mofchecker — MCP Edition

A lean, MCP-enabled repackaging of the outstanding mofchecker library by Kevin Jablonka and the lamalab-org team.

Standing on the shoulders of giants

The original mofchecker is, frankly, one of the most thoughtfully engineered tools in computational MOF science. In a field where "sanity check" usually means "did it crash?", Kevin and collaborators built a rigorous, composable framework that catches everything from overlapping atoms to suspiciously over-charged fragments — all in a clean, pythonic API that actually makes sense to use. The graph-hash deduplication alone is worth the price of admission. If you are doing any serious high-throughput MOF screening, the original library is essential reading; this fork would not exist without its solid foundation.

Original repository: https://github.com/lamalab-org/mofchecker
Original paper: Jablonka et al., Digital Discovery, 2023.

What is this fork?

This edition slims the original down to a focused MCP (Model Context Protocol) server so that AI agents — in particular those built with featherflow — can call structure checks as tools over stdio.

Changes relative to upstream:

| Change | Reason | |---|---| | Removed PorosityCheck / is_porous | Porosity analysis is provided by the separate zeopp-backend MCP service | | Added mcp_server.py with 8 MCP tools | Exposes every check category as an individual callable tool | | Migrated to pyproject.toml (PEP 621) | Modern packaging, single configuration file | | python_requires >= 3.9, dropped backports.cached-property | 3.8 is EOL; use functools.cached_property from stdlib | | Replaced black + isort + flake8 with ruff | Single, faster linter/formatter |

Porosity checks are intentionally not included here. Point your agent at zeopp-backend (http://localhost:9877/mcp) for those.

Installation

Important — virtual environment isolation Each MCP server must run in its own virtual environment. The command in your FeatherFlow config must point to this project's .venv/bin/python, not FeatherFlow's Python or the system Python.

0. Install uv (one-time, recommended)

# Linux / macOS
curl -LsSf https://astral.sh/uv/install.sh | sh

uv manages Python versions automatically — no need to install Python 3.9+ manually.

1. Clone and create a dedicated environment

git clone https://github.com/lichman0405/mofchecker-mcp.git
cd mofchecker-mcp
uv venv .venv --python 3.10        # pyeqeq requires Python <3.11
source .venv/bin/activate          # Linux/macOS
# .venv\Scripts\Activate.ps1      # Windows PowerShell

2. Install

uv pip install -e .

pyeqeq (EQeq charge check) requires Python < 3.11 and pybind11 >= 2.9 (older versions have a missing <cstdint> include that breaks on GCC 10+). Both constraints are handled automatically via pyproject.toml — no manual steps needed.

3. Verify

python -m mofchecker.mcp_server --help

MCP server

The primary use-case of this fork is running mofchecker as an MCP tool server for AI agents.

Start the server

# Activate the project's own venv first
source /path/to/mofchecker/.venv/bin/activate

python -m mofchecker.mcp_server   # stdio transport (for featherflow / Claude Desktop)

Available tools

| Tool | Description | |---|---| | list_available_descriptors | Returns the full list of descriptor keys | | get_basic_info | Formula, cell volume, density, space group, dimensionality | | check_global_structure | Floating atoms/solvent, graph connectivity | | check_atomic_overlaps | Overlapping atom pairs | | check_coordination | Over/under-coordinated C, N, H and rare-earth/alkaline metals | | check_geometry | Geometrically exposed metals (open metal sites) | | check_charges | EQeq partial-charge sanity (overcharged atoms) | | check_mof_full | Runs all checks and returns the complete descriptor dict |

Every tool accepts either a cif_path (absolute path on the server filesystem) or cif_content (raw CIF text) — whichever is more convenient for the caller.

featherflow integration

Edit ~/.featherflow/config.json. The command must be the absolute path to this project's .venv/bin/python — not mofchecker-mcp on $PATH and not FeatherFlow's own Python.

{
  "tools": {
    "mcpServers": {
      "mofchecker": {
        "command": "/path/to/mofchecker/.venv/bin/python",
        "args": ["-m", "mofchecker.mcp_server"],
        "toolTimeout": 120
      },
      "zeopp": {
        "url": "http://localhost:9877/mcp",
        "toolTimeout": 120
      }
    }
  },
  "channels": {
    "sendToolHints": true,
    "sendProgress": true
  }
}

On Windows replace the path with C:/path/to/mofchecker/.venv/Scripts/python.exe.

See mcp_config_example.json for a ready-to-use snippet.

Python API

The library is still fully usable as a regular Python package:

from mofchecker import MOFChecker

checker = MOFChecker.from_cif("path/to/structure.cif")

# Individual checks
print(checker.has_atomic_overlaps)     # bool
print(checker.has_oms)                 # bool
print(checker.has_overcoordinated_c)   # bool

# All descriptors at once
descriptors = checker.get_mof_descriptors()

Development

uv pip install -e ".[dev]"
pytest                            # run tests
ruff check mofchecker/ tests/            # lint
ruff format mofchecker/ tests/           # format

License

MIT — same as the original project.

MCP Servers