA"],
-  "synonym_limit": 5
-}
-```
-
-Limits: 1-100 identifiers. The response preserves input order and includes
-per-item errors:
-
-```json
-{
-  "valid": false,
-  "namespace": "name",
-  "properties_requested": ["CanonicalSMILES"],
-  "results": [
-    {
-      "input": "aspirin",
-      "valid": true,
-      "cid": 2244,
-      "properties": {
-        "CanonicalSMILES": "CC(=O)Oc1ccccc1C(=O)O",
-        "ConnectivitySMILES": "CC(=O)Oc1ccccc1C(=O)O",
-        "_aliases": {"CanonicalSMILES": "ConnectivitySMILES"},
-        "properties_raw": {}
-      },
-      "properties_raw": {},
-      "aliases": {"CanonicalSMILES": "ConnectivitySMILES"},
-      "synonyms": []
-    },
-    {
-      "input": "bad-name",
-      "valid": false,
-      "error": "not found"
-    }
-  ],
-  "count": 2,
-  "failed_count": 1
-}
-```
+信封，因此以下文档所说的业务 `data` 在 wrapper 结果中就是 `result["native"]`
+顶层；禁止再读取 `result["native"]["data"]`。本文件中的 URL 只用于说明 endpoint
+schema，不授权直接 HTTP。普通名称基础查询只调用一次 `compound-summary`；多个名称
+只调用一次 `compound-batch-summary`，默认 body 仅包含 `identifiers` 和
+`namespace:"name"`，不得先调用 health/schema。
+
+结果直接从 `native` 投影。批量记录位于 `native.results[*]`，原始标签在 `input`，
+属性在嵌套 `properties`。SMILES 回退顺序固定为
+`CanonicalSMILES -> ConnectivitySMILES -> SMILES -> IsomericSMILES`。
+PubChem `XLogP` 与 RDKit `MolLogP` 不得互换；not_found 不得用本地计算补值。
+
+Namespaces: `cid`, `name`, `smiles`, `inchi`, `inchikey`, `formula`.
+
+## Health
+
+operation：`health`，无 body。
+
+## Resolve CIDs
+
+operation：`compound-resolve-cids`。
+
+```json
+{"identifier": "aspirin", "namespace": "name", "max_records": 20}
+```
+
+`max_records`: 1-100.
+
+## Properties
+
+operation：`compound-properties`。
+
+```json
+{
+  "identifier": "2244",
+  "namespace": "cid",
+  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IUPACName"]
+}
+```
+
+Allowed properties include `MolecularFormula`, `MolecularWeight`,
+`CanonicalSMILES`, `IsomericSMILES`, `SMILES`, `ConnectivitySMILES`,
+`IUPACName`, `InChI`, `InChIKey`, `XLogP`, `TPSA`, `HBondDonorCount`,
+`HBondAcceptorCount`, `RotatableBondCount`, `ExactMass`, `MonoisotopicMass`,
+`Charge`, `HeavyAtomCount`, `Complexity`, `CovalentUnitCount`,
+`DefinedAtomStereoCount`, `UndefinedAtomStereoCount`, `DefinedBondStereoCount`,
+`UndefinedBondStereoCount`, and `IsotopeAtomCount`.
+
+## Synonyms
+
+operation：`compound-synonyms`。
+
+```json
+{"identifier": "2244", "namespace": "cid", "max_synonyms": 50}
+```
+
+`max_synonyms`: 1-500.
+
+## Summary
+
+operation：`compound-summary`。
+
+```json
+{
+  "identifier": "aspirin",
+  "namespace": "name",
+  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IUPACName"],
+  "synonym_limit": 20
+}
+```
+
+`synonym_limit`: 0-100. Use this endpoint for general compound lookup because
+it resolves CID, selected properties, and synonyms in one call.
+
+Response fields include `valid`, `cid`, `properties`, `properties_raw`,
+`aliases`, `synonyms`, and `metadata`. Numeric properties are coerced to JSON
+numbers when possible. Requested SMILES aliases are filled when PubChem returns
+an equivalent key such as `ConnectivitySMILES`.
