"""
An API for importing a ThermoML archive.
"""
import copy
import logging
import re
import traceback
from enum import unique, Enum
from urllib.error import HTTPError
from urllib.request import urlopen
from xml.etree import ElementTree
import numpy as np
from propertyestimator import unit
from propertyestimator.properties import PropertyPhase, MeasurementSource
from propertyestimator.substances import Substance
from propertyestimator.thermodynamics import ThermodynamicState
from propertyestimator.utils.openmm import openmm_quantity_to_pint
from .datasets import PhysicalPropertyDataSet
from .plugins import registered_thermoml_properties
def unit_from_thermoml_string(full_string):
"""A non-ideal way to convert a string to a propertyestimator.unit.Unit
Parameters
----------
full_string : str
The string to convert to a simtk Unit
Returns
----------
propertyestimator.unit.Unit
The parsed unit.
"""
full_string_split = full_string.split(',')
unit_string = full_string_split[1] if len(full_string_split) > 1 else ''
unit_string = unit_string.strip()
if unit_string == 'K':
return unit.kelvin
elif unit_string == '1/K':
return (1.0 / unit.kelvin).units
elif unit_string == 'kPa':
return unit.kilopascal
elif unit_string == 'kPa*dm3/mol':
return unit.kilopascal * unit.decimeter**3 / unit.mole
elif unit_string == 'kPa*kg/mol':
return unit.kilopascal * unit.kilogram / unit.mole
elif unit_string == 'kg/m3':
return unit.kilogram / unit.meter**3
elif unit_string == 'mol/kg':
return unit.mole / unit.kilogram
elif unit_string == 'mol/dm3':
return unit.mole / unit.decimeter ** 3
elif unit_string == 'kJ/mol':
return unit.kilojoule / unit.mole
elif unit_string == 'm3/kg':
return unit.meter ** 3 / unit.kilogram
elif unit_string == 'mol/m3':
return unit.mole / unit.meter ** 3
elif unit_string == 'm3/mol':
return unit.meter**3 / unit.mole
elif unit_string == 'J/K/mol':
return unit.joule / unit.kelvin / unit.mole
elif unit_string == 'J/K/kg':
return unit.joule / unit.kelvin / unit.kilogram
elif unit_string == 'J/K/m3':
return unit.joule / unit.kelvin / unit.meter ** 3
elif unit_string == '1/kPa':
return (1.0 / unit.kilopascal).units
elif unit_string == 'm/s':
return unit.meter / unit.second
elif unit_string == 'MHz':
return (1.0 / unit.megasecond).units
elif unit_string == 'N/m':
return unit.newton / unit.meter
elif len(unit_string) == 0:
return unit.dimensionless
else:
raise NotImplementedError('The unit (' + unit_string + ') is not currently supported')
def phase_from_thermoml_string(string):
"""Converts a ThermoML string to a PropertyPhase
Parameters
----------
string : str
The string to convert to a PropertyPhase
Returns
----------
PropertyPhase
The converted PropertyPhase
"""
phase_string = string.lower().strip()
phase = PropertyPhase.Undefined
if (phase_string == 'liquid' or
phase_string.find('fluid') >= 0 or phase_string.find('solution') >= 0):
phase = PropertyPhase.Liquid
elif phase_string.find('crystal') >= 0 and not phase_string.find('liquid') >= 0:
phase = PropertyPhase.Solid
elif phase_string.find('gas') >= 0:
phase = PropertyPhase.Gas
return phase
@unique
class ThermoMLConstraintType(Enum):
"""An enum containing the supported types of ThermoML constraints
"""
Undefined = 'Undefined'
Temperature = 'Temperature, K'
Pressure = 'Pressure, kPa'
ComponentMoleFraction = 'Mole fraction'
ComponentMassFraction = 'Mass fraction'
ComponentMolality = 'Molality, mol/kg'
SolventMoleFraction = 'Solvent: Mole fraction'
SolventMassFraction = 'Solvent: Mass fraction'
SolventMolality = 'Solvent: Molality, mol/kg'
@staticmethod
def from_node(node):
"""Converts either a ConstraintType or VariableType xml node to a ThermoMLConstraintType.
Parameters
----------
node : xml.etree.Element
The xml node to convert.
Returns
----------
ThermoMLConstraintType
The converted constraint type.
"""
try:
constraint_type = ThermoMLConstraintType(node.text)
except (KeyError, ValueError):
constraint_type = ThermoMLConstraintType.Undefined
if constraint_type == ThermoMLConstraintType.Undefined:
logging.debug(f'{node.tag}->{node.text} is an unsupported constraint type.')
return constraint_type
def is_composition_constraint(self):
"""Checks whether the purpose of this constraint is
to constrain the substance composition.
Returns
-------
bool
True if the constraint type is either a
- `ThermoMLConstraintType.ComponentMoleFraction`
- `ThermoMLConstraintType.ComponentMassFraction`
- `ThermoMLConstraintType.ComponentMolality`
- `ThermoMLConstraintType.SolventMoleFraction`
- `ThermoMLConstraintType.SolventMassFraction`
- `ThermoMLConstraintType.SolventMolality`
"""
return (self == ThermoMLConstraintType.ComponentMoleFraction or
self == ThermoMLConstraintType.ComponentMassFraction or
self == ThermoMLConstraintType.ComponentMolality or
self == ThermoMLConstraintType.SolventMoleFraction or
self == ThermoMLConstraintType.SolventMassFraction or
self == ThermoMLConstraintType.SolventMolality)
class ThermoMLConstraint:
"""A wrapper around a ThermoML Constraint node.
"""
def __init__(self):
self.type = ThermoMLConstraintType.Undefined
self.value = 0.0
self.solvents = []
# Describes which compound the variable acts upon.
self.compound_index = None
@classmethod
def from_node(cls, constraint_node, namespace):
"""Creates a ThermoMLConstraint from an xml node.
Parameters
----------
constraint_node : Element
The xml node to convert.
namespace : dict of str and str
The xml namespace.
Returns
----------
ThermoMLConstraint
The created constraint.
"""
# Extract the xml nodes.
type_node = constraint_node.find('.//ThermoML:ConstraintType/*', namespace)
value_node = constraint_node.find('./ThermoML:nConstraintValue', namespace)
solvent_index_nodes = constraint_node.find('./ThermoML:Solvent//ThermoML:nOrgNum', namespace)
compound_index_node = constraint_node.find('./ThermoML:ConstraintID/ThermoML:RegNum/*', namespace)
value = float(value_node.text)
# Determine what the default unit for this variable should be.
unit_type = unit_from_thermoml_string(type_node.text)
return_value = cls()
return_value.type = ThermoMLConstraintType.from_node(type_node)
return_value.value = value * unit_type
if compound_index_node is not None:
return_value.compound_index = int(compound_index_node.text)
if solvent_index_nodes is not None:
for solvent_index_node in solvent_index_nodes:
return_value.solvents.append(int(solvent_index_node))
return None if return_value.type is ThermoMLConstraintType.Undefined else return_value
@classmethod
def from_variable(cls, variable, value):
"""Creates a ThermoMLConstraint from an existing ThermoML variable definition.
