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Agent skill

Compound Name Retrieval

by InternScience in InternScience/scp

Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.

MITAuto-check passedResearch & Science

Install Compound Name Retrieval

skills CLI
$ npx skills add InternScience/scp --skill compound-name-retrieval -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install InternScience/scp compound-name-retrieval --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/compound-name-retrieval .claude/skills/compound-name-retrieval && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
compound-name-retrieval
GitHub stars
169
Used in
1 other repo
Token cost
~1.1k tokens
SKILL.md length
173 words
Files
1
Skills in repo
73
Repo updated
First seen
Licence
MIT

At a glance

Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.

  • Works in 2 steps: MCP Server Definition → Compound Name Retrieval Workflow
  • Tasks that involve Drug discovery and cheminformatics
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Compound Name Retrieval is an agent skill from InternScience/scp. Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Drug discovery and cheminformatics. The licence is MIT.

When your agent uses it

  • Tasks that involve Drug discovery and cheminformatics

Example prompts

  • “/compound-name-retrieval”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. MCP Server Definition
  2. Compound Name Retrieval Workflow

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are python).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Compound Name Retrieval loads about 1.1k tokens when it runs. Until then it costs about 37 tokens; SKILL.md has 173 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~37
When it runs · the whole SKILL.md, loaded when a task matches
~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 173 words, ~1,079 tokens.

Download SKILL.mdSave it as .claude/skills/compound-name-retrieval/SKILL.md (or your agent's skills folder).
name
compound-name-retrieval
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 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.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            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 self.session:
                await self.session_ctx.__aexit__(None, None, None)
            if hasattr(self, 'transport'):
                await self.transport.__aexit__(None, None, None)
        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

© InternScience, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/compound-name-retrieval of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Compound Name Retrieval next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Compound Name Retrieval compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Compound Name Retrieval this skillInternScience/scp1691 repos~1.1kAutomated safety check: PassMIT
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Drug DiscoveryTommy-yw/RunbookHermes5461 repos~2.3kAutomated safety check: PassMIT
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills48k1 repos~3kAutomated safety check: NotesMIT
Biomedical Analysis Dispatchxjtulyc/MedgeClaw6171 repos~2kAutomated safety check: PassNone
Edu Chem Reactionwy51ai/edulab1.4k—~1.2kAutomated safety check: PassApache-2.0

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Categories

Questions about Compound Name Retrieval

What does Compound Name Retrieval do?

Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names. Compound Name Retrieval is an agent skill from InternScience/scp. Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.

When should I use Compound Name Retrieval?

Compound Name Retrieval fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Compound Name Retrieval in Claude Code?

Run `npx skills add InternScience/scp --skill compound-name-retrieval -a claude-code`. Or copy the skill folder (skills/compound-name-retrieval in InternScience/scp) into .claude/skills/compound-name-retrieval in your project. Claude Code loads it when a task matches its description.

How do I install Compound Name Retrieval in Codex?

Run `npx skills add InternScience/scp --skill compound-name-retrieval -a codex`. Or copy the skill folder (skills/compound-name-retrieval in InternScience/scp) into .agents/skills/compound-name-retrieval in your project. Codex loads it when a task matches its description.

Can I use Compound Name Retrieval in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add InternScience/scp --skill compound-name-retrieval -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/compound-name-retrieval, .gemini/skills/compound-name-retrieval, .github/skills/compound-name-retrieval and .opencode/skills/compound-name-retrieval in your project.

What does Compound Name Retrieval need to run?

SKILL.md names no scripts, command-line tools or credentials: Compound Name Retrieval is instructions for the agent only. Our summary lists: Python 3.

Does Compound Name Retrieval access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Compound Name Retrieval safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Compound Name Retrieval use?

Compound Name Retrieval is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Compound Name Retrieval use?

About 1.1k tokens (SKILL.md is roughly 4.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Compound Name Retrieval?

Skills that share tags, products or a category with Compound Name Retrieval: Molecode (AtomFlow-AI/MoleCode, 305 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Compound Name Retrieval?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.