+
+## Batch Summary
+
+operation：`compound-batch-summary`。
+
+```json
+{
+  "identifiers": ["aspirin", "ibuprofen", "caffeine"],
+  "namespace": "name",
+  "properties": ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "XLogP", "TPSA"],
+  "synonym_limit": 5
+}
+```
+
+Limits: 1-100 identifiers. The response preserves input order and includes
+per-item errors:
+
+```json
+{
+  "valid": false,
+  "namespace": "name",
+  "properties_requested": ["CanonicalSMILES"],
+  "results": [
+    {
+      "input": "aspirin",
+      "valid": true,
+      "cid": 2244,
+      "properties": {
+        "CanonicalSMILES": "CC(=O)Oc1ccccc1C(=O)O",
+        "ConnectivitySMILES": "CC(=O)Oc1ccccc1C(=O)O",
+        "_aliases": {"CanonicalSMILES": "ConnectivitySMILES"},
+        "properties_raw": {}
+      },
+      "properties_raw": {},
+      "aliases": {"CanonicalSMILES": "ConnectivitySMILES"},
+      "synonyms": []
+    },
+    {
+      "input": "bad-name",
+      "valid": false,
+      "error": "not found"
+    }
+  ],
+  "count": 2,
+  "failed_count": 1
+}
+```

package/skills/delta-science/references/pymatgen.md

@@ -1,68 +1,68 @@
-# pymatgen 详细规则
-
-所有调用只走统一 wrapper。无机化学式、组成和式量优先使用 pymatgen，不用 PubChem
-或本地元素表替代。结构 operation 必须发送完整结构文本，不能发送本地文件路径；
-支持 `cif`、`poscar`、`json`、`cssr`、`xsf`，不接收 LAMMPS data/dump。
-
-## Health
-
-operation：`health`，无 body。
-
-## Composition Parse
-
-operation：`composition-parse`。
-
-```json
-{"formula": "LiFePO4", "format": "formula"}
-```
-
-Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
-`alphabetic_formula`, `anonymous_formula`, `chemical_system`,
-`number_of_atoms`, `weight`, `element_amounts`, `atomic_fractions`,
-`weight_fractions`, `error`.
-
-## Structure Parse / Summary
-
-operation：`structure-parse` 或 `structure-summary`。
-
-```json
-{"input": "<CIF text>", "format": "cif", "primitive": false}
-```
-
-Input formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
-
-Summary fields include `formula`, `reduced_formula`, `chemical_system`,
-`nsites`, `nelements`, `density`, `volume`, `lattice`, `element_amounts`, and
-`species`.
-
-## Structure Convert
-
-operation：`structure-convert`。
-
-```json
-{
-  "input": "<CIF text>",
-  "input_format": "cif",
-  "output_format": "poscar",
-  "primitive": false
-}
-```
-
-Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
-
-## Symmetry
-
-operation：`structure-symmetry`。
-
-```json
-{
-  "input": "<CIF text>",
-  "format": "cif",
-  "primitive": false,
-  "symprec": 0.01,
-  "angle_tolerance": 5.0
-}
-```
-
-Returns `space_group_symbol`, `space_group_number`, `crystal_system`,
-`point_group_symbol`, `hall`, and `nsites`.
+# pymatgen 详细规则
+
+所有调用只走统一 wrapper。无机化学式、组成和式量优先使用 pymatgen，不用 PubChem
+或本地元素表替代。结构 operation 必须发送完整结构文本，不能发送本地文件路径；
+支持 `cif`、`poscar`、`json`、`cssr`、`xsf`，不接收 LAMMPS data/dump。
+
+## Health
+
+operation：`health`，无 body。
+
+## Composition Parse
+
+operation：`composition-parse`。
+
+```json
+{"formula": "LiFePO4", "format": "formula"}
+```
+
+Key response fields in `data`: `valid`, `formula`, `reduced_formula`,
+`alphabetic_formula`, `anonymous_formula`, `chemical_system`,
+`number_of_atoms`, `weight`, `element_amounts`, `atomic_fractions`,
+`weight_fractions`, `error`.
+
+## Structure Parse / Summary
+
+operation：`structure-parse` 或 `structure-summary`。
+
+```json
+{"input": "<CIF text>", "format": "cif", "primitive": false}
+```
+
+Input formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
+
+Summary fields include `formula`, `reduced_formula`, `chemical_system`,
+`nsites`, `nelements`, `density`, `volume`, `lattice`, `element_amounts`, and
+`species`.
+
+## Structure Convert
+
+operation：`structure-convert`。
+
+```json
+{
+  "input": "<CIF text>",
+  "input_format": "cif",
+  "output_format": "poscar",
+  "primitive": false
+}
+```
+
+Output formats: `cif`, `poscar`, `json`, `cssr`, `xsf`.
+
+## Symmetry
+
+operation：`structure-symmetry`。
+
+```json
+{
+  "input": "<CIF text>",
+  "format": "cif",
+  "primitive": false,
+  "symprec": 0.01,
+  "angle_tolerance": 5.0
+}
+```
+
+Returns `space_group_symbol`, `space_group_number`, `crystal_system`,
+`point_group_symbol`, `hall`, and `nsites`.