Parameters
----------
variable : ThermoMLVariableDefinition
The variable to convert.
value : propertyestimator.unit.Quantity
The value of the constant.
Returns
----------
ThermoMLConstraint
The created constraint.
"""
return_value = cls()
return_value.type = variable.type
return_value.compound_index = variable.compound_index
return_value.solvents.extend(variable.solvents)
return_value.value = value
return return_value
class ThermoMLVariableDefinition:
"""A wrapper around a ThermoML Variable node.
"""
def __init__(self):
self.index = -1
self.type = ThermoMLConstraintType.Undefined
self.solvents = []
self.default_unit = None
# Describes which compound the variable acts upon.
self.compound_index = None
@classmethod
def from_node(cls, variable_node, namespace):
"""Creates a ThermoMLVariableDefinition from an xml node.
Parameters
----------
variable_node : xml.etree.Element
The xml node to convert.
namespace : dict of str and str
The xml namespace.
Returns
----------
ThermoMLVariableDefinition
The created variable definition.
"""
# Extract the xml nodes.
type_node = variable_node.find('.//ThermoML:VariableType/*', namespace)
index_node = variable_node.find('ThermoML:nVarNumber', namespace)
solvent_index_nodes = variable_node.find('./ThermoML:Solvent//ThermoML:nOrgNum', namespace)
compound_index_node = variable_node.find('./ThermoML:VariableID/ThermoML:RegNum/*', namespace)
return_value = cls()
return_value.default_unit = unit_from_thermoml_string(type_node.text)
return_value.index = int(index_node.text)
return_value.type = ThermoMLConstraintType.from_node(type_node)
if compound_index_node is not None:
return_value.compound_index = int(compound_index_node.text)
if solvent_index_nodes is not None:
for solvent_index_node in solvent_index_nodes:
return_value.solvents.append(int(solvent_index_node))
return None if return_value.type is ThermoMLConstraintType.Undefined else return_value
class ThermoMLPropertyUncertainty:
"""A wrapper around a ThermoML PropUncertainty node.
"""
# Reduce code redundancy by reusing this class for
# both property and combined uncertainties.
prefix = ''
def __init__(self):
self.index = -1
self.coverage_factor = None
@classmethod
def from_xml(cls, node, namespace):
"""Creates a ThermoMLPropertyUncertainty from an xml node.
Parameters
----------
node : Element
The xml node to convert.
namespace : dict of str and str
The xml namespace.
Returns
----------
ThermoMLCompound
The created property uncertainty.
"""
coverage_factor_node = node.find('ThermoML:n' + cls.prefix + 'CoverageFactor', namespace)
confidence_node = node.find('ThermoML:n' + cls.prefix + 'UncertLevOfConfid', namespace)
# As defined by https://www.nist.gov/pml/nist-technical-note-1297/nist-tn-1297-7-reporting-uncertainty
if coverage_factor_node is not None:
coverage_factor = float(coverage_factor_node.text)
elif confidence_node is not None and confidence_node.text == '95':
coverage_factor = 2
else:
return None
index_node = node.find('ThermoML:n' + cls.prefix + 'UncertAssessNum', namespace)
index = int(index_node.text)
return_value = cls()
return_value.coverage_factor = coverage_factor
return_value.index = index
return return_value
class ThermoMLCombinedUncertainty(ThermoMLPropertyUncertainty):
"""A wrapper around a ThermoML CombPropUncertainty node.
"""
prefix = 'Comb'
class ThermoMLCompound:
"""A wrapper around a ThermoML Compound node.
"""
def __init__(self):
self.smiles = None
self.index = -1
@staticmethod
def smiles_from_inchi_string(inchi_string):
"""Attempts to create a SMILES pattern from an inchi string.
Parameters
----------
inchi_string : str
The InChI string to convert.
Returns
----------
str, optional
None if the identifier cannot be converted, otherwise the converted SMILES pattern.
"""
from openeye import oechem
if inchi_string is None:
raise ValueError('The InChI string cannot be `None`.')
temp_molecule = oechem.OEMol()
if oechem.OEParseInChI(temp_molecule, inchi_string) is False:
raise ValueError('All InChI strings in ThermoML files must be valid.')
return oechem.OEMolToSmiles(temp_molecule)
@staticmethod
def smiles_from_thermoml_smiles_string(thermoml_string):
"""Attempts to create a SMILES pattern from a thermoml smiles string.
Parameters
----------
thermoml_string : str
The string to convert.
Returns
----------
str, optional
None if the identifier cannot be converted, otherwise the converted SMILES pattern.
"""
from openeye import oechem
if thermoml_string is None:
raise ValueError('The string cannot be `None`.')
temp_molecule = oechem.OEMol()
parse_smiles_options = oechem.OEParseSmilesOptions(quiet=True)
# Should make sure all smiles are OEChem consistent.
if oechem.OEParseSmiles(temp_molecule, thermoml_string, parse_smiles_options) is False:
raise ValueError('All SMILES strings in ThermoML files must be valid.')
return oechem.OEMolToSmiles(temp_molecule)
@staticmethod
def smiles_from_common_name(common_name):
"""Attempts to create a SMILES pattern from a common molecular name using
the `oechem.OEParseIUPACName` method.
Parameters
----------
common_name : str
The common name to convert.
Returns
----------
str, None
None if the identifier cannot be converted, otherwise the converted SMILES pattern.
"""
from openeye import oechem
from openeye import oeiupac
if common_name is None:
return None
temp_molecule = oechem.OEMol()
smiles = None
if oeiupac.OEParseIUPACName(temp_molecule, common_name) is True:
smiles = oechem.OEMolToSmiles(temp_molecule)
return smiles
@classmethod
def from_xml_node(cls, node, namespace):
"""Creates a ThermoMLCompound from an xml node.
Parameters
----------
node : Element
The xml node to convert.
namespace : dict of str and str
The xml namespace.
Returns
----------
ThermoMLCompound
The created compound wrapper.
"""
# Gather up all possible identifiers
inchi_identifier_nodes = node.findall('ThermoML:sStandardInChI', namespace)
smiles_identifier_nodes = node.findall('ThermoML:sSmiles', namespace)
common_identifier_nodes = node.findall('ThermoML:sCommonName', namespace)
if len(inchi_identifier_nodes) > 0 and inchi_identifier_nodes[0].text is not None:
# Convert InChI key to smiles.
smiles = cls.smiles_from_inchi_string(inchi_identifier_nodes[0].text)
elif len(smiles_identifier_nodes) > 0 and smiles_identifier_nodes[0].text is not None:
# Standardise the smiles pattern using OE.
smiles = cls.smiles_from_thermoml_smiles_string(smiles_identifier_nodes[0].text)
elif len(common_identifier_nodes) > 0 and common_identifier_nodes[0].text is not None:
# Standardise the smiles pattern using OE.
smiles = cls.smiles_from_common_name(common_identifier_nodes[0].text)
else:
logging.debug('A ThermoML:Compound node does not have a valid InChI identifier, '
'a valid SMILES pattern, or an understandable common name.')
return None
index_node = node.find('./ThermoML:RegNum/*', namespace)
if index_node is None:
raise ValueError('A ThermoML:Compound has a non-existent index')
compound_index = int(index_node.text)
return_value = cls()
return_value.smiles = smiles
return_value.index = compound_index
return return_value
class ThermoMLProperty:
"""A wrapper around a ThermoML Property node.
