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Agent skill

Molecular Format Conversion

by InternScience in InternScience/scp

Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications.

MITAuto-check passedResearch & Science

Install Molecular Format Conversion

skills CLI
$ npx skills add InternScience/scp --skill molecular-format-conversion -a claude-code

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

GitHub CLI
$ gh skill install InternScience/scp molecular-format-conversion --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/molecular-format-conversion .claude/skills/molecular-format-conversion && 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
molecular-format-conversion
GitHub stars
169
Used in
1 other repo
Token cost
~1.3k tokens
SKILL.md length
380 words
Files
1
Skills in repo
73
Repo updated
First seen
Licence
MIT

At a glance

Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications.

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

What it does

Molecular Format Conversion is an agent skill from InternScience/scp. Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications.

Its SKILL.md is about 1.3k 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

  • “/molecular-format-conversion”

Requirements

  • Python 3

Workflow steps

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

  1. MCP Server Definition
  2. Molecular Format Conversion 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

Molecular Format Conversion loads about 1.3k tokens when it runs. Until then it costs about 36 tokens; SKILL.md has 380 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~36
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k

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). 380 words, ~1,331 tokens.

Download SKILL.mdSave it as .claude/skills/molecular-format-conversion/SKILL.md (or your agent's skills folder).
name
molecular-format-conversion
description
Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications.
license
MIT license
metadata.skill-author
PJLab

Molecular Format Conversion

Usage

1. MCP Server Definition

Use the same ChemicalToolsClient class as defined in the molecular-properties-calculation skill.

2. Molecular Format Conversion Workflow

This workflow converts molecules between different chemical formats (SMILES, InChI, SELFIES) for database searching, machine learning, and cheminformatics applications.

Workflow Steps:

  1. SMILES to InChI - Convert SMILES to International Chemical Identifier
  2. InChI to SMILES - Convert InChI back to SMILES
  3. SMILES to SELFIES - Convert to string-based molecular representation

Implementation:

python
## Initialize client
HEADERS = {"SCP-HUB-API-KEY": "<your-api-key>"}

client = ChemicalToolsClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/31/SciToolAgent-Chem",
    HEADERS
)

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

print("=== Molecular Format Conversion ===\n")

## Test molecules
smiles = "CCO"  # Ethanol
inchi = "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"

## Step 1: SMILES to InChI
print("Step 1: SMILES to InChI")
result = await client.client.call_tool(
    "SMILESToInChI",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"SMILES: {smiles}")
print(f"{result_data}\n")

## Step 2: InChI to SMILES
print("Step 2: InChI to SMILES")
result = await client.client.call_tool(
    "InChIToSMILES",
    arguments={"inchi": inchi}
)
result_data = client.parse_result(result)
print(f"InChI: {inchi}")
print(f"{result_data}\n")

## Step 3: SMILES to SELFIES
print("Step 3: SMILES to SELFIES")
result = await client.client.call_tool(
    "SMILEStoSELFIES",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"SMILES: {smiles}")
print(f"{result_data}\n")

## Step 4: SELFIES to SMILES
print("Step 4: SELFIES to SMILES")
selfies = "[C][C][O]"
result = await client.client.call_tool(
    "SELFIEStoSMILES",
    arguments={"selfies": selfies}
)
result_data = client.parse_result(result)
print(f"SELFIES: {selfies}")
print(f"{result_data}\n")

await client.disconnect()
Tool Descriptions

SciToolAgent-Chem Server:

  • SMILESToInChI: Convert SMILES to InChI

    • Args: smiles (str)
    • Returns: InChI string

  • InChIToSMILES: Convert InChI to SMILES

    • Args: inchi (str)
    • Returns: SMILES string

  • SMILEStoSELFIES: Convert SMILES to SELFIES

    • Args: smiles (str)
    • Returns: SELFIES string

  • SELFIEStoSMILES: Convert SELFIES to SMILES

    • Args: selfies (str)
    • Returns: SMILES string

  • InChIToInChIKey: Convert InChI to InChIKey

    • Args: inchi (str)
    • Returns: InChIKey (27-character hash)

  • InChIKeyToInChI: Convert InChIKey to InChI

    • Args: inchikey (str)
    • Returns: InChI string
Input/Output

Input:

  • SMILES: Simplified Molecular Input Line Entry System (e.g., "CCO")
  • InChI: IUPAC International Chemical Identifier (e.g., "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3")
  • InChIKey: Hashed InChI (27 characters, e.g., "LFQSCWFLJHTTHZ-UHFFFAOYSA-N")
  • SELFIES: Self-Referencing Embedded Strings (e.g., "[C][C][O]")

Output:

  • Converted molecular representation in target format
Format Comparison
FormatCanonicalHuman-ReadableDatabase-FriendlyML-Friendly
SMILESPartialHighMediumMedium
InChIYesLowHighLow
InChIKeyYesNoVery HighNo
SELFIESYesLowLowVery High
Use Cases
  • SMILES: Standard format for most cheminformatics tools
  • InChI: Canonical representation for database searching
  • InChIKey: Fast database lookups and duplicate detection
  • SELFIES: Machine learning models (guarantees valid molecules)
Show full SKILL.md (139 more words)Show less
Format Details

SMILES (Simplified Molecular Input Line Entry System)

  • Pros: Human-readable, widely supported
  • Cons: Not canonical (multiple SMILES for same molecule)
  • Example: "CCO", "c1ccccc1", "CC(=O)O"

InChI (International Chemical Identifier)

  • Pros: Canonical, includes stereochemistry and isotopes
  • Cons: Long, not human-readable
  • Example: "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"

InChIKey

  • Pros: Fixed-length hash, fast comparison
  • Cons: Cannot reconstruct molecule from key
  • Example: "LFQSCWFLJHTTHZ-UHFFFAOYSA-N"
  • Structure: 14 characters (connectivity) + separator + 8 characters (stereo) + separator + version

SELFIES (Self-Referencing Embedded Strings)

  • Pros: Always generates valid molecules, ideal for ML
  • Cons: Less human-readable, newer format
  • Example: "[C][C][O]"
  • Used in: Generative models, molecular optimization
Additional Conversion Tools
  • ConvertSmilesToInchi: Alternative SMILES to InChI converter
  • GenerateMolKeyFromSmiles: Generate molecular key
  • InChIKeyToMOL: Convert InChIKey to MOL file
  • IsValidInChIKey: Validate InChIKey format
Error Handling

Some conversions may fail for:

  • Invalid input formats
  • Unsupported chemical features
  • Very large or complex molecules

Always check for errors in the returned data.

© 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/molecular-format-conversion 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

Molecular Format Conversion 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.

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Categories

Questions about Molecular Format Conversion

What does Molecular Format Conversion do?

Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications. Molecular Format Conversion is an agent skill from InternScience/scp. Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications.

When should I use Molecular Format Conversion?

Molecular Format Conversion fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Molecular Format Conversion in Claude Code?

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

How do I install Molecular Format Conversion in Codex?

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

Can I use Molecular Format Conversion 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 molecular-format-conversion -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/molecular-format-conversion, .gemini/skills/molecular-format-conversion, .github/skills/molecular-format-conversion and .opencode/skills/molecular-format-conversion in your project.

What does Molecular Format Conversion need to run?

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

Does Molecular Format Conversion 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 Molecular Format Conversion 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 Molecular Format Conversion use?

Molecular Format Conversion 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 Molecular Format Conversion use?

About 1.3k tokens (SKILL.md is roughly 5.3k 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 Molecular Format Conversion?

Skills that share tags, products or a category with Molecular Format Conversion: 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 Molecular Format Conversion?

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.