Chemical Systems and Components#

We describe a chemical system as being made up of one or more “components,” e.g., solvent, protein, or small molecule. The ChemicalSystem object joins components together into a simulation system.

Component

Base class for members of a ChemicalSystem.

SmallMoleculeComponent

Component representing a small molecule.

ProteinComponent

Component representing the contents of a PDB file, such as a protein.

SolventComponent

Component representing solvent molecules in a chemical system.

ChemicalSystem

A node of an alchemical network; represents a system of chemicals.

Chemical System Generators#

EasyChemicalSystemGenerator

Generate consistent chemical systems given a SmallMoleculeComponent.