"""
class SoluteStandardState(Enum):
"""Describes the standard state of a solute.
"""
Undefined = 'Undefined',
InfiniteDilutionSolute = 'Infinite dilution solute',
PureCompound = 'Pure compound',
PureLiquidSolute = 'Pure liquid solute',
StandardMolality = 'Standard molality (1 mol/kg) solute',
@staticmethod
def from_node(node):
"""Converts an `eStandardState` node a `ThermoMLProperty.SoluteStandardState`.
Parameters
----------
node : xml.etree.Element
The xml node to convert.
Returns
----------
ThermoMLProperty.SoluteStandardState
The converted state type.
"""
try:
standard_state = ThermoMLProperty.SoluteStandardState(node.text)
except (KeyError, ValueError):
standard_state = ThermoMLProperty.SoluteStandardState.Undefined
if standard_state == ThermoMLConstraintType.Undefined:
logging.debug(f'{node.tag}->{node.text} is an unsupported '
f'solute standard state type.')
return standard_state
def __init__(self, base_type):
self.thermodynamic_state = None
self.phase = PropertyPhase.Undefined
self.substance = None
self.value = None
self.uncertainty = None
self.source = None
self.index = None
self.type = base_type
self.solute_standard_state = ThermoMLProperty.SoluteStandardState.Undefined
self.solvents = []
self.target_compound_index = None
self.property_uncertainty_definitions = {}
self.combined_uncertainty_definitions = {}
self.default_unit = None
self.target_compound_index = None
@property
def temperature(self):
"""propertyestimator.unit.Quantity or None: The temperature at which the property was collected."""
return None if self.thermodynamic_state is None else self.thermodynamic_state.temperature
@property
def pressure(self):
"""propertyestimator.unit.Quantity or None: The pressure at which the property was collected."""
return None if self.thermodynamic_state is None else self.thermodynamic_state.pressure
@staticmethod
def extract_uncertainty_definitions(node, namespace,
property_uncertainty_definitions,
combined_uncertainty_definitions):
"""Extract any property or combined uncertainties from a property xml node.
Parameters
----------
node : Element
The xml node to convert.
namespace : dict of str and str
The xml namespace.
property_uncertainty_definitions : list(ThermoMLPropertyUncertainty)
A list of the extracted property uncertainties.
combined_uncertainty_definitions : list(ThermoMLPropertyUncertainty)
A list of the extracted combined property uncertainties.
"""
property_nodes = node.findall('ThermoML:CombinedUncertainty', namespace)
for property_node in property_nodes:
if property_node is None:
continue
uncertainty_definition = ThermoMLCombinedUncertainty.from_xml(property_node, namespace)
if uncertainty_definition is None:
continue
combined_uncertainty_definitions[uncertainty_definition.index] = uncertainty_definition
property_nodes = node.findall('ThermoML:PropUncertainty', namespace)
for property_node in property_nodes:
if property_node is None:
continue
uncertainty_definition = ThermoMLPropertyUncertainty.from_xml(property_node, namespace)
if uncertainty_definition is None:
continue
property_uncertainty_definitions[uncertainty_definition.index] = uncertainty_definition
@classmethod
def from_xml_node(cls, node, namespace, parent_phases):
"""Creates a ThermoMLProperty from an xml node.
Parameters
----------
node : Element
The xml node to convert.
namespace : dict of str and str
The xml namespace.
parent_phases: PropertyPhase
The phases specfied in the parent PureOrMixtureData node.
Returns
----------
ThermoMLCompound
The created property.
"""
# Gather up all possible identifiers
index_node = node.find('ThermoML:nPropNumber', namespace)
property_index = int(index_node.text)
phase_node = node.find('./ThermoML:PropPhaseID//ThermoML:ePropPhase', namespace)
phase = PropertyPhase.Undefined | parent_phases
if phase_node is not None:
phase |= phase_from_thermoml_string(phase_node.text)
reference_phase_node = node.find('./ThermoML:RefPhaseID//ThermoML:eRefPhase', namespace)
if reference_phase_node is not None:
phase |= phase_from_thermoml_string(reference_phase_node.text)
if phase == PropertyPhase.Undefined:
logging.debug(f'A property was measured in an unsupported phase '
f'({phase_node.text}) and will be skipped.')
return None
property_group_node = node.find('./ThermoML:Property-MethodID//ThermoML:PropertyGroup//*', namespace)
property_name_node = property_group_node.find('./ThermoML:ePropName', namespace)
method_name_node = property_group_node.find('./ThermoML:eMethodName', namespace)
if method_name_node is None:
method_name_node = property_group_node.find('./ThermoML:sMethodName', namespace)
if method_name_node is None or property_name_node is None:
raise RuntimeError('A property does not have a name / method entry.')
if property_name_node.text not in registered_thermoml_properties:
logging.debug(f'An unsupported property was found '
f'({property_name_node.text}) and will be skipped.')
return None
registered_plugin = registered_thermoml_properties[property_name_node.text]
if (registered_plugin.supported_phases & phase) != phase:
logging.debug(f'The {property_name_node.text} property is currently only supported '
f'when measured in the {str(registered_plugin.supported_phases)} phase, '
f'and not the {str(phase)} phase.')
return None
return_value = cls(registered_plugin.class_type)
return_value.index = property_index
return_value.phase = phase
return_value.default_unit = unit_from_thermoml_string(property_name_node.text)
return_value.type = registered_plugin.class_type
return_value.method_name = method_name_node.text
property_uncertainty_definitions = {}
combined_uncertainty_definitions = {}
cls.extract_uncertainty_definitions(node, namespace,
property_uncertainty_definitions,
combined_uncertainty_definitions)
return_value.combined_uncertainty_definitions = combined_uncertainty_definitions
return_value.property_uncertainty_definitions = property_uncertainty_definitions
solvent_index_nodes = node.findall('./ThermoML:Solvent//ThermoML:nOrgNum', namespace)
if solvent_index_nodes is not None:
for solvent_index_node in solvent_index_nodes:
return_value.solvents.append(int(solvent_index_node.text))
# The solute standard state appears to describe which a solute should
# be present in only trace amounts. It only seems to be relevant for
# activity based properties.
standard_state_node = node.find('./ThermoML:eStandardState', namespace)
if standard_state_node is not None:
return_value.solute_standard_state = ThermoMLProperty.SoluteStandardState.from_node(standard_state_node)
# Property->Property-MethodID->RegNum describes which compound is referred
# to if the property is based on one of the compounds e.g. the activity
# coefficient of compound 2.
target_compound_node = node.find('./ThermoML:Property-MethodID/ThermoML:RegNum/ThermoML:nOrgNum', namespace)
if target_compound_node is not None:
return_value.target_compound_index = int(target_compound_node.text)
return return_value
def set_value(self, value, uncertainty):
"""Set the value and uncertainty of this property, adding units if necessary.
