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Molecular Format Conversion

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molecular-format-conversion

Molecular Format Conversion is an Agent Skill for documents published in the SpectrAI-Initiative/InnoClaw repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

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

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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:

## 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)

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.