Source code for openff.evaluator.substances.substances

An API for defining and creating substances.
import operator
from collections import defaultdict

import numpy as np
from openff.units import unit

from openff.evaluator.attributes import Attribute, AttributeClass
from openff.evaluator.substances import Amount, Component, ExactAmount, MoleFraction

[docs]class Substance(AttributeClass): """Defines the components, their amounts, and their roles in a system. Examples -------- A neat liquid containing only a single component: >>> from openff.evaluator.substances import Component, ExactAmount, MoleFraction >>> liquid = Substance() >>> liquid.add_component(Component(smiles='O'), MoleFraction(1.0)) A binary mixture containing two components, where the mole fractions are explicitly stated: >>> binary_mixture = Substance() >>> binary_mixture.add_component(Component(smiles='O'), MoleFraction(0.2)) >>> binary_mixture.add_component(Component(smiles='CO'), MoleFraction(0.8)) The infinite dilution of one molecule within a bulk solvent or mixture may also be specified by defining the exact number of copies of that molecule, rather than a mole fraction: >>> benzene = Component(smiles='C1=CC=CC=C1', role=Component.Role.Solute) >>> water = Component(smiles='O', role=Component.Role.Solvent) >>> >>> infinite_dilution = Substance() >>> infinite_dilution.add_component(component=benzene, amount=ExactAmount(1)) # Infinite dilution. >>> infinite_dilution.add_component(component=water, amount=MoleFraction(1.0)) In this example we explicitly flag benzene as being the solute and the water component the solvent. This enables workflow's to easily identify key molecules of interest, such as the molecule which should be 'grown' into solution during solvation free energy calculations. """ components = Attribute( docstring="A list of all of the components in this substance.", type_hint=tuple, default_value=tuple(), read_only=True, ) amounts = Attribute( docstring="the amounts of the component in this substance", type_hint=dict, default_value=dict(), read_only=True, ) @property def identifier(self): """str: A unique str representation of this substance, which encodes all components and their amounts in the substance.""" return self._get_identifier() @property def number_of_components(self): """int: The number of different components in this substance.""" return len(self.components) def _get_identifier(self): """Generates a unique string identifier for this substance, which encodes all components and their amounts in the substance Returns ------- str The string identifier. """ component_identifiers = [component.identifier for component in self.components] component_identifiers.sort() identifier_split = [] for component_identifier in component_identifiers: component_amounts = sorted( self.amounts[component_identifier], key=lambda x: type(x).__name__ ) amount_identifier = ",".join( [component_amount.identifier for component_amount in component_amounts] ) identifier = f"{component_identifier}{{{amount_identifier}}}" identifier_split.append(identifier) return "|".join(identifier_split)
[docs] @classmethod def from_components(cls, *components): """Creates a new `Substance` object from a list of components. This method assumes that all components should be present with equal mole fractions. Parameters ---------- components: Component or str The components to add to the substance. These may either be full `Component` objects or just the smiles representation of the component. Returns ------- Substance The substance containing the requested components in equal amounts. """ if len(components) == 0: raise ValueError("At least one component must be specified") mole_fraction = 1.0 / len(components) return_substance = cls() for component in components: if isinstance(component, str): component = Component(smiles=component) return_substance.add_component(component, MoleFraction(mole_fraction)) return return_substance
[docs] def add_component(self, component, amount): """Add a component to the Substance. If the component is already present in the substance, then the mole fraction will be added to the current mole fraction of that component. Parameters ---------- component : Component The component to add to the system. amount : Amount The amount of this component in the substance. """ assert isinstance(component, Component) assert isinstance(amount, Amount) component.validate() amount.validate() if isinstance(amount, MoleFraction): total_mole_fraction = amount.value for component_identifier in self.amounts: total_mole_fraction += sum( [ amount.value for amount in self.amounts[component_identifier] if isinstance(amount, MoleFraction) ] ) if np.isclose(total_mole_fraction, 1.0): total_mole_fraction = 1.0 if total_mole_fraction > 1.0: raise ValueError( f"The total mole fraction of this substance {total_mole_fraction} exceeds 1.0" ) if component.identifier not in self.amounts: components = (*self.components, component) self._set_value("components", components) existing_amount_of_type = None all_amounts = ( [] if component.identifier not in self.amounts else self.amounts[component.identifier] ) remaining_amounts = [] # Check to see if an amount of the same type already exists in # the substance, such that this amount should be appended to it. for existing_amount in all_amounts: if not type(existing_amount) is type(amount): remaining_amounts.append(existing_amount) continue existing_amount_of_type = existing_amount break if existing_amount_of_type is not None: # Append any existing amounts to the new amount. amount = type(amount)(existing_amount_of_type.value + amount.value) remaining_amounts.append(amount) amounts = dict(self.amounts) amounts[component.identifier] = tuple(remaining_amounts) self._set_value("amounts", amounts)
[docs] def get_amounts(self, component): """Returns the amounts of the component in this substance. Parameters ---------- component: str or Component The component (or it's identifier) to retrieve the amount of. Returns ------- tuple of Amount The amounts of the component in this substance. """ assert isinstance(component, str) or isinstance(component, Component) identifier = component if isinstance(component, str) else component.identifier return self.amounts[identifier]
