- class openfe.ChemicalSystem(components: dict[str, gufe.components.component.Component], name: str | None = '')#
A combination of Components that form a system
Containing a combination of
SmallMoleculeComponent
,SolventComponent
andProteinComponent
, this object typically represents all the molecules in a simulation box.Used as a node for an
AlchemicalNetwork
.- Parameters:
components – The molecular representation of the chemical state, including connectivity and coordinates. Given as a dict with user-defined labels as keys,
Component
s 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
.
- property components: dict[str, gufe.components.component.Component]#
The individual components of the chemical system.
Components include atomic connectivity and coordinates. This is a dict 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
.
- property total_charge#
Formal charge for the ChemicalSystem.