pubchem-database

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PubChem Database

PubChem数据库

Prerequisites

前提条件

uv
: Read the
```
uv
```
skill and follow its Setup instructions to ensure
```
uv
```
is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file recording the notification text and timestamp.

uv
：阅读
```
uv
```
技能文档并按照其设置说明操作，确保
```
uv
```
已安装并添加至系统PATH。
用户通知：若当前技能目录中不存在LICENSE_NOTIFICATION.txt文件，则需：(1) 显著提醒用户查看https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines和https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest上的条款；(2) 创建该文件，记录通知内容及时间戳。

Quick Start

快速开始

PubChem queries are executed via a robust Python wrapper script to respect terms-of-service and handle complex JSON parsing. This script allows safe multi-agent use of APIs.

Example: Resolve a chemical name to its Compound ID (CID)

bash

uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.json

PubChem查询通过一个健壮的Python包装器脚本执行，以遵守服务条款并处理复杂的JSON解析。该脚本支持多Agent安全调用API。

示例：将化学名称解析为化合物ID（CID）

bash

uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.json

Core Rules

核心规则

Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
Read the generated JSON output file, and process it with jq or code.
Verify Facts: ALWAYS verify information retrieved from memory with a database query if the user asks for a specific fact that can be checked in PubChem. Do not rely solely on internal knowledge.
Notification: If this skill is used, ensure this is mentioned in the output.

使用包装器：务必通过提供的辅助脚本查询数据库，而非直接访问数据库。脚本会自动优雅地执行所需的速率限制。
读取生成的JSON输出文件，可使用jq或代码进行处理。
验证事实：若用户询问可在PubChem中核实的具体事实，务必通过数据库查询验证从内存中获取的信息，切勿仅依赖内部知识。
通知说明：若使用本技能，需在输出中提及这一点。

Core Capabilities

核心功能

1. Compound Resolution (Name or InChI to Identifiers) Convert chemical/trade names or InChI strings into PubChem CIDs, SMILES, and InChIKeys.

bash

uv run scripts/pubchem_api.py resolve --name "ibuprofen" --output result.json

1. 化合物解析（名称或InChI转换为标识符） 将化学/商品名称或InChI字符串转换为PubChem CID、SMILES和InChIKeys。

bash

uv run scripts/pubchem_api.py resolve --name "ibuprofen" --output result.json

OR

或

uv run scripts/pubchem_api.py resolve --inchi "InChI=1S/C3/c1-3-2/i1+1" --output result.json


**2. Physical & Chemical Property Retrieval** Fetch computed properties (e.g.,
MolecularWeight, XLogP, TPSA).

```bash
uv run scripts/pubchem_api.py properties --cid 2244 --output result.json

3. Synonyms and Trade Names Find alternative names and brand names.

bash

uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.json

uv run scripts/pubchem_api.py resolve --inchi "InChI=1S/C3/c1-3-2/i1+1" --output result.json


**2. 物理与化学属性检索** 获取计算属性（如分子量、XLogP、TPSA）。

```bash
uv run scripts/pubchem_api.py properties --cid 2244 --output result.json

3. 同义词与商品名称 查找替代名称和品牌名称。

bash

uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.json

Advanced Context

进阶内容

4. Safety and Hazard Information (GHS) Retrieve Global Harmonized System hazard statements and handling precautions (uses PUG-View).

bash

uv run scripts/pubchem_api.py safety --cid 2244 --output result.json

5. Drug and Medication Information Fetch FDA pharmacology data, mechanism of action, and therapeutic uses (uses PUG-View).

bash

uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json

6. Custom Heading (PUG-View) Retrieve any specific heading from the PUG-View system (e.g., 'Geometry', 'Crystal Structures').