Parameters
----------
value : float, unit.Quantity
The value of the property
uncertainty : float
The uncertainty in the value.
"""
value_quantity = value
uncertainty_quantity = uncertainty
if not isinstance(value_quantity, unit.Quantity):
value_quantity = value * self.default_unit
if not isinstance(uncertainty_quantity, unit.Quantity):
uncertainty_quantity = uncertainty * self.default_unit
self.value = value_quantity
self.uncertainty = uncertainty_quantity
class ThermoMLPureOrMixtureData:
"""A wrapper around a ThermoML PureOrMixtureData node.
"""
@staticmethod
def extract_compound_indices(node, namespace, compounds):
"""Extract a list of ThermoMLCompounds from a PureOrMixtureData node.
Parameters
----------
node : Element
The xml node to read.
namespace : dict of str and str
The xml namespace.
compounds :
The extracted compounds.
"""
component_nodes = node.findall('ThermoML:Component', namespace)
compound_indices = []
# Figure out which compounds are going to be associated with
# the property entries.
for component_node in component_nodes:
index_node = component_node.find('./ThermoML:RegNum/*', namespace)
compound_index = int(index_node.text)
if compound_index not in compounds:
logging.debug('A PureOrMixtureData entry depends on an '
'unsupported compound and has been ignored')
return None
if compound_index in compound_indices:
raise RuntimeError('A ThermoML:PureOrMixtureData entry defines the same compound twice')
compound_indices.append(compound_index)
return compound_indices
@staticmethod
def extract_property_definitions(node, namespace, parent_phases):
"""Extract a list of ThermoMLProperty from a PureOrMixtureData node.
Parameters
----------
node : Element
The xml node to read.
namespace : dict of str and str
The xml namespace.
parent_phases: PropertyPhase
The phases specified by the parent PureOrMixtureData node.
Returns
----------
dict(int, ThermoMLProperty)
The extracted properties.
"""
property_nodes = node.findall('ThermoML:Property', namespace)
properties = {}
for property_node in property_nodes:
property_definition = ThermoMLProperty.from_xml_node(property_node, namespace, parent_phases)
if property_definition is None:
continue
if property_definition.index in properties:
raise RuntimeError('A ThermoML data set contains two '
'properties with the same index')
properties[property_definition.index] = property_definition
return properties
@staticmethod
def extract_global_constraints(node, namespace, compounds):
"""Extract a list of ThermoMLConstraint from a PureOrMixtureData node.
Parameters
----------
node : Element
The xml node to read.
namespace : dict of str and str
The xml namespace.
compounds : dict(int, ThermoMLCompound)
A dictionary of the compounds this PureOrMixtureData was calculated for.
Returns
----------
dict(int, ThermoMLConstraint)
The extracted constraints.
"""
constraint_nodes = node.findall('ThermoML:Constraint', namespace)
constraints = []
for constraint_node in constraint_nodes:
constraint = ThermoMLConstraint.from_node(constraint_node, namespace)
if constraint is None or constraint.type is ThermoMLConstraintType.Undefined:
logging.debug('An unsupported constraint has been ignored.')
return None
if constraint.compound_index is not None and \
constraint.compound_index not in compounds:
logging.debug('A constraint exists upon a non-existent compound and will be ignored.')
return None
if constraint.type.is_composition_constraint() and constraint.compound_index is None:
logging.debug('An unsupported constraint has been ignored - composition constraints'
'need to have a corresponding compound_index.')
return None
constraints.append(constraint)
return constraints
@staticmethod
def extract_variable_definitions(node, namespace, compounds):
"""Extract a list of ThermoMLVariableDefinition from a PureOrMixtureData node.
Parameters
----------
node : Element
The xml node to read.
namespace : dict of str and str
The xml namespace.
compounds : dict(int, ThermoMLCompound)
A dictionary of the compounds this PureOrMixtureData was calculated for.
Returns
----------
dict(int, ThermoMLVariableDefinition)
The extracted constraints.
"""
variable_nodes = node.findall('ThermoML:Variable', namespace)
variables = {}
for variable_node in variable_nodes:
variable = ThermoMLVariableDefinition.from_node(variable_node, namespace)
if variable is None or variable.type is ThermoMLConstraintType.Undefined:
logging.debug('An unsupported variable has been ignored.')
continue
if variable.compound_index is not None and \
variable.compound_index not in compounds:
logging.debug('A constraint exists upon a non-existent compound and will be ignored.')
continue
if variable.type.is_composition_constraint() and variable.compound_index is None:
logging.debug('An unsupported variable has been ignored - composition variables'
'need to have a corresponding compound_index.')
continue
variables[variable.index] = variable
return variables
@staticmethod
def calculate_uncertainty(node, namespace, property_definition):
# Look for a standard uncertainty..
uncertainty_node = node.find('.//ThermoML:nCombStdUncertValue', namespace)
if uncertainty_node is None:
uncertainty_node = node.find('.//ThermoML:nStdUncertValue', namespace)
# We have found a std. uncertainty
if uncertainty_node is not None:
return float(uncertainty_node.text)
# Try to calculate uncertainty from a coverage factor if present
if len(property_definition.combined_uncertainty_definitions) == 0 and \
len(property_definition.property_uncertainty_definitions) == 0:
return None
combined = len(property_definition.combined_uncertainty_definitions) > 0
prefix = ThermoMLCombinedUncertainty.prefix if combined \
else ThermoMLPropertyUncertainty.prefix
if combined:
index_node = node.find('./ThermoML:CombinedUncertainty/ThermoML:nCombUncertAssessNum', namespace)
else:
index_node = node.find('./ThermoML:PropUncertainty/ThermoML:nUncertAssessNum', namespace)
expanded_uncertainty_node = node.find('.//ThermoML:n' + prefix + 'ExpandUncertValue', namespace)
if index_node is None or expanded_uncertainty_node is None:
return None
expanded_uncertainty = float(expanded_uncertainty_node.text)
index = int(index_node.text)
if combined and index not in property_definition.combined_uncertainty_definitions:
return None
if not combined and index not in property_definition.property_uncertainty_definitions:
return None
divisor = property_definition.combined_uncertainty_definitions[index].coverage_factor if combined \
else property_definition.property_uncertainty_definitions[index].coverage_factor
return expanded_uncertainty / divisor
@staticmethod
def _smiles_to_molecular_weight(smiles):
"""Calculates the molecular weight of a substance specified
by a smiles string.
