ChemicalSystem — OpenFE documentation

class openfe.setup.system.ChemicalSystem(components: Dict[str, Component], name: str | None = '')#

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

Create a node for an alchemical network.

Parameters:

components – The molecular representation of the chemical state, including connectivity and coordinates. Given as a dict with user-defined labels as keys, Components as values.
name – Optional identifier for the chemical state; included with the other attributes as part of the (hashable) graph node itself when the chemical state is added to an AlchemicalNetwork.

Methods

`as_protein_smallmolecule_solvent`
`as_smallmolecule_solvent`

Attributes

`components`	The molecular representation of the chemical system.
`name`	Optional identifier for the chemical system.
`total_charge`	Formal charge for the ChemicalSystem.

property components: dict[str, Component]#

The molecular representation of the chemical system.

Components include atomic connectivity and coordinates. This is a frozendict with user-defined labels as keys and Component instances as values.

property name#

Optional identifier for the chemical system.

Used as part of the (hashable) graph node itself when the chemical state is added to an AlchemicalNetwork.

ChemicalSystem#