gatewizard 1.0.3

A tool for membrane protein preparation and molecular dynamics analysis

GateWizard

A library and GUI application tool for membrane protein preparation and molecular dynamics analysis.

📖 Read the Documentation

Features

• Protein Structure Preparation: Clean PDB files, add missing atoms, and optimize structures
• Propka Integration: pKa calculations with automatic protonation state assignment
• Protein Capping: Add ACE/NME caps to protein termini before analysis
• Force Field Support: Compatible with Amber force fields (ff14SB, ff19SB, etc.)
• Membrane System Building: Automated membrane protein insertion and equilibration
• Modern GUI: Built with CustomTkinter for an intuitive user experience

Installation

Quick Installation from PyPI (Recommended)

1. Create a conda environment with scientific dependencies:

   conda create -n gatewizard -c conda-forge python sqlite ambertools=24 parmed=4.3.0 -y
   

2. Activate the environment:

   conda activate gatewizard
   

3. Install GateWizard from PyPI:

   pip install gatewizard
   

Alternative: Development Installation

For developers or to install from source:

1. Clone the repository:

   git clone https://github.com/maurobedoya/gatewizard.git
   cd gatewizard
   

2. Create environment from file:

   conda env create -f environment.yml
   conda activate gatewizard
   

3. Install in development mode:

   pip install -e .
   

Dependencies

Core Dependencies (Automatically Installed)

• Python ≥ 3.8
• CustomTkinter ≥ 5.0.0 - Modern GUI framework
• NumPy ≥ 1.21.0 - Numerical computing
• Matplotlib ≥ 3.5.0 - Plotting and visualization
• MDAnalysis ≥ 2.0.0 - Molecular analysis toolkit
• Propka ≥ 3.2.0 - pKa calculations
• BioPython - PDB file handling

Scientific Computing Dependencies (Via Conda)

• AmberTools 24 - Molecular dynamics preparation and analysis
• Parmed 4.3.0 - Parameter/topology file manipulation (must be from conda-forge for compatibility)

Usage

Launch the GUI

gatewizard

Command Line Options

gatewizard --help              # Show all options
gatewizard --screen 1          # Launch on secondary monitor
gatewizard --debug             # Enable debug logging
gatewizard --version           # Show version

Upgrading

To upgrade to the latest version:

# Activate your environment
conda activate gatewizard

# Upgrade GateWizard
pip install --upgrade gatewizard

To check your current version:

gatewizard --version

Key Features

Propka Analysis

• Automatic pKa calculations for protein residues
• Protonation state assignment at specified pH
• Optional protein capping with ACE/NME groups
• Export results for molecular dynamics simulations

System Building

• Automated protein preparation workflow
• Integration with AmberTools for force field assignment
• Support for different membrane types
• Equilibration protocol generation
• Analysis of the equilibrated and production MDs

Troubleshooting

Common Issues

ImportError with numpy.compat: This indicates a version conflict between NumPy and Parmed. Make sure to install Parmed via conda-forge as shown in the installation instructions.

pdb4amber command not found: Ensure AmberTools is installed via conda-forge and the gatewizard environment is activated.

GUI not launching: Check that CustomTkinter is properly installed. Try reinstalling with pip install --force-reinstall customtkinter.

Development

Setting up for Development

# Clone the repository
git clone https://github.com/maurobedoya/gatewizard.git
cd gatewizard

# Create and activate environment
conda env create -f environment.yml
conda activate gatewizard

# Install in development mode
pip install -e .

Project Structure

gatewizard/
├── gatewizard/          # Main source code
│   ├── gui/             # GUI components
│   ├── analysis/        # Analysis modules
│   └── ...
├── docs/                # Documentation (GitHub Pages)
├── tests/               # Test suite
├── environment.yml      # Conda environment
├── pyproject.toml      # Project configuration
└── README.md           # This file

Running Tests

All tests are in the tests/ directory. See tests/README.md for detailed testing documentation.

# Run all tests
python -m pytest tests/

# Run with verbose output
python -m pytest tests/ -v

# Run specific test file
python -m pytest tests/test_propka_improvements.py

# Run with coverage
python -m pytest tests/ --cov=gatewizard --cov-report=html

Documentation

Documentation is built with MkDocs and hosted on GitHub Pages.

# Install MkDocs
pip install mkdocs mkdocs-material

# Serve documentation locally
mkdocs serve

# Build documentation
mkdocs build

# Deploy to GitHub Pages
mkdocs gh-deploy

View documentation at: http://localhost:8000 (when serving locally)

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Add/update tests
5. Update documentation
6. Commit your changes (git commit -m 'Add amazing feature')
7. Push to the branch (git push origin feature/amazing-feature)
8. Open a Pull Request

Code Style

• Follow PEP 8 guidelines
• Add docstrings to functions and classes
• Include type hints where appropriate
• Write tests for new features

License

GateWizard is licensed under the MIT License.

Copyright (c) 2025 Constanza González and Mauricio Bedoya

Authors

• Constanza González [e-mail]
• Mauricio Bedoya [e-mail]