Parameters
----------
smiles: str
The smiles string to calculate the molecular weight of.
Returns
-------
propertyestimator.unit.Quantity
The molecular weight.
"""
from simtk import unit as simtk_unit
from openforcefield.topology import Molecule
try:
molecule = Molecule.from_smiles(smiles)
except Exception as e:
formatted_exception = traceback.format_exception(None, e, e.__traceback__)
raise ValueError(f'The toolkit raised an exception for the {smiles} smiles pattern: {formatted_exception}')
molecular_weight = 0.0 * simtk_unit.dalton
for atom in molecule.atoms:
molecular_weight += atom.mass
return openmm_quantity_to_pint(molecular_weight)
@staticmethod
def _solvent_mole_fractions_to_moles(solvent_mass, solvent_mole_fractions, solvent_compounds):
"""Converts a set of solvent mole fractions to moles for a
given mass of solvent.
Parameters
----------
solvent_mass: propertyestimator.unit.Quantity
The total mass of the solvent in units compatible with kg.
solvent_mole_fractions: dict of int and float
The mole fractions of any solvent compounds in the system.
solvent_compounds: dict of int and float
A dictionary of any solvent compounds in the system.
Returns
-------
dict of int and unit.Quantity
A dictionary of the moles of each solvent compound.
"""
weighted_molecular_weights = 0.0 * unit.gram / unit.mole
number_of_moles = {}
for solvent_index in solvent_compounds:
solvent_smiles = solvent_compounds[solvent_index].smiles
solvent_fraction = solvent_mole_fractions[solvent_index]
solvent_weight = ThermoMLPureOrMixtureData._smiles_to_molecular_weight(solvent_smiles)
weighted_molecular_weights += solvent_weight * solvent_fraction
total_solvent_moles = solvent_mass / weighted_molecular_weights
for solvent_index in solvent_compounds:
moles = solvent_mole_fractions[solvent_index] * total_solvent_moles
number_of_moles[solvent_index] = moles
return number_of_moles
@staticmethod
def _convert_mole_fractions(constraints, compounds, solvent_mole_fractions=None):
"""Converts a set of `ThermoMLConstraint` to mole fractions.
Parameters
----------
constraints: list of ThermoMLConstraint
The constraints to convert.
compounds: dict of int and ThermoMLCompound
The compounds in the system.
solvent_mole_fractions: dict of int and float
The mole fractions of any solvent compounds in the system,
where the total mole fraction of all solvents must be equal
to one.
Returns
-------
dict of int and float
A dictionary of compound indices and mole fractions.
"""
# noinspection PyTypeChecker
number_of_constraints = len(constraints)
mole_fractions = {}
total_mol_fraction = 0.0
for constraint in constraints:
mole_fraction = constraint.value
if isinstance(mole_fraction, unit.Quantity):
mole_fraction = mole_fraction.to(unit.dimensionless).magnitude
mole_fractions[constraint.compound_index] = mole_fraction
total_mol_fraction += mole_fractions[constraint.compound_index]
if ((number_of_constraints != len(compounds) and solvent_mole_fractions is not None) or
(number_of_constraints != len(compounds) - 1 and number_of_constraints != len(compounds) and
solvent_mole_fractions is None)):
raise ValueError(f'The number of mole fraction constraints ({number_of_constraints}) must be one '
f'less than or equal to the number of compounds being constrained ({len(compounds)}) '
f'if a solvent list is not present, otherwise there must be an equal number.')
# Handle the case were a single mole fraction constraint is missing.
if number_of_constraints == len(compounds) - 1:
for compound_index in compounds:
if compound_index in mole_fractions:
continue
mole_fractions[compound_index] = 1.0 - total_mol_fraction
# Recompute the total mole fraction to be safe.
total_mol_fraction = 0.0
for compound_index in mole_fractions:
total_mol_fraction += mole_fractions[compound_index]
# Account for any solvent present.
if solvent_mole_fractions is not None:
# Assume the remainder of the mole fraction is the solvent.
remaining_mole_fraction = 1.0 - total_mol_fraction
for solvent_index in solvent_mole_fractions:
mole_fractions[solvent_index] = solvent_mole_fractions[solvent_index] * remaining_mole_fraction
return mole_fractions
@staticmethod
def _convert_mass_fractions(constraints, compounds, solvent_mole_fractions=None, solvent_compounds=None):
"""Converts a set of `ThermoMLConstraint` to mole fractions.
Parameters
----------
constraints: list of ThermoMLConstraint
The constraints to convert.
compounds: dict of int and ThermoMLCompound
The compounds in the system.
solvent_mole_fractions: dict of int and float
The mole fractions of any solvent compounds in the system,
where the total mole fraction of all solvents must be equal
to one.
solvent_compounds: dict of int and float
A dictionary of any explicitly defined solvent compounds in the
system.
Returns
-------
dict of int and float
A dictionary of compound indices and mole fractions.
"""
# noinspection PyTypeChecker
number_of_constraints = len(constraints)
mass_fractions = {}
total_mass_fraction = 0.0
for constraint in constraints:
mass_fraction = constraint.value
if isinstance(mass_fraction, unit.Quantity):
mass_fraction = mass_fraction.to(unit.dimensionless).magnitude
mass_fractions[constraint.compound_index] = mass_fraction
total_mass_fraction += mass_fraction
if ((number_of_constraints != len(compounds) and solvent_mole_fractions is not None) or
(number_of_constraints != len(compounds) - 1 and number_of_constraints != len(compounds) and
solvent_mole_fractions is None)):
raise ValueError(f'The number of mass fraction constraints ({number_of_constraints}) must be one '
f'less than or equal to the number of compounds being constrained ({len(compounds)}) '
f'if a solvent list is not present, otherwise there must be an equal number.')
# Handle the case were a single mass fraction constraint is missing.
if number_of_constraints == len(compounds) - 1:
for compound_index in compounds:
if compound_index in mass_fractions:
continue
mass_fractions[compound_index] = (1.0 - total_mass_fraction)\
if isinstance(mass_fractions[compound_index], unit.Quantity):
mass_fractions[compound_index] = mass_fractions[compound_index].to(unit.dimensionless).magnitude
total_mass = 1 * unit.gram
total_solvent_mass = total_mass
moles = {}
total_moles = 0.0 * unit.mole
for compound_index in compounds:
compound_smiles = compounds[compound_index].smiles
compound_weight = ThermoMLPureOrMixtureData._smiles_to_molecular_weight(compound_smiles)
moles[compound_index] = total_mass * mass_fractions[compound_index] / compound_weight
total_moles += moles[compound_index]
total_solvent_mass -= total_mass * mass_fractions[compound_index]
if number_of_constraints == len(compounds) and solvent_mole_fractions is not None:
solvent_moles = ThermoMLPureOrMixtureData._solvent_mole_fractions_to_moles(total_solvent_mass,
solvent_mole_fractions,
solvent_compounds)
for solvent_index in solvent_moles:
moles[solvent_index] = solvent_moles[solvent_index]
total_moles += solvent_moles[solvent_index]
mole_fractions = {}
for compound_index in moles:
mole_fraction = moles[compound_index] / total_moles
mole_fractions[compound_index] = mole_fraction
return mole_fractions
@staticmethod
def _convert_molality(constraints, compounds, solvent_mole_fractions=None, solvent_compounds=None):
"""Converts a set of `ThermoMLConstraint` to mole fractions.
