molmcp

<h1 align="center">molmcp</h1>

<p align="center"> <strong>The MCP foundation for the MolCrafts ecosystem</strong> </p>

<p align="center"> <a href="https://pypi.org/project/molcrafts-molmcp/"><img alt="PyPI" src="https://img.shields.io/pypi/v/molcrafts-molmcp?logo=python&logoColor=white&label=PyPI"></a> <a href="https://pypi.org/project/molcrafts-molmcp/"><img alt="Python" src="https://img.shields.io/pypi/pyversions/molcrafts-molmcp.svg"></a> <a href="https://github.com/MolCrafts/molmcp/blob/master/LICENSE"><img alt="License" src="https://img.shields.io/badge/license-BSD--3--Clause-blue"></a> <a href="https://github.com/MolCrafts/molmcp/actions"><img alt="CI" src="https://github.com/MolCrafts/molmcp/actions/workflows/ci.yml/badge.svg"></a> </p>

<p align="center"> <a href="https://molcrafts.github.io/molmcp/"><strong>Documentation</strong></a> · <a href="https://molcrafts.github.io/molmcp/get-started/quickstart/"><strong>Quickstart</strong></a> · <a href="https://github.com/MolCrafts/molmcp/issues"><strong>Issues</strong></a> </p>

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Why molmcp

The MolCrafts ecosystem ships many packages — molpy, molcfg, molexp, molpack, mollog, molq, molrec, molvis — and each of them benefits from being callable by an LLM agent. The hard part is discovery: an agent needs to find out what a codebase actually provides instead of guessing function, class, or tool names.

molmcp solves this with a graph-based codebase capability discovery engine. It statically indexes a repository into a code graph — symbols, signatures, docstrings, relationships, examples, and tests — and exposes that graph to agents over the Model Context Protocol.

It does two things:

1. Runs a discovery engine that indexes any codebase (a local path, an installed package, or — soon — a GitHub repository) into a snapshot-cached code graph, and answers structured queries against it.
2. Defines a Provider plugin contract for the narrow class of capabilities discovery cannot answer — stateful queries against local runtime state (a jobs DB, a workspace catalog) — under a single coordinated MCP server with shared security defaults.

molmcp core imports nothing from the MolCrafts packages. That's the point — it's pure infrastructure, and any codebase can be indexed without molmcp depending on it.

Discovery, not guessing

The discovery engine is built so an agent resolves capabilities from indexed code structure rather than guessing names:

• It parses source with a per-language analyzer (Python today on the stdlib ast module; TypeScript, Rust, and C++ slot in behind the same LanguageAnalyzer interface) into a shared graph of nodes and edges.
• A two-phase pipeline — extraction then resolution — links calls, base classes, imports, tests, and docstring examples into a connected graph.
• The graph is stored as one SQLite database per source snapshot, keyed on a content hash (local) or commit SHA (GitHub) — never a branch name — so cached results are always tied to exact source.
• Every tool response carries a snapshot block, so an agent always knows which revision it is looking at.

Discovery tools

When discovery sources are configured, molmcp exposes six composable, graph-backed tools (all read-only):

Tool	Purpose
molmcp_find_capability	Primary tool — describe a task, get ranked symbol matches with signatures, examples, tests, and callers.
molmcp_search_symbols	Search indexed symbols by name, qualname, or summary.
molmcp_describe_symbol	Full detail for one symbol, optionally with source code.
molmcp_relations	Walk the graph from a symbol: callers, callees, implementers, subclasses, references, examples, tests, impact.
molmcp_outline	Map a source's packages/modules to their symbols — the "where do I look" tool.
molmcp_refresh	Force a fresh re-index of a source.

Provider plugin contract

Discovery answers most questions. For the rest — queries that depend on local runtime state no static analysis can recover — molmcp defines a Provider plugin contract. A Provider earns a tool slot only when all four conditions hold: stable signature, read-only/idempotent, every-session frequency, single-shot answer. See docs/concepts/provider-design.md.

Install

pip install molcrafts-molmcp

Requires Python ≥ 3.12. The PyPI distribution is molcrafts-molmcp; the import name is molmcp. The discovery engine adds no required runtime dependency — it uses the standard library.

60-second quickstart

Start an MCP server that indexes the installed MolCrafts packages:

python -m molmcp

molmcp auto-detects whichever of {molpy, molpack, molrs, molq, molexp} are importable and registers discovery over them. Point it anywhere with --source:

python -m molmcp --source pkg:molpy --source /path/to/a/repo

Wire it into Claude Code:

claude mcp add molcrafts -- python -m molmcp

Inspect the engine — or verify it works — without an MCP client:

molmcp discovery verify pkg:molpy   # self-check: counts, FTS, sample query
molmcp discovery index pkg:molpy
molmcp discovery outline pkg:molpy
molmcp discovery query pkg:molpy "radial distribution function"

molmcp discovery verify prints a health report and exits non-zero on failure, so it doubles as a CI/setup check. See the discovery engine guide for the full verification walkthrough.

Source specs

A discovery source is one of:

• path/to/repo — a local directory.
• pkg:<name> — an installed Python package (resolved by import name).
• github:owner/repo[@ref] — a GitHub repository (downloaded at a resolved commit; GITHUB_TOKEN is used when set).

Architecture

                ┌────────────────────────────────────┐
                │  MCP clients                       │
                │  (Claude Code, Claude Desktop, …)  │
                └──────────────┬─────────────────────┘
                               │   stdio / http / sse
                               ▼
                ┌────────────────────────────────────┐
                │  molmcp                            │
                │  • DiscoveryProvider (molmcp_* )   │
                │  • Discovery engine core           │
                │      source → snapshot → extract   │
                │      → resolve → SQLite graph      │
                │  • Provider contract + discovery   │
                │  • PathSafety / ResponseLimit      │
                │  • Annotations validator           │
                └──────────────┬─────────────────────┘
                               │
            ┌──────────────────┼──────────────────────┐
            ▼                  ▼                      ▼
      MolqProvider      MolexpProvider     third-party providers
      (jobs.db)         (workspace.json     (entry-point group
                         catalog)            molmcp.providers)

The discovery engine core (molmcp.discovery) is MCP-free — it can be imported, scripted, and tested without FastMCP. Only molmcp.discovery.provider touches MCP.

Adding domain tools

Before adding a Provider tool, check it against the four-condition rule in docs/concepts/provider-design.md. If a tool earns a slot:

from fastmcp import FastMCP
from mcp.types import ToolAnnotations

class MolpackProvider:
    name = "molpack"

    def register(self, mcp: FastMCP) -> None:
        @mcp.tool(annotations=ToolAnnotations(readOnlyHint=True))
        def list_pack_targets(workdir: str) -> list[dict]:
            """Return the in-progress pack targets cached under workdir."""
            from molpack import workspace
            return [t.to_dict() for t in workspace.scan(workdir).targets]

Declare the entry point in the package's pyproject.toml:

[project.entry-points."molmcp.providers"]
molpack = "molpack_mcp:MolpackProvider"

python -m molmcp discovers it automatically.

Status

Alpha. The discovery engine and Provider contract may shift before 1.0. Pin to molcrafts-molmcp >= 0.2, < 0.3.

Contributing

git clone https://github.com/MolCrafts/molmcp.git
cd molmcp
pip install -e ".[dev]"
pytest

License

BSD-3-Clause. See LICENSE.

Acknowledgements

molmcp is part of the MolCrafts project. It implements the Model Context Protocol using the fastmcp server library.