SolventComponent

class openfe.setup.system.SolventComponent(*, smiles: str = 'O', positive_ion: str = 'Na+', negative_ion: str = 'Cl-', neutralize: bool = True, ion_concentration: unit.Quantity = <Quantity(0.15, 'molar')>)

Bases: Component

Component representing solvent molecules in a chemical system.

This component represents the abstract idea of the solvent and ions present around the other components, rather than a list of specific water molecules and their coordinates. This abstract representation is later made concrete by specific MD engine methods.

Parameters:

• smiles (str, optional) – smiles of the solvent, default ‘O’ (water)

• positive_ion (str) – the pair of ions which is used to neutralize (if neutralize=True) and bring the solvent to the required ionic concentration. Must be a positive and negative monoatomic ions, defaults “Na+”, “Cl-”

• negative_ion (str) – the pair of ions which is used to neutralize (if neutralize=True) and bring the solvent to the required ionic concentration. Must be a positive and negative monoatomic ions, defaults “Na+”, “Cl-”

• neutralize (bool, optional) – if the net charge on the chemical state is neutralized by the ions in this solvent component. Default True

• ion_concentration (openff-units.unit.Quantity, optional) – ionic concentration required, default 0.15 * unit.molar this must be supplied with units, e.g. “1.5 * unit.molar”

Examples

To create a sodium chloride solution at 0.2 molar concentration:

>>> s = SolventComponent(position_ion='Na', negative_ion='Cl',
...                      ion_concentration=0.2 * unit.molar)

Attributes

ion_concentration	Concentration of ions in the solvent state
name
negative_ion	The anion in the solvent state
neutralize	If the solvent neutralizes the system overall
positive_ion	The cation in the solvent state
smiles	SMILES representation of the solvent molecules
total_charge	Solvents don't have a formal charge defined so this returns None

property ion_concentration: Quantity

Concentration of ions in the solvent state

property name: str

property negative_ion: str | None

The anion in the solvent state

property neutralize: bool

If the solvent neutralizes the system overall

property positive_ion: str | None

The cation in the solvent state

property smiles: str

SMILES representation of the solvent molecules

property total_charge

Solvents don’t have a formal charge defined so this returns None