[docs] def get_molecules_per_component( self, maximum_molecules, tolerance=None, count_exact_amount=True, truncate_n_molecules=True, ): """Returns the number of molecules for each component in this substance, given a maximum total number of molecules. Parameters ---------- maximum_molecules: int The maximum number of molecules. tolerance: float, optional The tolerance within which this amount should be represented. 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. count_exact_amount: bool Whether components present in an exact amount (i.e. defined with an ``ExactAmount``) should be considered when apply the maximum number of molecules constraint. This may be set false, for example, when building a separate solvated protein (n = 1) and solvated protein + ligand complex (n = 2) system but wish for both systems to have the same number of solvent molecules. truncate_n_molecules: bool Whether or not to attempt to truncate the number of molecules in the substance if the total number is over the specified maximum. If False, an exception will be raised in this case. The truncation works by iteratively removing one molecule of the predominant component up to a limit of removing a total number of molecules equal to the number of components in the substance (e.g. for a binary substance a maximum of two molecules can be removed). An exception is raised if the number of molecules cannot be sensibly truncated. Returns ------- dict of str and int A dictionary of molecule counts per component, where each key is a component identifier. """ remaining_molecule_slots = maximum_molecules for index, component in enumerate(self.components): amounts = self.amounts[component.identifier] for amount in amounts: if not isinstance(amount, ExactAmount) or not count_exact_amount: continue remaining_molecule_slots -= amount.value if remaining_molecule_slots < 0: raise ValueError( f"The required number of molecules {maximum_molecules - remaining_molecule_slots} " f"exceeds the provided maximum number ({maximum_molecules})." ) # Track the total number of molecules. n_molecules = defaultdict(int) # Track the number of molecules added from mole fraction amounts. n_mole_fractions = defaultdict(int) for component in self.components: for amount in self.amounts[component.identifier]: n_amount_molecules = amount.to_number_of_molecules( remaining_molecule_slots, tolerance ) n_molecules[component.identifier] += n_amount_molecules if isinstance(amount, MoleFraction): n_mole_fractions[component.identifier] += n_amount_molecules # Attempt to fix rounding issues which lead to more molecules being added than # the maximum. total_molecules = ( sum(n_molecules.values()) if count_exact_amount else sum(n_mole_fractions.values()) ) max_truncation_attempts = len(self.components) n_truncation_attempts = 0 while ( truncate_n_molecules and total_molecules > maximum_molecules and sum(n_mole_fractions.values()) > 0 and n_truncation_attempts < max_truncation_attempts ): largest_component = max( n_mole_fractions.items(), key=operator.itemgetter(1) )[0] n_molecules[largest_component] -= 1 n_mole_fractions[largest_component] -= 1 total_molecules = ( sum(n_molecules.values()) if count_exact_amount else sum(n_mole_fractions.values()) ) n_truncation_attempts += 1 if total_molecules > maximum_molecules: raise ValueError( f"The total number of molecules ({total_molecules}) exceeds the maximum " f"number ({maximum_molecules}). This should not be able to happen." ) return n_molecules
[docs] @staticmethod def calculate_aqueous_ionic_mole_fraction(ionic_strength): """Determines what mole fraction of ions is needed to yield an aqueous system of a given ionic strength. Parameters ---------- ionic_strength: openff.evaluator.unit.Quantity The ionic string in units of molar. Returns ------- float The mole fraction of ions. """ # Taken from YANK: # water_molarity = (998.23 * unit.gram / unit.litre) / ( 18.01528 * unit.gram / unit.mole ) ionic_mole_fraction = ionic_strength / (ionic_strength + water_molarity) return ionic_mole_fraction
def __str__(self): return self.identifier def __repr__(self): return f"<Substance {str(self)}>" def __hash__(self): return hash(self.identifier) def __eq__(self, other): return type(self) is type(other) and hash(self) == hash(other) def __ne__(self, other): return not (self == other) def __setstate__(self, state): # Handle the list -> tuple conversion manually. assert "amounts" in state for key in state["amounts"]: assert isinstance(state["amounts"][key], (list, tuple)) state["amounts"][key] = tuple(state["amounts"][key]) super(Substance, self).__setstate__(state) def __len__(self): return len(self.components) def __iter__(self): return iter(self.components)
[docs] def validate(self, attribute_type=None): super(Substance, self).validate(attribute_type) # Validate all of the components. assert all(isinstance(x, Component) for x in self.components) assert all(x.identifier in self.amounts for x in self.components) # Validate the amounts assert all(x.identifier in self.amounts for x in self.components) assert all(isinstance(x, tuple) for x in self.amounts.values()) assert all(len(x) > 0 for x in self.amounts.values()) for component in self.components: component.validate(attribute_type) amounts = self.amounts[component.identifier] assert all(isinstance(x, Amount) for x in amounts) for amount in amounts: amount.validate(attribute_type) contains_mole_fraction = any( isinstance(x, MoleFraction) for y in self.amounts.values() for x in y ) if contains_mole_fraction: total_mole_fraction = 0.0 for component_identifier in self.amounts: total_mole_fraction += sum( [ amount.value for amount in self.amounts[component_identifier] if isinstance(amount, MoleFraction) ] ) if not np.isclose(total_mole_fraction, 1.0): raise ValueError( f"The total mole fraction of this substance " f"({total_mole_fraction}) must equal 1.0" )