Molecule 2D Tools

Configuration File: molecule_2d_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the molecule_2d_tools.json configuration file.

Available Tools

visualize_molecule_2d (Type: Molecule2DTool)

Visualize 2D molecular structures using RDKit. Supports SMILES, InChI, molecule names, and variou…

visualize_molecule_2d tool specification

Tool Information:

  • Name: visualize_molecule_2d

  • Type: Molecule2DTool

  • Description: Visualize 2D molecular structures using RDKit. Supports SMILES, InChI, molecule names, and various output formats including PNG, SVG, and interactive HTML.

Parameters:

  • smiles (string) (required) SMILES string representation of the molecule

  • inchi (string) (required) InChI string representation of the molecule

  • molecule_name (string) (required) Common name of the molecule (will be resolved to SMILES via PubChem)

  • width (integer) (optional) Width of the visualization in pixels

  • height (integer) (optional) Height of the visualization in pixels

  • output_format (string) (optional) Output format

  • show_atom_numbers (boolean) (optional) Whether to show atom numbers

  • show_bond_numbers (boolean) (optional) Whether to show bond numbers

  • include_stereo (boolean) (optional) Whether to include stereochemistry information

Example Usage:

query = {
    "name": "visualize_molecule_2d",
    "arguments": {
        "smiles": "example_value",
        "inchi": "example_value",
        "molecule_name": "example_value"
    }
}
result = tu.run(query)