gatewizard 1.0.39

A tool for membrane protein preparation and molecular dynamics analysis

GateWizard (API)

Python library for membrane protein preparation, system building, equilibration setup, and MD trajectory analysis.

This repository is the API only. It does not include a graphical interface.

If you want a desktop app, use gatewizard-gui, a separate project that calls this library. You can use the API without the GUI, and the GUI without cloning this repo (it installs the API via pip).

📖 Documentation

Features

• Preparation — clean structures, pKa (PROPKA), protonation, and termini capping
• Membrane builder — orient protein, pack lipids and solvent, Amber parametrization (tleap)
• Equilibration — CHARMM-GUI-style protocols for NAMD, GROMACS, and OpenMM (NVT, NPT, NPAT, NPγT)
• Analysis — trajectory metrics, structural analysis, and plotting helpers
• Force fields — Amber protein models (e.g. ff14SB, ff19SB) and common water/lipid setups

Install

conda create -n gatewizard -c conda-forge python sqlite ambertools=24 parmed=4.3.0 openmm cudatoolkit -y
conda activate gatewizard
pip install "gatewizard[full]"
pip install -r requirements-orientation.txt

MemPrO is installed from the MemPrO GitHub release (v0.1.0).

For optional extras without OpenMM (NAMD/GROMACS only):

pip install gatewizard

From source (includes openmm + cudatoolkit via conda):

git clone https://github.com/maurobedoya/gatewizard.git
cd gatewizard
conda env create -f environment.yml
conda activate gatewizard
pip install -e .

Check the version:

python -c "import gatewizard; print(gatewizard.__version__)"

Dependencies

GateWizard is split across two repositories (API + GUI). Below is the full dependency stack; subsections mark what this repo installs automatically.

Python — core (pip install gatewizard) · this repo

Installed automatically:

Package	Role
Python ≥ 3.8	Runtime
NumPy	Numerical arrays
Matplotlib	Plots and analysis figures
MDAnalysis	Trajectories and topologies
lipyphilic	Membrane / lipid analysis
PROPKA	pKa and protonation
RDKit	Ligand 2D structures
Pillow	Image I/O
psique	Structure / sequence tools
requests	HTTP helpers

Python — optional [full] · this repo

Package	Role
ParmEd	Topology conversion (GROMACS, etc.)
OpenMM	Equilibration / MD (Python; use with conda cudatoolkit for GPU)
MemPrO	Membrane orientation (GitHub)

Install: pip install "gatewizard[full]" then pip install -r requirements-orientation.txt for MemPrO.

Python — GUI backend · gatewizard-gui

Package	Role
FastAPI	Local HTTP API for the desktop app
Uvicorn	ASGI server
gatewizard[full]	This API (installed into the embedded runtime)

Conda (building + OpenMM GPU) · this repo via environment.yml; GUI embeds on Linux/WSL/macOS

Package	Role
AmberTools 24	tleap, antechamber, packmol, pdb4amber, …
ParmEd 4.3.0	From conda-forge (AmberTools-compatible)
OpenMM ≥ 8.0	MD engine (Python)
cudatoolkit	OpenMM CUDA platform (Linux/WSL + NVIDIA driver)

Desktop app · gatewizard-gui

Package	Role
Electron	Desktop shell
Node.js 20+	App and build runtime
Svelte 5	UI framework
Vite	Frontend bundler
Tailwind CSS	Styling
Three.js + Threlte	3D structure viewer
electron-updater	In-app update checks

External MD engines (install separately · neither repo)

Tool	Role
NAMD	Run NAMD equilibration — namd3 / namd2 on PATH
GROMACS	Run GROMACS equilibration — gmx on PATH

OpenMM needs no separate binary — use openmm + cudatoolkit (conda) with gatewizard[full]. Auto-selects CUDA → OpenCL → CPU; override with PLATFORM=CUDA bash run_equilibration.sh.

python -c "import openmm; print([openmm.Platform.getPlatform(i).getName() for i in range(openmm.Platform.getNumPlatforms())])"

Provided by this repository

Component	Included
gatewizard Python package (core + [full] extras)	yes
environment.yml (AmberTools, OpenMM, cudatoolkit, …)	yes
Desktop app (Electron, Svelte, viewer)	no — gatewizard-gui
FastAPI backend	no — GUI repo
NAMD / GROMACS binaries	no — user install

Desktop GUI

gatewizard-gui — Electron app for the same workflow with a visual interface. It manages its own Python runtime and can update the API from the app.