vdw-surfgen 0.2

Generate van der Waals surface points from XYZ molecules

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 built on logic 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:
  • .txt coordinate file
  • .xyz pseudo-atom file
  • .png 3D scatter plot
• Command-line interface (CLI) with full control

🚀 Installation

pip install vdw-surfgen

🔨Usage

vsg molecule.xyz --scale 1 --density 2.0 --save_txt --save_xyz --save_img

soajagbe.