Skillget

mcp-atom-of-thoughts

mcp
Security Audit
Fail
Health Pass
  • License — License: MIT
  • Description — Repository has a description
  • Active repo — Last push 0 days ago
  • Community trust — 26 GitHub stars
Code Fail
  • os.homedir — User home directory access in src/approval.ts
  • process.env — Environment variable access in src/approval.ts
  • os.homedir — User home directory access in src/config.ts
Permissions Pass
  • Permissions — No dangerous permissions requested
Purpose
This server provides a structured reasoning framework for LLMs. It decomposes problems into trackable "atoms" with dependency graphs, confidence scoring, and interactive browser-based visualizations.

Security Assessment
The tool reads the user's home directory path (`os.homedir`) and accesses environment variables to manage configuration and an approval system. This is standard for MCP servers, but flagged as it can reveal local system paths. The visualization feature opens a local HTTP server to render D3.js graphs in your browser and receive approve/reject feedback. No dangerous permissions, hardcoded secrets, or shell command execution were detected. Overall risk: Low.

Quality Assessment
The project is under the permissive MIT license and is actively maintained. It demonstrates strong engineering practices with TypeScript 5.9, excellent documentation, and a robust test suite (183 passing tests). The repository currently has 26 GitHub stars, indicating early but growing community adoption.

Verdict
Safe to use — a well-engineered reasoning tool with standard local server behavior and no dangerous permission requirements.
SUMMARY

MCP server for structured AI reasoning — decompose problems into atomic thoughts with dependency graphs, confidence tracking, and interactive D3.js visualization

README.md

Atom of Thoughts

Structured reasoning for LLMs. Decompose, track confidence, visualize, approve.

npm version
license
node
tests
TypeScript

Atom of Thoughts — interactive D3 visualization

Setup

Add to your MCP config:

{
  "mcpServers": {
    "atom-of-thoughts": {
      "command": "npx",
      "args": ["-y", "@dioptx/mcp-atom-of-thoughts"]
    }
  }
}

[!TIP]
Works with Claude Code, Cursor, Windsurf, or any MCP client.

How it works

graph LR
    P["P · Premise"]:::premise --> R["R · Reasoning"]:::reasoning
    R --> H["H · Hypothesis"]:::hypothesis
    H --> V["V · Verification"]:::verification
    V --> C["C · Conclusion"]:::conclusion

    classDef premise fill:#6b7280,stroke:#9ca3af,color:#fff,font-weight:bold
    classDef reasoning fill:#3b82f6,stroke:#60a5fa,color:#fff,font-weight:bold
    classDef hypothesis fill:#eab308,stroke:#facc15,color:#000,font-weight:bold
    classDef verification fill:#06b6d4,stroke:#22d3ee,color:#fff,font-weight:bold
    classDef conclusion fill:#22c55e,stroke:#4ade80,color:#fff,font-weight:bold

Chain atoms together. Each carries a confidence score (0-1). Reasoning terminates when a high-confidence conclusion is reached or max depth is hit. Sessions isolate separate problems so they don't interfere.

Tools

Three tools:

Tool When to reach for it
AoT-fast Default. Tradeoffs, debugging, decisions, option evaluation. Depth 3.
AoT-full Plans, architecture, decomposition into sub-problems. Depth 5.
atomcommands Sessions, export, approval polling, decomposition lifecycle.

Quick example

AoT-fast({atomId:"P1", content:"API returns 500 on POST /users",     atomType:"premise"})
AoT-fast({atomId:"R1", content:"Unhandled exception in route handler", atomType:"reasoning", dependencies:["P1"]})
AoT-fast({atomId:"C1", content:"Add try-catch in POST handler",       atomType:"conclusion", dependencies:["R1"], confidence:0.9})

Only atomId, content, and atomType are required. Everything else has defaults.

Visualization

Set viz: true on any call to open an interactive D3 graph in the browser:

AoT-fast({atomId:"C1", ..., viz: true})

The approve/reject UI posts decisions back to the server over HTTP. No filesystem polling.

Configuration 
{
  "args": ["-y", "@dioptx/mcp-atom-of-thoughts", "--mode", "fast", "--viz", "never"]
}
Flag Default Effect
--mode full|fast|both both Which tools to register
--viz auto|always|never auto auto = render on viz:true; always = every call; never = skip (CI)
--max-depth <n> 5 / 3 Override depth limit
--output-dir <path> OS temp Where to write viz HTML
--downloads-dir <path> ~/Downloads Approval JSON fallback
Sessions

Each reasoning chain gets its own session. Default: "default".

  • atomcommands new_session creates and activates a new one.
  • atomcommands switch_session / list_sessions / reset_session for management.
  • When reasoning terminates, the session auto-archives. The next zero-dep atom auto-spawns default-2, default-3, etc.
  • Or pass sessionId on any AoT call to target explicitly.

Two problems in one MCP process stay isolated without manual session management.

Visualization & Approval

viz: true generates a self-contained HTML file (D3 bundled inline, works offline) and opens your browser. The UI shows:

  • Force-directed graph colored by atom type with confidence rings
  • Sidebar to approve/reject phases or individual atoms
  • Approve/reject POSTs to a local 127.0.0.1 listener (ephemeral port)

Poll results via atomcommands check_approval. Falls back to ~/Downloads file scan if the HTTP listener can't bind.

Install Methods

npx (zero install):

{ "command": "npx", "args": ["-y", "@dioptx/mcp-atom-of-thoughts"] }

npm global:

npm install -g @dioptx/mcp-atom-of-thoughts

Smithery:

npx -y @smithery/cli install @dioptx/mcp-atom-of-thoughts --client claude

Docker:

docker build -t aot . && docker run -i --rm aot
Development 
git clone https://github.com/dioptx/mcp-atom-of-thoughts.git
cd mcp-atom-of-thoughts
npm install
npm test        # 183 tests (unit + e2e)
npm run build
Migrating from v2

See MIGRATION_v2_to_v3.md for the full lookup table. The short version:

  • AoT-light is now AoT-fast
  • AoT is now AoT-full
  • generate_visualization is now viz: true on any AoT call
  • export_graph and check_approval are now atomcommands subcommands
  • --no-viz / --no-approval replaced by --viz auto|always|never

MIT · Based on Atom of Thoughts

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