Simple code to convert a .xyz file to lammps topology. It basically guess the bonds and angles using cassadra. Bonds and angles with same atomic number are ignored (H-H or O-O are ignored, H-O-H works fine).
The current code pipeline is:
graph LR
A[.xyz with steps] --> B[extract last .xyz] --> C[split to two .xyz's, water and silica] --> D[.xyz to .pdb] --> É[use utils/pdb2lmp.py to generate the topologies]