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    • Select atoms
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    • ChemicalSystem Complete API
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  • Chemical System

Chemical SystemΒΆ

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.

  • 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
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