Chemical System
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The ChemicalSystem class serves as a versatile representation of a
chemical system. It is designed to handle various types of chemical
structures, such as molecules, surfaces, or crystals.

Tip:

  For copy-pasteable "ChemicalSystem" workflows, start with Python
  Examples.

* Overview

* Read, write, file formats

* Atoms, Bonds, Elements, Electrostatic Embedding

  * Atoms

  * Bonds

  * Elements

  * Electrostatic Embedding

* Lattice, Periodic Boundary Conditions

  * The "lattice" attribute

  * Lattice class

  * ChemicalSystem methods for periodic systems

* Charge, mass, formula

* Combine and split

  * Combining two ChemicalSystems

  * Splitting ChemicalSystems into parts

* Geometry Manipulation

  * Internal coordinates manipulation policy

  * Distances between atoms

  * Angles

  * Dihedral angles

  * Translate, rotate, align, RMSD

  * Geometric center, moments of inertia

  * Perturb coordinates or lattice

  * Symmetry

* Comparison of systems

* Regions

* Select atoms

* ASE, RDKit and PLAMS

  * ASE Atoms

  * RDKit Molecule

  * PLAMS Molecule

* GUI and notebook integration

* ChemicalSystem Complete API

  * "ChemicalSystem"

  * "InternalCoordinateManipulationPolicy"

  * "Atom"

  * "Lattice"

  * "Bond"

  * "Bonds"
