---
name: compound-name-retrieval-5c3e2d66069f
description: Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.
license: MIT license
metadata:
    skill-author: PJLab
---

# Compound Name to SMILES Retrieval

## Usage

### 1. MCP Server Definition

```python
import asyncio
import json
from contextlib import AsyncExitStack
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class DrugSDAClient:
    """DrugSDA-Tool MCP Client"""

    def __init__(self, server_url: str, api_key: str):
        self.server_url = server_url
        self.api_key = api_key
        self.session = None

    async def connect(self):
        """Establish connection and initialize session"""
        try:
            self.transport = streamablehttp_client(
                url=self.server_url,
                headers={"SCP-HUB-API-KEY": self.api_key}
            )
            self._stack = AsyncExitStack()
            await self._stack.__aenter__()
            self.read, self.write, self.get_session_id = await self._stack.enter_async_context(self.transport)
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self._stack.enter_async_context(self.session_ctx)
            await self.session.initialize()
            return True
        except Exception as e:
            print(f"✗ connect failure: {e}")
            return False

    async def disconnect(self):
        """Disconnect from server"""
        try:
            if hasattr(self, '_stack'):
                await self._stack.aclose()
            print("✓ already disconnect")
        except Exception as e:
            print(f"✗ disconnect error: {e}")
    def parse_result(self, result):
        """Parse MCP tool call result"""
        try:
            if hasattr(result, 'content') and result.content:
                content = result.content[0]
                if hasattr(content, 'text'):
                    return json.loads(content.text)
            return str(result)
        except Exception as e:
            return {"error": f"parse error: {e}", "raw": str(result)}
```

### 2. Compound Name Retrieval Workflow

This workflow retrieves SMILES strings from PubChem using common chemical names.

**Workflow Steps:**

1. **Input Compound Names** - Provide list of chemical names
2. **Query PubChem** - Search for each compound in PubChem database
3. **Extract SMILES** - Retrieve canonical SMILES representations

**Implementation:**

```python
## Initialize client
client = DrugSDAClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool",
    "<your-api-key>"
)

if not await client.connect():
    print("connection failed")
    exit()

## Input: List of compound names
compound_names = ["aspirin", "caffeine", "ibuprofen"]

## Retrieve SMILES from compound names
result = await client.session.call_tool(
    "retrieve_smiles_from_name",
    arguments={
        "compound_names": compound_names
    }
)

result_data = client.parse_result(result)
smiles_list = result_data["retrieve_smiles"]

## Display results
print("Retrieved SMILES strings:")
for item in smiles_list:
    print(f"Name: {item['compound_name']}")
    print(f"SMILES: {item['smiles']}\n")

await client.disconnect()
```

### Tool Descriptions

**DrugSDA-Tool Server:**
- `retrieve_smiles_from_name`: Retrieve SMILES from PubChem by compound name
  - Args:
    - `compound_names` (list): List of chemical compound names
  - Returns:
    - `retrieve_smiles` (list): List of name-SMILES pairs
      - `compound_name` (str): Input compound name
      - `smiles` (str): Canonical SMILES string

### Input/Output

**Input:**
- `compound_names`: List of chemical names (common names, IUPAC names, or synonyms)

**Output:**
- List of results:
  - `compound_name`: Query compound name
  - `smiles`: Canonical SMILES representation

### Use Cases

- Convert chemical names to machine-readable formats
- Batch retrieve molecular structures
- Validate compound names against PubChem
- Prepare datasets for computational chemistry
- Integration with molecular analysis pipelines

### Performance Notes

- **Data source**: PubChem public database
- **Name matching**: Supports common names, IUPAC names, and synonyms
- **Execution time**: ~1-2 seconds per compound
- **Availability**: Requires internet connection to PubChem API


---
Source attribution: SpectrAI-Initiative
Original project: https://github.com/SpectrAI-Initiative/InnoClaw
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: SpectrAI-Initiative
Original project: https://github.com/SpectrAI-Initiative/InnoClaw
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Development & Engineering, Education & Research
Roles: Data Scientist, ML / AI Engineer, Researcher
Specialties: API
Tools: Pubchem
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: f818f823404f91205aa3f960b6c268382c0a35893bb1c7c12c0ff06ef8a5fcc5