Structures and Data Model

Examples in this section focus on building, modifying, converting, and representing molecular or periodic structures in Python.

• Building Surfaces and Slabs
• Building Packed Systems with Packmol
• Breaking bonds in a ring molecule and modifying distances for NEB
• Substituting Functional Groups in Molecules
• Balancing Reaction Equations from Formulas and Structures
• 2D Reaction Schematics from PLAMS Molecules
• Complete guide to storing and converting PLAMS Molecules between Python libraries and file formats