acatome-chat 0.4.0

AI research assistant — local Ollama or Claude/GPT-4o, switchable. Paper library, doc editing, web search.

acatome-chat

A local-first AI research assistant for scientific literature.

Runs with a local Ollama model by default — or switch to Claude, GPT-4o, or any litellm-compatible provider with a single flag. One install gives you an interactive shell with 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

1. Build your paper library

Extract PDFs and ingest them into the searchable store:

# Extract a single PDF (or a whole directory)
acatome-extract extract paper.pdf
acatome-extract extract ~/Downloads/papers/

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

Optional enrichment steps:

# Watch a folder for new PDFs (auto-extracts on arrival)
acatome-extract watch ~/Downloads/papers/

# Add LLM-generated summaries to your bundles
acatome-extract enrich ~/.acatome/papers/

2. Start the chat

# Default: local Ollama model (ollama/qwen3.5:9b)
acatome-chat

# Or use Claude / GPT-4o / any litellm provider
acatome-chat --model anthropic/claude-sonnet-4-20250514
acatome-chat --model openai/gpt-4o
acatome-chat --model ollama/llama3.1:8b

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

3. Use slash commands

The shell has / commands with tab autocomplete:

Command	What it does
/tools	List all available MCP tools
/status	Show connected model and servers
/model <spec>	Switch LLM provider on the fly
/think / /nothink	Toggle reasoning mode
/db	Show paper library connection info and stats
/review <prompt>	Review the active document (see below)
/help	Show command help
/quit	Exit the shell

4. Review documents

› /review check scientific rigor and paragraph structure
› /review fix grammar and clarity --fix
› /review verify citations --comments-only
› /review improve transitions --section S2.3

The assistant reads each section, applies fixes as tracked changes, and adds margin comments for issues needing human judgment.

5. Talk to your papers

After ingesting papers, the LLM has direct access to your library. Example prompts:

› Find papers about CO2 conversion and write a summary with citations into co2review.docx
› Search for MOFs with high CO2 uptake and compare their pore sizes
› Read the abstract of li2024mof and summarize the key findings
› Open my draft.docx and add a new section about these results
› Search the web for recent advances in direct air capture

The assistant can read your papers, search the web, query chemistry databases, and write results directly into .docx or .tex files — all in one conversation.

Note: Document editing supports .docx and .tex formats. For Word files, changes are written as tracked changes. Be aware that Word may overwrite the file if it's open — save and close Word before asking the assistant to edit.

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

GPL-3.0-or-later