gatewizard 1.0.0__tar.gz

gatewizard-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Constanza González and Mauricio Bedoya
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gatewizard-1.0.0/MANIFEST.in

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+# Exclude potentially problematic files and directories
+include gatewizard/
+recursive-include gatewizard *.py
+recursive-include gatewizard/crystal_analysis *.cr *.yml *.lock *.md
+include gatewizard/run_crystal_with_system_libs.sh
+global-exclude *.pyc
+global-exclude __pycache__
+global-exclude *.log
+global-exclude .git*
+global-exclude *.pdb
+global-exclude *.pka
+prune equilibration
+prune restraints
+prune docs
+exclude *.md
+exclude test_*.py
+exclude *.sh
+exclude *.bat

gatewizard-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: gatewizard
+Version: 1.0.0
+Summary: A tool for membrane protein preparation and molecular dynamics analysis
+Author-email: Constanza González <constanza.gonzalez.villagra@gmail.com>, Mauricio Bedoya <mbedoya@ucm.cl>
+License: MIT License
+        
+        Copyright (c) 2025 Constanza González and Mauricio Bedoya
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: customtkinter>=5.0.0
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: requests>=2.25.0
+Requires-Dist: MDAnalysis>=2.0.0
+Requires-Dist: propka>=3.2.0
+Provides-Extra: analysis
+Requires-Dist: MDAnalysis>=2.0.0; extra == "analysis"
+Provides-Extra: all
+Requires-Dist: MDAnalysis>=2.0.0; extra == "all"
+Dynamic: license-file
+
+# Gatewizard
+
+A library and GUI application tool for membrane protein preparation and molecular dynamics analysis.
+
+## 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 (Recommended)
+
+1. **Create a conda environment with all dependencies:**
+   ```bash
+   conda create -n gatewizard -c conda-forge python sqlite ambertools=24 parmed=4.3.0 -y
+   ```
+
+2. **Activate the environment:**
+   ```bash
+   conda activate gatewizard
+   ```
+
+3. **Install Gatewizard:**
+   ```bash
+   pip install -e .
+   ```
+
+### Alternative: Using environment.yml
+
+1. **Create environment from file:**
+   ```bash
+   conda env create -f environment.yml
+   ```
+
+2. **Activate the environment:**
+   ```bash
+   conda activate gatewizard
+   ```
+
+3. **Install Gatewizard:**
+   ```bash
+   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
+```bash
+gatewizard
+```
+
+### Command Line Options
+```bash
+gatewizard --help              # Show all options
+gatewizard --screen 1          # Launch on secondary monitor
+gatewizard --debug             # Enable debug logging
+gatewizard --version           # Show 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
+```bash
+git clone <repository>
+cd gatewizard
+conda env create -f environment.yml
+conda activate gatewizard
+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](tests/README.md) for detailed testing documentation.
+
+```bash
+# 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.
+
+```bash
+# 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](LICENSE).
+
+Copyright (c) 2025 Constanza González and Mauricio Bedoya
+
+## Authors
+
+- Constanza González <constanza.gonzalez.villagra@gmail.com>
+- Mauricio Bedoya <mbedoya@ucm.cl>
+

gatewizard-1.0.0/README.md

@@ -0,0 +1,202 @@
+# Gatewizard
+
+A library and GUI application tool for membrane protein preparation and molecular dynamics analysis.
+
+## 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 (Recommended)
+
+1. **Create a conda environment with all dependencies:**
+   ```bash
+   conda create -n gatewizard -c conda-forge python sqlite ambertools=24 parmed=4.3.0 -y
+   ```
+
+2. **Activate the environment:**
+   ```bash
+   conda activate gatewizard
+   ```
+
+3. **Install Gatewizard:**
+   ```bash
+   pip install -e .
+   ```
+
+### Alternative: Using environment.yml
+
+1. **Create environment from file:**
+   ```bash
+   conda env create -f environment.yml
+   ```
+
+2. **Activate the environment:**
+   ```bash
+   conda activate gatewizard
+   ```
+
+3. **Install Gatewizard:**
+   ```bash
+   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
+```bash
+gatewizard
+```
+
+### Command Line Options
+```bash
+gatewizard --help              # Show all options
+gatewizard --screen 1          # Launch on secondary monitor
+gatewizard --debug             # Enable debug logging
+gatewizard --version           # Show 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
+```bash
+git clone <repository>
+cd gatewizard
+conda env create -f environment.yml
+conda activate gatewizard
+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](tests/README.md) for detailed testing documentation.
+
+```bash
+# 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.
+
+```bash
+# 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](LICENSE).
+
+Copyright (c) 2025 Constanza González and Mauricio Bedoya
+
+## Authors
+
+- Constanza González <constanza.gonzalez.villagra@gmail.com>
+- Mauricio Bedoya <mbedoya@ucm.cl>
+

gatewizard-1.0.0/gatewizard/__init__.py

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+# SPDX-License-Identifier: MIT
+# Copyright (c) 2025 Constanza González and Mauricio Bedoya
+
+"""
+Gatewizard - A tool for membrane protein preparation and analysis.
+"""
+
+__version__ = "1.0.0"
+__author__ = "Constanza González, Mauricio Bedoya"
+__email__ = ""
+__license__ = "MIT"
+
+# Import main classes for easier access
+from gatewizard.core.preparation import (
+    run_propka,
+    extract_summary_section,
+    parse_summary_section,
+    modify_pdb_based_on_summary,
+)
+
+from gatewizard.core.builder import Builder
+from gatewizard.core.job_monitor import JobMonitor
+
+# GUI imports (optional, only if GUI dependencies are available)
+try:
+    from gatewizard.gui.app import ProteinViewerApp
+    GUI_AVAILABLE = True
+except ImportError:
+    GUI_AVAILABLE = False
+    ProteinViewerApp = None
+
+__all__ = [
+    "__version__",
+    "__author__",
+    "__email__",
+    "__license__",
+    "run_propka",
+    "extract_summary_section", 
+    "parse_summary_section",
+    "modify_pdb_based_on_summary",
+    "Builder",
+    "JobMonitor",
+    "GUI_AVAILABLE",
+]
+
+# Add ProteinViewerApp to __all__ if GUI is available
+if GUI_AVAILABLE:
+    __all__.append("ProteinViewerApp")

gatewizard-1.0.0/gatewizard/core/__init__.py

@@ -0,0 +1,29 @@
+"""
+Core functionality module for Gatewizard.
+
+This module contains the core business logic for protein preparation,
+system building, and job monitoring. It is independent of the GUI
+and can be used programmatically.
+"""
+
+from gatewizard.core.preparation import (
+    run_propka,
+    extract_summary_section,
+    parse_summary_section,
+    modify_pdb_based_on_summary,
+)
+
+from gatewizard.core.builder import Builder
+from gatewizard.core.job_monitor import JobMonitor, JobStatus
+from gatewizard.core.file_manager import FileManager
+
+__all__ = [
+    "run_propka",
+    "extract_summary_section",
+    "parse_summary_section", 
+    "modify_pdb_based_on_summary",
+    "Builder",
+    "JobMonitor",
+    "JobStatus",
+    "FileManager",
+]