pymcce 0.2.0

Python implementation of core functions from Gunner Lab's MCCE

PyMCCE

Python implementation of core functions from Gunner Lab's MCCE

Overview

PyMCCE is a Python package that provides core functionality for molecular dynamics calculations and continuum electrostatics, inspired by the Multi-Conformation Continuum Electrostatics (MCCE) method from Gunner Lab.

Features

• Core MCCE Functions: Python implementation of essential MCCE algorithms
• MCCE Tools: MCCE tools: PBE solver, SAS calculator, PDB donwloader, etc

Installation

From PyPI (when available)

pip install pymcce

From Source

git clone https://github.com/newbooks/PyMCCE.git
cd PyMCCE
pip install -e .

Project Structure

├── CONTRIBUTING.md                       # How to develop code
├── docs                                  # Documentation source files
│   └── README.md                         # How to write and deploy documentation
├── LICENSE                               # License
├── Makefile                              # Shortcut commands using make utility
├── pyproject.toml                        # Pip packaging configuration
├── README.md                             # Readme
├── src                                   # Project source
│   └── pymcce                            # Main project pymcce
│       ├── cli.py                        # App commands
│       ├── core.py                       # Pseudo code like program flow for the app commands
│       ├── data                          # Data file: default prm and ftpl
│       │   ├── ftpl
│       │   │   ├── ala.ftpl
│       │   │   ├── arg.ftpl
│       │   │   ├── asn.ftpl
│       │   │   ├── asp.ftpl
│       │   └── prm
│       │       └── run.prm.default
│       ├── mcce.py                       # MCCE class - MCCE specific structure and functions
│       ├── __init__.py                   # Define accessible modules for other programs to import
│       └── utils.py                      # Support functions - Not protein structure related
└── tests

Development

Setting up Development Environment

1. Clone the repository:

   git clone https://github.com/newbooks/PyMCCE.git
   cd PyMCCE
   

2. Install in development mode:

   pip install -e .
   

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• Gunner Lab's MCCE for the original implementation
• The scientific computing community for the tools and libraries that make this work possible

Contact

• Author: Junjun Mao
• Email: [e-mail]
• GitHub: newbooks/PyMCCE

Roadmap

• Develop core MCCE algorithms — estimated 16 weeks
• Build MCCE tools — 4 weeks for pdbtools, 4 weeks for mccetools
• Write user documentation — estimated 2 weeks
• Prepare developer documentation — estimated 2 weeks
• Produce tutorial materials — estimated 2 weeks
• Optimize performance — ongoing