vdw-surfgen
vdw-surfgen is a Python CLI tool to generate points on the van der Waals (VDW) surface of a molecule using its XYZ geometry file.
Surface points are generated at a scaled VDW radius and can be used for visualization, machine learning, or molecular modeling.
It is inspired by Robert T. McGibbon's pyvdwsurface.
🔧 Features
- 🧬 Read atomic coordinates from
.xyzfiles - ⚛️ Compute VDW surface points using Fibonacci sphere sampling
- 🔬 Set surface density (points per Ų)
- 💾 Save results as:
.xyzpseudo-atom file (always saved).txtcoordinate file (optional).png3D scatter plot (optional)
- 🎨 Beautiful colored terminal output with progress bars
- ⚡ Command-line interface (CLI) with full control
🚀 Installation
pip install vdw-surfgen
🔨Usage
# Basic usage (XYZ file always saved)
vsg molecule.xyz
# With additional formats and custom parameters
vsg molecule.xyz --scale 1.2 --density 2.0 --txt --img
Options:
--scale: Scale factor for VDW radii (default: 1.0)--density: Point density per Ų (default: 1.0)--txt: Save as TXT coordinate file--img: Save 3D visualization as PNG
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