# RDKit 3D Molecular Viewer

> Use this tool when you need to visualize and analyze molecular structures in 3D, generating interactive models from SMILES or InChI inputs. It solves problems in cheminformatics and molecular modeling, providing features like geometry optimization, molecular measurements, and file exports. The tool accepts SMILES or InChI strings as input and outputs interactive HTML viewers with various rendering styles and export options.

Canonical page: https://skillsregistry.net/skills/milsonson-rdkit-3d-molecular-viewer  
JSON: https://api.skillsregistry.net/v1/skills/milsonson-rdkit-3d-molecular-viewer

## Description

Generates 3D molecular structures from SMILES or InChI inputs and provides interactive HTML viewers for visualization. Leverages RDKit's conformer generation and geometry optimization to create 3D molecular models, then generates rich HTML viewers using 3Dmol.js that support multiple rendering styles (ball-and-stick, stick, sphere), VDW surface visualization, molecular measurements (distances, angles, dihedrals), and file exports (MOL, SDF, PNG). Supports SSE, streamable HTTP, and stdio transports with Docker and Google Cloud Run deployment options.

## Trust

- **Trust score (0–1):** 0.95
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** cloud-infra
- **Updated:** 2026-09-28

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/milsonson-rdkit-3d-molecular-viewer)
- **Repository:** <https://github.com/milsonson/rdkit-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "milsonson-rdkit-3d-molecular-viewer"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/milsonson-rdkit-3d-molecular-viewer` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/milsonson-rdkit-3d-molecular-viewer/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt