Contributing

git clone https://github.com/emdgroup/mdfactory.git
cd mdfactory
pixi install

pixi run -e dev test

git clone https://github.com/emdgroup/mdfactory.git
cd mdfactory
conda create -n mdfactory -c conda-forge python rdkit \
    openff-toolkit openff-interchange openff-nagl openff-units openmm
conda activate mdfactory
pip install -e .[dev]

ruff format .
ruff check .

ruff check --fix .

def build_system(config, molecules):
    """
    Build a simulation system from configuration and molecules.

    Parameters
    ----------
    config : dict
        System configuration with box_size, engine, etc.
    molecules : list of dict
        Molecule specifications with SMILES and counts.

    Returns
    -------
    positions : ndarray
        Molecule positions in the simulation box.

    Raises
    ------
    ValueError
        If box_size is negative or molecules list is empty.

    Examples
    --------
    >>> config = {"box_size": [3.0, 3.0, 3.0]}
    >>> molecules = [{"smiles": "O", "count": 100}]
    >>> positions = build_system(config, molecules)
    """
    pass

pytest mdfactory/tests/

pytest --cov=mdfactory --cov-report=html

## Changes
- Implements NAMDEngine class
- Adds PSF topology generation
- Updates engine registry

## Testing
- Added test_namd_engine.py
- All existing tests pass
- Tested with sample protein system

Closes #123

# Make changes
git add .
git commit -m "Address review feedback"
git push origin feature/my-feature

cd docs
bun run dev

---
title: New Feature
description: Description of the feature
---

## Usage

Explain how to use the feature...