vdw-surfgen 0.3

Generate van der Waals surface points from XYZ files.

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 .xyz files
• ⚛️ Compute VDW surface points using Fibonacci sphere sampling
• 🔬 Set surface density (points per Ų)
• 💾 Save results as:
  • .xyz pseudo-atom file (always saved)
  • .txt coordinate file (optional)
  • .png 3D 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

Note:

• 🧬 .xyz files are always saved automatically
• 🎨 Enjoy beautiful colored output with progress bars!

🧪 Testing

A sample test file test.xyz (FMN molecule with 50 atoms) is included. You can use it to test the functionality:

vsg test.xyz --txt --img

soajagbe.