Source code for openff.evaluator.substances.amounts

An API for defining and creating substances.

import abc
import math
import typing

import numpy as np

from openff.evaluator.attributes import UNDEFINED, Attribute, AttributeClass

[docs]class Amount(AttributeClass, abc.ABC): """A representation of the amount of a given component in a `Substance`. """ value = Attribute( docstring="The value of this amount.", type_hint=typing.Union[float, int], read_only=True, )
[docs] def __init__(self, value=UNDEFINED): """ Parameters ---------- value: float or int The value of this amount. """ self._set_value("value", value)
@property def identifier(self): """A string identifier for this amount.""" raise NotImplementedError()
[docs] @abc.abstractmethod def to_number_of_molecules(self, total_substance_molecules, tolerance=None): """Converts this amount to an exact number of molecules Parameters ---------- total_substance_molecules: int The total number of molecules in the whole substance. This amount will contribute to a portion of this total number. tolerance: float, optional The tolerance with which this amount should be in. As an example, when converting a mole fraction into a number of molecules, the total number of molecules may not be sufficiently large enough to reproduce this amount. Returns ------- int The number of molecules which this amount represents, given the `total_substance_molecules`. """ raise NotImplementedError()
def __str__(self): return self.identifier def __repr__(self): return f"<{self.__class__.__name__} {str(self)}>" def __eq__(self, other): return type(self) is type(other) and np.isclose(self.value, other.value) def __ne__(self, other): return not (self == other) def __hash__(self): return hash(self.identifier)
[docs]class MoleFraction(Amount): """The mole fraction of a `Component` in a `Substance`.""" value = Attribute(docstring="The value of this amount.", type_hint=float) @property def identifier(self): return f"x={self.value:.6f}"
[docs] def to_number_of_molecules(self, total_substance_molecules, tolerance=None): # Determine how many molecules of each type will be present in the system. number_of_molecules = self.value * total_substance_molecules fractional_number_of_molecules = number_of_molecules % 1 if np.isclose(fractional_number_of_molecules, 0.5): number_of_molecules = int(number_of_molecules) else: number_of_molecules = int(round(number_of_molecules)) if number_of_molecules == 0: raise ValueError( "The total number of substance molecules was not large enough, " "such that this non-zero amount translates into zero molecules " "of this component in the substance." ) if tolerance is not None: mole_fraction = number_of_molecules / total_substance_molecules if abs(mole_fraction - self.value) > tolerance: raise ValueError( f"The mole fraction ({mole_fraction}) given a total number of molecules " f"({total_substance_molecules}) is outside of the tolerance {tolerance} " f"of the target mole fraction {self.value}" ) return number_of_molecules
[docs] def validate(self, attribute_type=None): super(MoleFraction, self).validate(attribute_type) if self.value <= 0.0 or self.value > 1.0: raise ValueError( "A mole fraction must be greater than zero, and less than or " "equal to one." ) if math.floor(self.value * 1e6) < 1: raise ValueError( "Mole fractions are only precise to the sixth " "decimal place within this class representation." )
[docs]class ExactAmount(Amount): """The exact number of instances of a `Component` in a `Substance`. An assumption is made that this amount is for a component which is infinitely dilute (such as ligands in binding calculations), and hence do not contribute to the total mole fraction of a `Substance`. """ value = Attribute(docstring="The value of this amount.", type_hint=int) @property def identifier(self): return f"n={int(round(self.value)):d}"
[docs] def to_number_of_molecules(self, total_substance_molecules, tolerance=None): return self.value