package/skills/delta-science/references/rdkit.md

@@ -1,139 +1,139 @@
-# RDKit 详细规则
-
+# RDKit 详细规则
+
 只能通过当前 Skill 目录下的 `scripts/invoke.py` 调用。wrapper 已解包服务
-信封，因此以下业务响应在 wrapper 结果中位于 `result["native"]` 顶层；禁止读取
-`result["native"]["data"]`。这里只记录 operation schema，不授权直接 HTTP。
-
-一个请求只执行完成目标所需的最少调用。同时校验、规范化并计算基础描述符时使用一次
-`batch-parse-describe`，payload 使用 `molecules:[{id,smiles}]`，不得拆成 parse 和
-descriptors。多个分子的全对相似度使用一次 `similarity-matrix`；排名字段固定为
-`a`、`b`、`similarity`，不是 `i`、`j`、`score`。
-
-只报告 native 实际存在的描述符。渲染 PNG 时只解码文档指定字段，并验证字节以
-`89 50 4e 47 0d 0a 1a 0a` 开头；不得把 JSON envelope 保存成图片。
-
-## Health
-
-operation：`health`，无 body。
-
-## Parse
-
-operation：`parse`。
-
-```json
-{"input": "CCO", "format": "smiles", "sanitize": true}
-```
-
-Formats: `smiles`, `inchi`, `molblock`.
-
-Key response fields in `data`: `valid`, `canonical_smiles`, `formula`,
-`molecular_weight`, `exact_molecular_weight`, `inchi_key`, `atom_count`,
-`heavy_atom_count`, `bond_count`, `warnings`, `error`.
-
-## Descriptors
-
-operation：`descriptors`。
-
-```json
-{"smiles": "CCO", "descriptor_set": "basic", "sanitize": true}
-```
-
-`descriptor_set` currently supports `basic`. Descriptor keys include `Formula`,
-`MolWt`, `ExactMolWt`, `HeavyAtomMolWt`, `TPSA`, `MolLogP`, `NumHDonors`,
-`NumHAcceptors`, `NumRotatableBonds`, `RingCount`, `FractionCSP3`,
-`HeavyAtomCount`, `AtomCount`, and `BondCount`.
-
-## Batch Descriptors
-
-operation：`batch-descriptors`。
-
-```json
-{"smiles": ["CCO", "c1ccccc1"], "descriptor_set": "basic", "sanitize": true}
-```
-
-Limits: 1-500 SMILES.
-
-## Batch Parse Describe
-
-operation：`batch-parse-describe`。
-
-```json
-{
-  "molecules": [
-    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
-    {"id": "caffeine", "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C"}
-  ],
-  "descriptor_set": "basic",
-  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
-  "sanitize": true
-}
-```
-
-Limits: 1-500 molecules. Returns per-item `valid`, `canonical_smiles`, parse
-fields, `descriptors`, optional `fingerprint_metadata`, `on_bits`, `bit_count`,
-`warnings`, and `error`.
-
-## Render
-
-operation：`render`。
-
-```json
-{"smiles": "CCO", "image_format": "svg", "width": 450, "height": 320}
-```
-
-Image formats: `svg`, `png`. SVG returns text; PNG returns base64.
-Width/height range: 150-2000.
-
-## Fingerprint
-
-operation：`fingerprint`。
-
-```json
-{"smiles": "CCO", "radius": 2, "n_bits": 2048}
-```
-
-Morgan fingerprint parameters: `radius` 1-6, `n_bits` 128-8192.
-
-## Similarity
-
-operation：`similarity`。
-
-```json
-{"query_smiles": "CCO", "target_smiles": "CCCO", "radius": 2, "n_bits": 2048}
-```
-
-Returns Tanimoto similarity.
-
-## Similarity Matrix
-
-operation：`similarity-matrix`。
-
-```json
-{
-  "molecules": [
-    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
-    {"id": "ibuprofen", "smiles": "CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O"}
-  ],
-  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
-  "sanitize": true
-}
-```
-
-Returns `matrix` in input order and `ranked_pairs` sorted by descending
-Tanimoto similarity. Each ranked record is named, not index-based:
-
-```json
-{"a":"aspirin","b":"ibuprofen","similarity":0.195122}
-```
-
-Do not expect `i`, `j`, or `score` fields.
-
-## Substructure
-
-operation：`substructure`。
-
-```json
-{"query_smarts": "c1ccccc1", "target_smiles": ["c1ccccc1", "CCO"]}
-```
-
-Limits: SMARTS max length 5000; target list size 1-500.
