Cortexa research tool·structure·visualization_molecule_3d

Visualize Molecule 3d

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

Livelast probed 2026-04-30 23:07Z· 151msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 151ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "anyOf": [
    {
      "required": [
        "smiles"
      ]
    },
    {
      "required": [
        "mol_content"
      ]
    },
    {
      "required": [
        "sdf_content"
      ]
    }
  ],
  "properties": {
    "color_scheme": {
      "default": "default",
      "description": "Color scheme for the molecule",
      "enum": [
        "default",
        "spectrum",
        "rainbow",
        "ssPyMOL",
        "ssJmol",
        "Jmol",
        "amino",
        "shapely",
        "nucleic",
        "chain"
      ],
      "type": "string"
    },
    "conformer_count": {
      "default": 1,
      "description": "Number of conformers to generate",
      "type": "integer"
    },
    "generate_conformers": {
      "default": true,
      "description": "Whether to generate multiple conformers",
      "type": "boolean"
    },
    "height": {
      "default": 600,
      "description": "Height of the visualization in pixels",
      "type": "integer"
    },
    "mol_content": {
      "description": "MOL file content as string",
      "type": "string"
    },
    "sdf_content": {
      "description": "SDF file content as string",
      "type": "string"
    },
    "show_hydrogens": {
      "default": true,
      "description": "Whether to show hydrogen atoms",
      "type": "boolean"
    },
    "show_surface": {
      "default": false,
      "description": "Whether to show molecular surface",
      "type": "boolean"
    },
    "smiles": {
      "description": "SMILES string representation of the molecule",
      "type": "string"
    },
    "style": {
      "default": "stick",
      "description": "Visualization style",
      "enum": [
        "stick",
        "sphere",
        "cartoon",
        "line",
        "spacefill"
      ],
      "type": "string"
    },
    "width": {
      "default": 800,
      "description": "Width of the visualization in pixels",
      "type": "integer"
    }
  },
  "type": "object"
}

Examples (1)

Default Visualize Molecule 3d call

public-safeinput

{
  "conformer_count": 1,
  "generate_conformers": false,
  "height": 1,
  "show_hydrogens": false,
  "show_surface": false,
  "smiles": "CC(=O)Oc1ccccc1C(=O)O",
  "width": 1
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_visualize_molecule_3d
Tool name: visualize_molecule_3d
Added: 2026-04-30 22:47Z
Tags: tooluniverse

Schema

JSON Schema the agent (or your API call) must match.

{ "anyOf": [ { "required": [ "smiles" ] }, { "required": [ "mol_content" ] }, { "required": [ "sdf_content" ] } ], "properties": { "color_scheme": { "default": "default", "description": "Color scheme for the molecule", "enum": [ "default", "spectrum", "rainbow", "ssPyMOL", "ssJmol", "Jmol", "amino", "shapely", "nucleic", "chain" ], "type": "string" }, "conformer_count": { "default": 1, "description": "Number of conformers to generate", "type": "integer" }, "generate_conformers": { "default": true, "description": "Whether to generate multiple conformers", "type": "boolean" }, "height": { "default": 600, "description": "Height of the visualization in pixels", "type": "integer" }, "mol_content": { "description": "MOL file content as string", "type": "string" }, "sdf_content": { "description": "SDF file content as string", "type": "string" }, "show_hydrogens": { "default": true, "description": "Whether to show hydrogen atoms", "type": "boolean" }, "show_surface": { "default": false, "description": "Whether to show molecular surface", "type": "boolean" }, "smiles": { "description": "SMILES string representation of the molecule", "type": "string" }, "style": { "default": "stick", "description": "Visualization style", "enum": [ "stick", "sphere", "cartoon", "line", "spacefill" ], "type": "string" }, "width": { "default": 800, "description": "Width of the visualization in pixels", "type": "integer" } }, "type": "object" }

Examples (1)

Default Visualize Molecule 3d call

public-safeinput

{
  "conformer_count": 1,
  "generate_conformers": false,
  "height": 1,
  "show_hydrogens": false,
  "show_surface": false,
  "smiles": "CC(=O)Oc1ccccc1C(=O)O",
  "width": 1
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.