deepseekplugins

DeepSeek Harness plugin

dsh-molecule-viewer

Interactive 3D molecule viewer for DeepSeek Harness: view PDB/SDF/MOL2/MOL structures with 3Dmol.js

Tools & Capabilities
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Source facts

Repository
PandaAIDD/dsh-molecule-viewer
Latest update
Aug 17, 2026
Category
Tools & Capabilities
GitHub stars
1
Format
plugin
Catalog evidence
Upstream dsh.bundle evidence
Evidence path
package.json#dsh.bundle
Checked against
0.1.0-rc.8
Upstream check date
2026-08-20

This evidence comes from the upstream catalog. This site has not installed, run, or security-reviewed the plugin.

Install

Start with a prompt that asks an agent to review the GitHub repository and source. Switch to the command if you want to install it yourself.

Copy this prompt into DSH, Codex, or another agent and ask it to review the GitHub repository and source first.

Do not install or run any commands yet. Read this plugin's GitHub repository, README, and relevant source code. Then answer the questions below clearly and directly so I can decide whether it fits my needs:

1. What is this plugin, and what problem does it solve?
2. Who is it for, and what are its typical use cases?
3. How is it used after installation? Include one minimal example.
4. What known limitations or privacy, security, compatibility, or maintenance risks does it have?
5. Give a clear recommendation: recommend, conditionally recommend, or do not recommend, with reasons.

Distinguish statements documented by the repository, inferences from source code, and unknowns. If evidence is insufficient, say so explicitly. Do not guess or simply repeat the README.

GitHub: https://github.com/PandaAIDD/dsh-molecule-viewer
Plugin: dsh-molecule-viewer
Author: PandaAIDD

Check the source files

Read the README and other files from this plugin directory before installing.

File explorer4 files
README.en.mdSource · read only
README language

dsh-molecule-viewer

English | 简体中文

An interactive 3D molecule viewer plugin for DSH (DeepSeek Harness): pass a molecular file path or PDB/SDF/MOL2/MOL data, and an interactive 3D viewer (3Dmol.js — rotate/zoom, style switching, coloring) renders right in the conversation.

![2AFW protein rendered in cartoon style](assets/fig1.png)

Features

  • 🧬 Four formats: PDB (proteins/large molecules), SDF, MOL2, MOL
  • 📁 Path-first: pass the file path and the tool reads it server-side — Windows (D:\dir\x.pdb), WSL (/mnt/d/dir/x.pdb), and ~/ spellings are recognized and cross-converted automatically
  • 🖱️ Interactive viewer: rotate, zoom, and switch cartoon / stick / line / sphere styles, background color, and molecule coloring live
  • 🔄 Survives restarts: the viewer payload persists with the tool/result event and re-renders when history is reloaded (official slots only — installs on a stock harness)
  • ⚡ Lightweight parsing: the host side only counts atoms and validates; real parsing and rendering happen in the browser via 3Dmol.js
  • 📦 3Dmol.js bundled locally: vendor/3Dmol-min.cjs (2.4.2) is compiled into the client bundle at build time — no CDN requests at runtime, fast loads, works offline, immune to tracking-prevention blocks

Install

dsh plugin --profile web add git+https://github.com/PandaAIDD/dsh-molecule-viewer.git

Restart to activate:

dsh --profile web

After installation the view_molecule tool is available automatically; the model calls it based on its description.

> dsh plugin is a pnpm forwarder: clone the repo → install into the profile's node_modules → detect the dsh.bundle.patch declaration → add it to dsh.profile.bundles automatically. peerDependencies resolve from the profile's healed node_modules.

Usage

Just describe what you want in the conversation and the model calls the tool:

> "Visualize this molecule: D:\project\Dock\data\3IPQ.pdb"

Or be explicit:

> "Use the view_molecule tool to view this SDF data: ..."

Supported formats

FormatExtensionsNotes
PDB.pdb .entProteins/large molecules (ATOM/HETATM records)
SDF.sdf .sdMulti-molecule structures (V2000/V3000)
MOL2.mol2TRIPOS format
MOL.molMDL MOL (V2000/V3000)

> SMILES is not supported yet — a format with 3D coordinates is required. > > Molecular content above 2 MB is not inlined into the session log; the viewer slot shows a summary card instead (atom count and format remain visible).

Tool parameters

| Parameter | Type | Required | Description | |---|---|---|---| | path | string | one of path/data (preferred) | Path to the molecular file, exactly as the user wrote it (Windows/WSL both work, ~/ expands); read server-side, fast | | data | string | one of path/data | Raw molecular file content as plain text — only for molecules with no file on disk (e.g. pasted in chat); do not base64-encode | | format | pdb \| sdf \| mol2 \| mol | required with data | Input format; inferred from the extension when path is given, may be omitted | | name | string | no | Display name (e.g. "1CRN"), shown as the viewer title | | style | stick \| line \| sphere \| cartoon | no | Initial rendering style (default stick; cartoon recommended for proteins) |

License

MIT

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