+信封，因此以下业务响应在 wrapper 结果中位于 `result["native"]` 顶层；禁止读取
+`result["native"]["data"]`。这里只记录 operation schema，不授权直接 HTTP。
+
+一个请求只执行完成目标所需的最少调用。同时校验、规范化并计算基础描述符时使用一次
+`batch-parse-describe`，payload 使用 `molecules:[{id,smiles}]`，不得拆成 parse 和
+descriptors。多个分子的全对相似度使用一次 `similarity-matrix`；排名字段固定为
+`a`、`b`、`similarity`，不是 `i`、`j`、`score`。
+
+只报告 native 实际存在的描述符。渲染 PNG 时只解码文档指定字段，并验证字节以
+`89 50 4e 47 0d 0a 1a 0a` 开头；不得把 JSON envelope 保存成图片。
+
+## Health
+
+operation：`health`，无 body。
+
+## Parse
+
+operation：`parse`。
+
+```json
+{"input": "CCO", "format": "smiles", "sanitize": true}
+```
+
+Formats: `smiles`, `inchi`, `molblock`.
+
+Key response fields in `data`: `valid`, `canonical_smiles`, `formula`,
+`molecular_weight`, `exact_molecular_weight`, `inchi_key`, `atom_count`,
+`heavy_atom_count`, `bond_count`, `warnings`, `error`.
+
+## Descriptors
+
+operation：`descriptors`。
+
+```json
+{"smiles": "CCO", "descriptor_set": "basic", "sanitize": true}
+```
+
+`descriptor_set` currently supports `basic`. Descriptor keys include `Formula`,
+`MolWt`, `ExactMolWt`, `HeavyAtomMolWt`, `TPSA`, `MolLogP`, `NumHDonors`,
+`NumHAcceptors`, `NumRotatableBonds`, `RingCount`, `FractionCSP3`,
+`HeavyAtomCount`, `AtomCount`, and `BondCount`.
+
+## Batch Descriptors
+
+operation：`batch-descriptors`。
+
+```json
+{"smiles": ["CCO", "c1ccccc1"], "descriptor_set": "basic", "sanitize": true}
+```
+
+Limits: 1-500 SMILES.
+
+## Batch Parse Describe
+
+operation：`batch-parse-describe`。
+
+```json
+{
+  "molecules": [
+    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
+    {"id": "caffeine", "smiles": "Cn1cnc2c1c(=O)n(C)c(=O)n2C"}
+  ],
+  "descriptor_set": "basic",
+  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
+  "sanitize": true
+}
+```
+
+Limits: 1-500 molecules. Returns per-item `valid`, `canonical_smiles`, parse
+fields, `descriptors`, optional `fingerprint_metadata`, `on_bits`, `bit_count`,
+`warnings`, and `error`.
+
+## Render
+
+operation：`render`。
+
+```json
+{"smiles": "CCO", "image_format": "svg", "width": 450, "height": 320}
+```
+
+Image formats: `svg`, `png`. SVG returns text; PNG returns base64.
+Width/height range: 150-2000.
+
+## Fingerprint
+
+operation：`fingerprint`。
+
+```json
+{"smiles": "CCO", "radius": 2, "n_bits": 2048}
+```
+
+Morgan fingerprint parameters: `radius` 1-6, `n_bits` 128-8192.
+
+## Similarity
+
+operation：`similarity`。
+
+```json
+{"query_smiles": "CCO", "target_smiles": "CCCO", "radius": 2, "n_bits": 2048}
+```
+
+Returns Tanimoto similarity.
+
+## Similarity Matrix
+
+operation：`similarity-matrix`。
+
+```json
+{
+  "molecules": [
+    {"id": "aspirin", "smiles": "CC(=O)Oc1ccccc1C(=O)O"},
+    {"id": "ibuprofen", "smiles": "CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O"}
+  ],
+  "fingerprint": {"type": "morgan", "radius": 2, "n_bits": 2048},
+  "sanitize": true
+}
+```
+
+Returns `matrix` in input order and `ranked_pairs` sorted by descending
+Tanimoto similarity. Each ranked record is named, not index-based:
+
+```json
+{"a":"aspirin","b":"ibuprofen","similarity":0.195122}
+```
+
+Do not expect `i`, `j`, or `score` fields.
+
+## Substructure
+
+operation：`substructure`。
+
+```json
+{"query_smarts": "c1ccccc1", "target_smiles": ["c1ccccc1", "CCO"]}
+```
+
+Limits: SMARTS max length 5000; target list size 1-500.