Parameters
----------
constraints: list of ThermoMLConstraint
The constraints to convert.
compounds: dict of int and ThermoMLCompound
The compounds in the system.
solvent_mole_fractions: dict of int and float
The mole fractions of any solvent compounds in the system,
where the total mole fraction of all solvents must be equal
to one.
solvent_compounds: dict of int and float
A dictionary of any explicitly defined solvent compounds in the
system.
Returns
-------
dict of int and float
A dictionary of compound indices and mole fractions.
"""
number_of_moles = {}
# noinspection PyTypeChecker
number_of_constraints = len(constraints)
mole_fractions = {}
total_number_of_moles = 0.0 * unit.moles
total_solvent_mass = 1.0 * unit.kilograms
for constraint in constraints:
molality = constraint.value
moles = molality * total_solvent_mass
number_of_moles[constraint.compound_index] = moles
total_number_of_moles += moles
if ((number_of_constraints != len(compounds) - 1 and solvent_mole_fractions is None) or
(number_of_constraints != len(compounds) and solvent_mole_fractions is not None)):
raise ValueError(f'The number of molality constraints ({number_of_constraints}) must be one '
f'less than the number of compounds being constrained ({len(compounds)}) if a '
f'solvent list is not present, otherwise there must be an equal number.')
if number_of_constraints == len(compounds) - 1 and solvent_mole_fractions is None:
# In this case, there is no explicit solvent entry and the last component
# whose molality has not been constrained is considered to be the 'solvent'
for compound_index in compounds:
if compound_index in number_of_moles:
continue
compound_smiles = compounds[compound_index].smiles
compound_weight = ThermoMLPureOrMixtureData._smiles_to_molecular_weight(compound_smiles)
moles = total_solvent_mass / compound_weight
number_of_moles[compound_index] = moles
total_number_of_moles += moles
elif number_of_constraints == len(compounds) and solvent_mole_fractions is not None:
solvent_moles = ThermoMLPureOrMixtureData._solvent_mole_fractions_to_moles(total_solvent_mass,
solvent_mole_fractions,
solvent_compounds)
for solvent_index in solvent_moles:
number_of_moles[solvent_index] = solvent_moles[solvent_index]
total_number_of_moles += solvent_moles[solvent_index]
for compound_index in number_of_moles:
mole_fraction = number_of_moles[compound_index] / total_number_of_moles
mole_fractions[compound_index] = mole_fraction
return mole_fractions
@staticmethod
def build_mixture(thermoml_property, constraints, compounds):
"""Build a Substance object from the extracted constraints and compounds.
Parameters
----------
thermoml_property: ThermoMLProperty
The property to which this mixture belongs.
constraints : list of ThermoMLConstraint
The ThermoML constraints.
compounds : dict of int and ThermoMLCompound
A dictionary of the compounds this PureOrMixtureData was calculated for.
Returns
----------
Substance
The constructed mixture.
"""
# TODO: We need to take into account `thermoml_property.target_compound_index` and
# `thermoml_property.solute_standard_state` to properly identify infinitely
# diluted solutes in the system (if any). Otherwise the solute will be
# assigned a mole fraction of zero.
solvent_constraint_type = ThermoMLConstraintType.Undefined
component_constraint_type = ThermoMLConstraintType.Undefined
solvent_indices = set()
for solvent_index in thermoml_property.solvents:
if solvent_index in solvent_indices:
continue
solvent_indices.add(solvent_index)
# Determine which types of solvent and component constraints are
# being applied.
for constraint in constraints:
# Make sure we hunt down solvent indices.
for solvent_index in constraint.solvents:
if solvent_index in solvent_indices:
continue
solvent_indices.add(solvent_index)
# Only composition type restraints apply here, skip
# the rest.
if not constraint.type.is_composition_constraint():
continue
if (constraint.type == ThermoMLConstraintType.SolventMassFraction or
constraint.type == ThermoMLConstraintType.SolventMoleFraction or
constraint.type == ThermoMLConstraintType.SolventMolality):
if solvent_constraint_type == ThermoMLConstraintType.Undefined:
solvent_constraint_type = constraint.type
if solvent_constraint_type != constraint.type:
logging.debug(f'A property with different types of solvent composition constraints '
f'was found - {solvent_constraint_type} vs {constraint.type}). This '
f'is likely a bug in the ThermoML file and so this property will be '
f'skipped.')
return None
else:
if component_constraint_type == ThermoMLConstraintType.Undefined:
component_constraint_type = constraint.type
if component_constraint_type != constraint.type:
logging.debug(f'A property with different types of composition constraints '
f'was found - {component_constraint_type} vs {constraint.type}). This '
f'is likely a bug in the ThermoML file and so this property will be '
f'skipped.')
return None
# If no constraint was applied, this very likely means a pure substance
# was found.
if (component_constraint_type == ThermoMLConstraintType.Undefined and
solvent_constraint_type == ThermoMLConstraintType.Undefined):
component_constraint_type = ThermoMLConstraintType.ComponentMoleFraction
elif (component_constraint_type == ThermoMLConstraintType.Undefined and
solvent_constraint_type != ThermoMLConstraintType.Undefined):
logging.debug(f'A property with only solvent composition '
f'constraints {solvent_constraint_type} was found.')
return None
solvent_mole_fractions = {}
solvent_constraints = [constraint for constraint in constraints if
constraint.type == solvent_constraint_type]
solvent_compounds = {}
for solvent_index in solvent_indices:
if solvent_index in compounds:
solvent_compounds[solvent_index] = compounds[solvent_index]
continue
logging.debug('The composition of a non-existent solvent was '
'found. This usually only occurs in cases were '
'the solvent component could not be understood '
'by the framework.')
return None
# Make sure all of the solvents have not been removed.
if solvent_constraint_type != ThermoMLConstraintType.Undefined and len(solvent_indices) == 0:
logging.debug('The composition of a solvent was found, however the '
'solvent list is empty. This usually only occurs in '
'cases were the solvent component could not be understood '
'by the framework.')
