lnb-mdt 1.0.1

Lipid Nanobubble Molecular Dynamics Toolkit

LNB-MDT v1.0

LNB-MDT (Lipid NanoBubble Molecular Dynamics Toolkit) is a comprehensive toolkit designed for molecular dynamics simulations of lipid nanobubbles.

Installation

Method 1: Install from PyPI (Recommended)

The easiest way to install LNB-MDT is using pip:

pip install lnb-mdt

Method 2: Install from Source

If you want to install the latest development version or contribute to the project:

# Clone the repository
git clone https://github.com/xinyuren-bio/LNB-MDT.git
cd LNB-MDT

# Install in editable mode
pip install -e .

Note: For editable installation, you need Python 3.7+ and pip. It's recommended to use a virtual environment:

# Create virtual environment (using conda)
conda create -n LNB-MDT python=3.11
conda activate LNB-MDT

# Or using venv
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install
pip install -e .

Verify Installation

After installation, verify that LNB-MDT is correctly installed:

# Check if command is available
LNB-MDT --help

# Or test in Python
python -c "import LNB_MDT; print('LNB-MDT installed successfully!')"

Quick Start

After installation, you can use LNB-MDT in two ways:

1. Command Line Interface (CLI)

# Launch GUI
LNB-MDT UI

# Run area analysis
LNB-MDT AREA --help

# Run with test data
LNB-MDT AREA -test

# Configure VMD path
LNB-MDT VMD --path /path/to/vmd

2. Python API

from LNB_MDT.analysis import Area
import MDAnalysis as mda

# Load trajectory
u = mda.Universe("system.gro", "trajectory.xtc")

# Run analysis
area_analysis = Area(u, {'DPPC': ['PO4'], 'CHOL': ['ROH']})
area_analysis.run()

Documentation

For detailed documentation, including installation guide, quick start, user guide, and command line tools, please visit:

📚 Read the Docs - LNB-MDT Documentation

File Structure

LNB-MDT/
├── main.py                 # Main program entry
├── requirements.txt        # Python dependencies
├── analysis/              # Analysis modules
│   ├── area.py           # Area analysis
│   ├── height.py         # Height analysis
│   ├── cluster.py        # Cluster analysis
│   ├── anisotropy.py     # Anisotropy analysis
│   ├── gyration.py       # Gyration analysis
│   ├── sz.py             # Sz order parameter analysis
│   └── density.py        # Density analysis (time and radius)
├── preparation/            # Preparation module
└── cases_lnb/             # Example lipid nanobubble data
    ├── lnb.gro           # Example topology file (Martini 3.0, DPPC:DAPC:CHOL=5:3:2)
    ├── lnb.xtc           # Example trajectory file (50-60 ns time window)
    └── README.md         # Example data description

License

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

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LNB-MDT v1.0 - Making lipid nanobubble simulations simpler and more efficient!