SmilesCanonicalization (canonicalize_smiles)

Example

Input:

smiles: 'C(O)C'
isomeric: True
kekulization: True
keep_atom_map: False

Text Input (used for the run_text function in the Python calling mode):

smiles: 'C(O)C'

Output:

'CCO'

Usage

The tool supports both MCP mode and Python calling mode.

MCP Mode

Configure your MCP client following its instructions with something like:

{
    "command": "/ABSTRACT/PATH/TO/uv",  // Use `which uv` to get its path
    "args": ["--directory", "/ABSTRACT/PATH/TO/ChemMCP", "run", "--tools", "SmilesCanonicalization"],
    "toolCallTimeoutMillis": 300000,
    "env": {}
}

Python Calling Mode

import os
from chemmcp.tools import SmilesCanonicalization

# Initialize the tool
tool = SmilesCanonicalization()

# The tool has two alternative ways to run:
# 1. Run with separate input domains (recommended)
output = tool.run_code(
    smiles='C(O)C'
    isomeric=True
    kekulization=True
    keep_atom_map=False
)
# 2. Run with text-only input
output = tool.run_text(
    smiles='C(O)C'
)

Each tool in ChemMCP has two ways to run:

• run_code (recommended): The inputs contain one or more domains, each of which can be a str, an int, a float, etc.
• run_text: The inputs are a single string in a specific format. The tool will parse the string to extract the input domains. This is useful in scenarios where an agent framework calls tools only with text input. The output is the same in both cases.

For the input and output domains, please refer to the tool’s signature.

Tool Signature

Input

Used in the MCP mode, as well as the run_code function in the Python calling mode.

Text Input

Used in the run_text function in the Python calling mode.

Output

The output is the same in both input cases.

Envs

No required environment variables for this tool.

Implementation Details

• Implementation Description: Uses a customized version of RDKit’s SMILES canonicalization functionality to convert a SMILES string into its canonical form.
• Open-source dependencies (code source or required libraries):
  • LlaSMol (MIT)
• Hosted services and software (required for running the tool): None