How to integrate PDF Vector MCP with Atomic Agent

Connect Atomic Agent to PDF Vector MCP. Summarize key findings from research paper, extract tables from grant pdf into json, and more using natural language, with authentication handled for you.

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Api Key

PDF Vector is a document parsing and vector-search service that converts PDFs into markdown and structured data. Use it to quickly find, extract, and index details from academic papers and grant documents.

10 Tools

Introduction

Atomic Agent is an open-source AI agent that runs on your machine and supports local models through llama.cpp. Connect it to 1,500+ apps through Composio, including PDF Vector.

This guide uses Atomic Agent's built-in Composio integration. You need Atomic Agent v0.5.6 or later, your own Composio API key, and a PDF Vector account. See the Atomic Agent documentation for installation instructions.

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How Atomic Agent connects to PDF Vector

Atomic Agent connects to Composio's Tool Router over Streamable HTTP MCP. It discovers the tools needed for your request, and Composio handles account authentication.

Execution and account-connection tools follow Atomic Agent's configured approval policy. Review any approval prompt before allowing an action on your connected account.

Connect PDF Vector to Atomic Agent

  1. Sign up or sign in to the Composio dashboard. Copy your API key.
  2. In Atomic Agent, open the Integrations tab and select Composio. Select API key, press e, paste the key, and press Enter. The tools become available immediately, without a restart.
  3. Ask Atomic Agent to do something in PDF Vector. It searches Composio for the right tool.
  4. On first use, open the sign-in link returned in the chat. Connect your PDF Vector account, then return to Atomic Agent to continue.

Headless setup

Add the following line to ~/.atomic-agent/.env, replacing YOUR_COMPOSIO_API_KEY with your key. Start Atomic Agent after saving the file.

bash
COMPOSIO_API_KEY=YOUR_COMPOSIO_API_KEY

What is the PDF Vector MCP server, and what's possible with it?

The PDF Vector MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your PDF Vector account. It provides structured and secure access so your agent can perform PDF Vector operations on your behalf.

Use PDF Vector from Atomic Agent

With your account connected, ask Atomic Agent to work with PDF Vector in natural language. You can connect more apps through the same Composio integration as you need them.

Visit the Atomic Agent website or inspect the Atomic Agent source code.

Troubleshooting

Why is my API key rejected?

Copy the key directly from the Composio dashboard. Atomic Agent requires ASCII characters because it sends the key in an HTTP header. Remove any extra characters introduced when copying.

Why are Composio tools unavailable after saving a key?

Check that you use Atomic Agent v0.5.6 or later and that Composio is enabled in your configuration. A "composio": { "enabled": false } setting disables the integration while keeping the saved key on disk.

Does Composio have a free plan?

The Hobby plan includes 100,000 tool calls per month. Composio-managed OAuth apps have a lower included allowance. See Composio pricing for the current limits that apply to your connection.

TOOLS

Supported Tools

Every PDF Vector action and event your agent gets out of the box.

Ask Document

Answer one question from a general, identity, invoice, or bank-statement document.

Extract Document Data

Extract schema-constrained structured data from a general, identity, invoice, or bank-statement document.

Fetch Publications

Resolve up to 100 publication identifiers with provider auto-detection and return both resolved records and per-identifier errors.

Find Citations

Find relevant academic citations for each sentence in a paragraph and preserve provider-specific partial errors.

Find Similar Papers

Find papers related to a seed publication using citation-network similarity, optionally including relationship edges.

Get Paper Graph

Retrieve a publication plus one independently offset-controlled page of citing papers and one page of referenced papers.

Parse Academic Paper

Resolve an academic identifier or provider URL to a public PDF and parse it to markdown.

Parse Document

Convert a general, identity, invoice, or bank-statement document to markdown.

Search Publications

Search academic publications across selected databases and return one offset-controlled page, including any provider-specific partial errors.

Search Research Grants

Search US, EU, and UK research-grant providers and return one explicit offset-controlled page with partial provider errors.

FAQ

Frequently asked questions

With a standalone PDF Vector MCP server, the agents and LLMs can only access a fixed set of PDF Vector tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from PDF Vector and many other apps based on the task at hand, all through a single MCP endpoint.

Yes, you can. Atomic Agent fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right PDF Vector tools.

Yes, absolutely. You can configure which PDF Vector scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your PDF Vector data and credentials are handled as safely as possible.

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