acatome-chat 0.2.2

Acatome research assistant — acatome-lambic shell with MCP tools

acatome-chat

A local-first AI research assistant for scientific literature.

One install gives you an interactive shell backed by a local LLM, a searchable paper library, document editing, live web search, and domain-specific databases — all wired together through the Model Context Protocol (MCP).

What you get

Capability	Powered by	What it does
Paper library	acatome-mcp + acatome-store	Semantic search over your papers. Navigate by slug, DOI, or arXiv ID. Read abstracts, TOCs, full chunks, figures. Add notes.
PDF extraction	acatome-extract	Drop a PDF, get structured text with metadata lookup (CrossRef + Semantic Scholar), RAKE keywords, and optional LLM summaries. Supports articles, datasheets, tech reports.
Document writing	precis-mcp	Open, navigate, and edit Word (.docx) and LaTeX (.tex) documents. Tracked changes in Word. Auto-numbered headings. Citation support.
Web search	perplexity-sonar-mcp	Live web queries via Perplexity Sonar — quick lookups, deep research with citations, academic and finance focus modes.
Catalysis DB	catapult-mcp	Query DFT reaction energies, activation barriers, and catalyst comparisons from CatHub and Materials Project.
MOF DB	grandmofty-mcp	Search Metal-Organic Frameworks by pore size, surface area, void fraction, gas isotherms. Data from CoRE, hMOF, QMOF.
LLM shell	acatome-lambic	Provider-agnostic chat with tool use, thinking mode, and MCP server management. Works with Ollama, OpenAI, Anthropic, and any litellm-compatible provider.

Install

pip install acatome-chat
# or
uv add acatome-chat

That's it. All MCP servers and the paper store are included. Default backend is SQLite + Chroma — no external services needed.

For heavier setups:

uv add "acatome-chat[postgres]"     # PostgreSQL + pgvector
uv add "acatome-chat[embeddings]"   # sentence-transformers

Quick start

# Start the shell (default: ollama/qwen3.5:9b)
acatome-chat

# Use a different model
acatome-chat --model ollama/llama3.1:8b
acatome-chat --model anthropic/claude-sonnet-4-20250514
acatome-chat --model openai/gpt-4o

# Disable thinking/reasoning mode
acatome-chat --no-think

Build your paper library

# Extract a single PDF
acatome-extract extract paper.pdf

# Watch a folder for new PDFs
acatome-extract watch ~/Downloads/papers/

# Enrich with LLM summaries
acatome-extract enrich ~/.acatome/papers/

# Ingest into the searchable store
acatome-store ingest ~/.acatome/papers/

Talk to your papers

Once inside the shell, the LLM has direct access to your library:

> Find papers about CO2 capture in MOFs from 2020 onwards
> Read the abstract of li2024mof
> Summarize the key findings from chunks 12-18
> Search the web for recent advances in direct air capture
> Open my review draft and add a paragraph about these results

Architecture

acatome-chat (you are here)
├── acatome-lambic        LLM shell engine (MCP client)
├── acatome-mcp           Paper query MCP server
│   └── acatome-store     SQLite/Postgres + Chroma/pgvector storage
│       └── acatome-meta  Shared config and metadata
├── acatome-extract       PDF → structured bundle pipeline
│   └── precis-summary    RAKE keyword extraction
├── precis-mcp            Document editor MCP server
├── perplexity-sonar-mcp  Web search MCP server
├── catapult-mcp          Catalysis database MCP server
│   └── chemdb-common     Shared chemistry DB utilities
└── grandmofty-mcp        MOF database MCP server
    └── chemdb-common

Environment variables

Variable	Required	Purpose
PERPLEXITY_API_KEY	For web search	Perplexity Sonar API key
OPENAI_API_KEY	For OpenAI models	OpenAI API key
ANTHROPIC_API_KEY	For Anthropic models	Anthropic API key

For local models via Ollama, no API keys are needed.

License

MIT