bash

uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json

7. Image Generation Retrieve 2D chemical structure images. The script returns a Markdown-formatted image link.

bash

uv run scripts/pubchem_api.py image --cid 2244 --output result.json

4. 安全与危害信息（GHS） 获取全球化学品统一分类和标签制度（GHS）的危害说明及操作注意事项（使用PUG-View）。

bash

uv run scripts/pubchem_api.py safety --cid 2244 --output result.json

5. 药物与医疗信息 获取FDA药理学数据、作用机制及治疗用途（使用PUG-View）。

bash

uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json

6. 自定义标题查询（PUG-View） 从PUG-View系统中检索特定标题下的内容（如“几何结构”、“晶体结构”）。

bash

uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json

7. 图像生成 获取二维化学结构图像。脚本会返回Markdown格式的图片链接。

bash

uv run scripts/pubchem_api.py image --cid 2244 --output result.json

Complex Search & Biology

复杂搜索与生物学相关功能

8. Structure-Based Searching (Similarity & Substructure) Find molecules similar to a SMILES string or containing a specific substructure.

bash

uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.json

and

bash

uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json

9. BioAssay & Target Interactions Identify genes or proteins a chemical interacts with.

bash

uv run scripts/pubchem_api.py assays --cid 2244 --output result.json

8. 基于结构的搜索（相似性与子结构） 查找与指定SMILES字符串相似的分子，或包含特定子结构的分子。

bash

uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.json

以及

bash

uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json

9. 生物测定与靶点相互作用 识别与化学品相互作用的基因或蛋白质。

bash

uv run scripts/pubchem_api.py assays --cid 2244 --output result.json

Advanced Usage & Workflows

进阶用法与工作流

10. Cross-references (Xrefs) Fetch identifiers cross-referenced with a CID (e.g., PatentID, PubMedID).

bash

uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json

11. Property Range Search Find CIDs within a specific property range. Supported features include:

molecular_weight

heavy_atom_count

xlogp

tpsa

h_bond_donor_count

h_bond_acceptor_count

rotatable_bond_count

exact_mass

monoisotopic_mass

, and

complexity

bash

uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json

12. Custom PUG-REST Query Execute a raw path against the PUG-REST API.

bash

uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.json

10. 交叉引用（Xrefs） 获取与CID关联的其他标识符（如专利ID、PubMedID）。

bash

uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json

11. 属性范围搜索 查找属性值在特定范围内的CID。支持的属性包括：

molecular_weight

、

heavy_atom_count

、

xlogp

、

tpsa

、

h_bond_donor_count

、

h_bond_acceptor_count

、

rotatable_bond_count

、

exact_mass

、

monoisotopic_mass

和

complexity

。

bash

uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json

12. 自定义PUG-REST查询 针对PUG-REST API执行原始路径查询。

bash

uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.json

Fallback Search Strategies

备选搜索策略

If direct resolution by name or formula fails (e.g., for complex compounds or specific ions):

Search for parent/neutral molecule: If searching for an ion or salt, try searching for the neutral parent compound.
Deconstruct complex formulas: If a complex formula returns no results, try searching for major components or ligands.
Use substructure or similarity search: If you have a SMILES string or can generate one for a component, use it to find related compounds.

若直接通过名称或分子式解析失败（如针对复杂化合物或特定离子）：

搜索母体/中性分子：若搜索离子或盐类，尝试搜索其中性母体化合物。
拆解复杂分子式：若复杂分子式无结果，尝试搜索主要成分或配体。
使用子结构或相似性搜索：若拥有SMILES字符串或可为某成分生成SMILES字符串，使用其查找相关化合物。

Complex Queries and Multi-Step Tasks

复杂查询与多步骤任务

Custom/Complex Queries: For more details, read references/endpoints.md to construct raw PUG-REST URLs.
Multi-Step Tasks: For complex tasks like drug discovery pipelines, follow the checklists in references/workflows.md.

自定义/复杂查询：如需更多细节，请阅读references/endpoints.md以构建原始PUG-REST URL。
多步骤任务：针对药物发现流程等复杂任务，请遵循references/workflows.md中的检查清单。