Molecule 3D Tools

Configuration File: molecule_3d_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the molecule_3d_tools.json configuration file.

Available Tools

visualize_molecule_3d (Type: Molecule3DTool)

Visualize 3D molecular structures using RDKit and py3Dmol. Supports SMILES, MOL files, SDF conten…

visualize_molecule_3d tool specification

Tool Information:

  • Name: visualize_molecule_3d

  • Type: Molecule3DTool

  • Description: Visualize 3D molecular structures using RDKit and py3Dmol. Supports SMILES, MOL files, SDF content, and various visualization styles with interactive 3D viewing capabilities.

Parameters:

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

  • mol_content (string) (required) MOL file content as string

  • sdf_content (string) (required) SDF file content as string

  • style (string) (optional) Visualization style

  • color_scheme (string) (optional) Color scheme for the molecule

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

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

  • show_hydrogens (boolean) (optional) Whether to show hydrogen atoms

  • show_surface (boolean) (optional) Whether to show molecular surface

  • generate_conformers (boolean) (optional) Whether to generate multiple conformers

  • conformer_count (integer) (optional) Number of conformers to generate

Example Usage:

query = {
    "name": "visualize_molecule_3d",
    "arguments": {
        "smiles": "example_value",
        "mol_content": "example_value",
        "sdf_content": "example_value"
    }
}
result = tu.run(query)