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.

ChemicalSystem	A combination of Components that form a system
Transformation	Two chemical states with a method for estimating the free energy difference between them.
Component	Base class for an individual item in a larger chemical system
SmallMoleculeComponent	Component representing a small molecule, used for ligands and cofactors.
ProteinComponent	Component representing the contents of a PDB file, such as a protein.
ProteinMembraneComponent	Solvated PDB component with an explicit membrane and periodic box.
SolventComponent	Component representing solvation in a chemical system.
SolvatedPDBComponent	PDB component with explicit solvent and box vectors.

Chemical System Generators

EasyChemicalSystemGenerator

Generate consistent chemical systems given a SmallMoleculeComponent.