gufe.components.solventcomponent

Classes

BaseSolventComponent(*args, **kwargs)	Base class for solvated components.
SolventComponent(*, smiles, positive_ion, ...)	Component representing solvation in a chemical system.

class gufe.components.solventcomponent.BaseSolventComponent(*args, **kwargs)

Base class for solvated components.

This base class is used both for explicitly solvated components and “abstractly” solvated components (i.e. SolventComponent).

abstract property name: str

abstract property total_charge: int | None

Net formal charge for the Component, if defined.

validate()

Validate this Component.

This method may be overridden by subclasses to implement component-specific consistency or sanity checks.

Implementations should raise an exception if validation fails. The base implementation performs no checks.

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

Component representing solvation 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)

property name: str

property smiles: str

SMILES representation of the solvent molecules

property positive_ion: str | None

The cation in the solvent state

property negative_ion: str | None

The anion in the solvent state

property neutralize: bool

If the solvent neutralizes the system overall

property ion_concentration: Quantity

Concentration of ions in the solvent state

validate()

Validate this Component.

This method may be overridden by subclasses to implement component-specific consistency or sanity checks.

Implementations should raise an exception if validation fails. The base implementation performs no checks.

property total_charge

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