return None
remaining_constraints = [constraint for constraint in constraints if
constraint.type == component_constraint_type]
remaining_compounds = {}
for compound_index in compounds:
if compound_index in solvent_indices:
continue
remaining_compounds[compound_index] = compounds[compound_index]
# Determine the mole fractions of the solvent species, if any.
if solvent_constraint_type == ThermoMLConstraintType.SolventMoleFraction:
solvent_mole_fractions = ThermoMLPureOrMixtureData._convert_mole_fractions(solvent_constraints,
solvent_compounds)
elif solvent_constraint_type == ThermoMLConstraintType.SolventMassFraction:
solvent_mole_fractions = ThermoMLPureOrMixtureData._convert_mass_fractions(solvent_constraints,
solvent_compounds)
elif solvent_constraint_type == ThermoMLConstraintType.SolventMolality:
solvent_mole_fractions = ThermoMLPureOrMixtureData._convert_molality(solvent_constraints,
solvent_compounds)
elif solvent_constraint_type == ThermoMLConstraintType.Undefined:
solvent_mole_fractions = None
solvent_compounds = None
remaining_compounds = compounds
# Determine the mole fractions of the remaining compounds.
mole_fractions = {}
if component_constraint_type == ThermoMLConstraintType.ComponentMoleFraction:
mole_fractions = ThermoMLPureOrMixtureData._convert_mole_fractions(remaining_constraints,
remaining_compounds,
solvent_mole_fractions)
elif component_constraint_type == ThermoMLConstraintType.ComponentMassFraction:
mole_fractions = ThermoMLPureOrMixtureData._convert_mass_fractions(remaining_constraints,
remaining_compounds,
solvent_mole_fractions,
solvent_compounds)
elif component_constraint_type == ThermoMLConstraintType.ComponentMolality:
mole_fractions = ThermoMLPureOrMixtureData._convert_molality(remaining_constraints,
remaining_compounds,
solvent_mole_fractions,
solvent_compounds)
if len(mole_fractions) != len(compounds):
raise ValueError(f'The number of mole fractions ({len(mole_fractions)}) does not '
f'equal the total number of compounds ({len(compounds)})')
# Make sure we haven't picked up a dimensionless unit be accident.
for compound_index in mole_fractions:
if isinstance(mole_fractions[compound_index], unit.Quantity):
mole_fractions[compound_index] = mole_fractions[compound_index].to(unit.dimensionless).magnitude
total_mol_fraction = sum([value for value in mole_fractions.values()])
if not np.isclose(total_mol_fraction, 1.0):
raise ValueError(f'The total mole fraction {total_mol_fraction} is not equal to 1.0')
substance = Substance()
for compound_index in compounds:
compound = compounds[compound_index]
if np.isclose(mole_fractions[compound_index], 0.0):
continue
substance.add_component(component=Substance.Component(smiles=compound.smiles),
amount=Substance.MoleFraction(mole_fractions[compound_index]))
return substance
@staticmethod
def extract_measured_properties(node, namespace,
property_definitions,
global_constraints,
variable_definitions,
compounds):
"""Extract the measured properties defined by a ThermoML PureOrMixtureData node.
Parameters
----------
node : Element
The xml node to read.
namespace : dict of str and str
The xml namespace.
property_definitions
The extracted property definitions.
global_constraints
The extracted constraints.
variable_definitions
The extracted variable definitions.
compounds
The extracted compounds.
Returns
----------
list(MeasuredPhysicalProperty)
The extracted measured properties.
"""
value_nodes = node.findall('ThermoML:NumValues', namespace)
measured_properties = []
# Each value_node corresponds to one MeasuredProperty
for value_node in value_nodes:
constraints = []
temperature_constraint = None
pressure_constraint = None
for global_constraint in global_constraints:
constraint = copy.deepcopy(global_constraint)
constraints.append(constraint)
if constraint.type == ThermoMLConstraintType.Temperature:
temperature_constraint = constraint
elif constraint.type == ThermoMLConstraintType.Pressure:
pressure_constraint = constraint
# First extract the values of any variable constraints
variable_nodes = value_node.findall('ThermoML:VariableValue', namespace)
skip_entry = False
for variable_node in variable_nodes:
variable_index = int(variable_node.find('./ThermoML:nVarNumber', namespace).text)
if variable_index not in variable_definitions:
# The property was constrained by an unsupported variable and
# so will be skipped for now.
skip_entry = True
break
variable_definition = variable_definitions[variable_index]
variable_value = float(variable_node.find('ThermoML:nVarValue', namespace).text)
value_as_quantity = unit.Quantity(variable_value, variable_definition.default_unit)
"Convert the 'variable' into a full constraint entry"
constraint = ThermoMLConstraint.from_variable(variable_definition, value_as_quantity)
constraints.append(constraint)
if constraint.type == ThermoMLConstraintType.Temperature:
temperature_constraint = constraint
elif constraint.type == ThermoMLConstraintType.Pressure:
pressure_constraint = constraint
if skip_entry:
continue
# Extract the thermodynamic state that the property was measured at.
if temperature_constraint is None:
logging.debug('A property did not report the temperature or the pressure it '
'was measured at and will be ignored.')
continue
temperature = temperature_constraint.value
pressure = None if pressure_constraint is None else pressure_constraint.value
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure)
# Now extract the actual values of the measured properties, and their
# uncertainties
property_nodes = value_node.findall('ThermoML:PropertyValue', namespace)
for property_node in property_nodes:
property_index = int(property_node.find('./ThermoML:nPropNumber', namespace).text)
if property_index not in property_definitions:
# Most likely the property was dropped earlier due to an unsupported phase / type
continue
property_definition = property_definitions[property_index]
uncertainty = ThermoMLPureOrMixtureData.calculate_uncertainty(property_node,
namespace,
property_definition)
if uncertainty is None:
logging.debug('A property ({str(property_definition.type)}) '
'without uncertainties was ignored')
continue
measured_property = copy.deepcopy(property_definition)
# measured_property = json.loads(json.dumps(property_definition))
measured_property.thermodynamic_state = thermodynamic_state
property_value_node = property_node.find('.//ThermoML:nPropValue', namespace)
measured_property.set_value(float(property_value_node.text),
float(uncertainty))
mixture = ThermoMLPureOrMixtureData.build_mixture(measured_property,
constraints,
compounds)
if mixture is None:
continue
measured_property.substance = mixture
measured_properties.append(measured_property)
# By this point we now have the measured properties and the thermodynamic state
# they were measured at converted to standardised classes.
return measured_properties
@staticmethod
def from_xml_node(node, namespace, compounds):
"""Extracts all of the data in a ThermoML PureOrMixtureData node.
Parameters
----------
node : Element
The xml node to read.
namespace : dict of str and str
The xml namespace.
compounds : dict of int and ThermoMLCompound
A list of the already extracted `ThermoMLCompound`'s.
Returns
----------
list(MeasuredPhysicalProperty)
A list of extracted properties.
"""
# Figure out which compounds are going to be associated with
# the property entries.
compound_indices = ThermoMLPureOrMixtureData.extract_compound_indices(node, namespace, compounds)
if compound_indices is None:
# Most likely this entry depended on a non-parsable compound
# and will be skipped entirely
return None
if len(compound_indices) == 0:
logging.debug('A PureOrMixtureData entry with no compounds was ignored.')
return None
phase_nodes = node.findall('./ThermoML:PhaseID/ThermoML:ePhase', namespace)
all_phases = None
for phase_node in phase_nodes:
phase = phase_from_thermoml_string(phase_node.text)
if phase == PropertyPhase.Undefined:
logging.debug(f'A property was measured in an unsupported phase '
f'({phase_node.text}) and will be skipped.')
return None
all_phases = phase if all_phases is None else all_phases | phase
# Extract property definitions - values come later!
property_definitions = ThermoMLPureOrMixtureData.extract_property_definitions(node, namespace, all_phases)
if len(property_definitions) == 0:
return None
for property_index in property_definitions:
all_phases |= property_definitions[property_index].phase
property_definitions[property_index].phase |= all_phases
# Extract any constraints on the system e.g pressure, temperature
global_constraints = ThermoMLPureOrMixtureData.extract_global_constraints(node, namespace, compounds)
if global_constraints is None:
return None
# Extract any variables set on the system e.g pressure, temperature
# Only the definition entry and not the value of the variable is extracted
variable_definitions = ThermoMLPureOrMixtureData.extract_variable_definitions(node, namespace, compounds)
if len(global_constraints) == 0 and len(variable_definitions) == 0:
logging.debug('A PureOrMixtureData entry with no constraints was ignored.')
return None
used_compounds = {}
for compound_index in compounds:
if compound_index not in compound_indices:
continue
used_compounds[compound_index] = compounds[compound_index]
measured_properties = ThermoMLPureOrMixtureData.extract_measured_properties(node, namespace,
property_definitions,
global_constraints,
variable_definitions,
used_compounds)
return measured_properties
[docs]class ThermoMLDataSet(PhysicalPropertyDataSet):
"""A dataset of physical property measurements created from a ThermoML dataset.
Examples
--------
For example, we can use the DOI `10.1016/j.jct.2005.03.012` as a key
for retrieving the dataset from the ThermoML Archive:
>>> dataset = ThermoMLDataSet.from_doi('10.1016/j.jct.2005.03.012')
You can also specify multiple ThermoML Archive keys to create a dataset from multiple ThermoML files:
>>> thermoml_keys = ['10.1021/acs.jced.5b00365', '10.1021/acs.jced.5b00474']
>>> dataset = ThermoMLDataSet.from_doi(*thermoml_keys)
"""
[docs] def __init__(self):
"""Constructs a new ThermoMLDataSet object."""
super().__init__()
[docs] @classmethod
def from_doi(cls, *doi_list):
"""Load a ThermoML data set from a list of DOIs
Parameters
----------
doi_list : str
The list of DOIs to pull data from
Returns
-------
ThermoMLDataSet
The loaded data set.
"""
return_value = None
for doi in doi_list:
# E.g https://trc.nist.gov/ThermoML/10.1016/j.jct.2016.12.009.xml
doi_url = 'https://trc.nist.gov/ThermoML/' + doi + '.xml'
data_set = cls._from_url(doi_url, MeasurementSource(doi=doi))
if data_set is None or len(data_set.properties) == 0:
continue
if return_value is None:
return_value = data_set
else:
return_value.merge(data_set)
return return_value
[docs] @classmethod
def from_url(cls, *url_list):
"""Load a ThermoML data set from a list of URLs
Parameters
----------
url_list : str
The list of URLs to pull data from
Returns
-------
ThermoMLDataSet
The loaded data set.
"""
return_value = None
for url in url_list:
data_set = cls._from_url(url)
if data_set is None or len(data_set.properties) == 0:
continue
if return_value is None:
return_value = data_set
else:
return_value.merge(data_set)
return return_value
@classmethod
def _from_url(cls, url, source=None):
"""Load a ThermoML data set from a given URL
Parameters
----------
url : str
The URL to pull data from
source : Source, optional
An optional source which gives more information (e.g DOIs) for the url.
Returns
----------
ThermoMLDataSet
The loaded data set.
"""
if source is None:
source = MeasurementSource(reference=url)
return_value = None
try:
with urlopen(url) as response:
return_value = cls.from_xml(response.read(), source)
except HTTPError:
logging.warning('No ThermoML file could not be found at ' + url)
return return_value
[docs] @classmethod
def from_file(cls, *file_list):
"""Load a ThermoML data set from a list of files
Parameters
----------
file_list : str
The list of files to pull data from
Returns
-------
ThermoMLDataSet
The loaded data set.
"""
return_value = None
counter = 0
for file in file_list:
data_set = cls._from_file(file)
counter += 1
if data_set is None or len(data_set.properties) == 0:
continue
if return_value is None:
return_value = data_set
else:
return_value.merge(data_set)
return return_value
@classmethod
def _from_file(cls, path):
"""Load a ThermoML data set from a given file
Parameters
----------
path : str
The file path to pull data from
Returns
-------
ThermoMLDataSet
The loaded data set.
"""
source = MeasurementSource(reference=path)
return_value = None
try:
with open(path) as file:
return_value = ThermoMLDataSet.from_xml(file.read(), source)
except FileNotFoundError:
logging.warning('No ThermoML file could not be found at ' + path)
return return_value
[docs] @classmethod
def from_xml(cls, xml, source):
"""Load a ThermoML data set from an xml object.
Parameters
----------
xml : str
The xml string to parse.
source : Source
The source of the xml object.
Returns
-------
ThermoMLDataSet
The loaded ThermoML data set.
"""
root_node = ElementTree.fromstring(xml)
if root_node is None:
logging.warning('The ThermoML XML document could not be parsed.')
return None
if root_node.tag.find('DataReport') < 0:
logging.warning('The ThermoML XML document does not contain the expected root node.')
return None
# Extract the namespace that will prefix all type names
namespace_string = re.search(r'{.*\}', root_node.tag).group(0)[1:-1]
namespace = {'ThermoML': namespace_string}
return_value = ThermoMLDataSet()
compounds = {}
# Extract the base compounds present in the xml file
for node in root_node.findall('ThermoML:Compound', namespace):
compound = ThermoMLCompound.from_xml_node(node, namespace)
if compound is None:
continue
if compound.index in compounds:
raise RuntimeError('A ThermoML data set contains two '
'compounds with the same index')
compounds[compound.index] = compound
# Pull out any and all properties in the file.
for node in root_node.findall('ThermoML:PureOrMixtureData', namespace):
properties = ThermoMLPureOrMixtureData.from_xml_node(node,
namespace,
compounds)
if properties is None or len(properties) == 0:
continue
for measured_property in properties:
substance_id = measured_property.substance.identifier
if substance_id not in return_value._properties:
return_value._properties[substance_id] = []
if measured_property.type is None:
raise ValueError('An unexepected property type managed to slip through the cracks.')
final_property = measured_property.type()
final_property.value = measured_property.value
final_property.uncertainty = measured_property.uncertainty
final_property.phase = measured_property.phase
final_property.thermodynamic_state = measured_property.thermodynamic_state
final_property.substance = measured_property.substance
final_property.source = source
return_value._properties[substance_id].append(final_property)
return_value._sources.append(source)
return return_value