"""
Model classes for physical properties.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import logging
import six
from .base import BaseModel, StringType, ListType, ModelType, SetType
from .units.temperature import TemperatureModel
from .units.length import LengthModel
from ..parse.cem import CompoundParser, CompoundHeadingParser, ChemicalLabelParser, CompoundTableParser, names_only, labels_only, roles_only
from ..parse.ir import IrParser
from ..parse.mp_new import MpParser
from ..parse.nmr import NmrParser
from ..parse.tg import TgParser
from ..parse.uvvis import UvvisParser
from ..parse.elements import R, I, Optional, W, Group, NoMatch
from ..parse.actions import merge, join
from ..model.units.quantity_model import QuantityModel, DimensionlessModel
from ..parse.auto import AutoTableParser, AutoSentenceParser
from ..parse.apparatus import ApparatusParser
log = logging.getLogger(__name__)
[docs]class Compound(BaseModel):
names = SetType(StringType(), parse_expression=names_only, updatable=True)
labels = SetType(StringType(), parse_expression=NoMatch(), updatable=True)
roles = SetType(StringType(), parse_expression=roles_only, updatable=True)
parsers = [CompoundParser(), CompoundHeadingParser(), ChemicalLabelParser(), CompoundTableParser()]
# parsers = [CompoundParser(), CompoundHeadingParser(), ChemicalLabelParser()]
# parsers = [CompoundParser()]
[docs] def merge(self, other):
"""Merge data from another Compound into this Compound."""
log.debug('Merging: %s and %s' % (self.serialize(), other.serialize()))
if type(other) != type(self):
return self
for k in self.keys():
if other[k] is not None:
if self[k] is not None:
for new_item in other[k]:
if new_item not in self[k]:
self[k].add(new_item)
log.debug('Result: %s' % self.serialize())
return self
@property
def is_unidentified(self):
if not self.names and not self.labels:
return True
return False
@property
def is_id_only(self):
"""Return True if identifier information only."""
for key, value in self.items():
if key not in {'names', 'labels', 'roles'} and value:
return False
if self.names or self.labels:
return True
return False
[docs] @classmethod
def update(cls, definitions, strict=True):
"""Update the Compound labels parse expression
Arguments:
definitions {list} -- list of definitions found in this element
"""
log.debug("Updating Compound")
for definition in definitions:
label = definition['label']
if strict:
new_label_expression = Group(W(label)('labels'))
else:
new_label_expression = Group(I(label)('labels'))
if not cls.labels.parse_expression:
cls.labels.parse_expression = new_label_expression
else:
cls.labels.parse_expression = cls.labels.parse_expression | new_label_expression
return
[docs] def construct_label_expression(self, label):
return W(label)('labels')
[docs]class Apparatus(BaseModel):
name = StringType()
parsers = [ApparatusParser()]
[docs]class UvvisPeak(BaseModel):
#: Peak value, i.e. wavelength
value = StringType()
#: Peak value units
units = StringType(contextual=True)
# Extinction value
extinction = StringType()
# Extinction units
extinction_units = StringType(contextual=True)
# Peak shape information (e.g. shoulder, broad)
shape = StringType()
[docs]class UvvisSpectrum(BaseModel):
solvent = StringType(contextual=True)
temperature = StringType(contextual=True)
temperature_units = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
peaks = ListType(ModelType(UvvisPeak))
compound = ModelType(Compound)
parsers = [UvvisParser()]
[docs]class IrPeak(BaseModel):
value = StringType()
units = StringType(contextual=True)
strength = StringType()
bond = StringType()
[docs]class IrSpectrum(BaseModel):
solvent = StringType(contextual=True)
temperature = StringType(contextual=True)
temperature_units = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
peaks = ListType(ModelType(IrPeak))
compound = ModelType(Compound)
parsers = [IrParser()]
[docs]class NmrPeak(BaseModel):
shift = StringType()
intensity = StringType()
multiplicity = StringType()
coupling = StringType()
coupling_units = StringType(contextual=True)
number = StringType()
assignment = StringType()
[docs]class NmrSpectrum(BaseModel):
nucleus = StringType(contextual=True)
solvent = StringType(contextual=True)
frequency = StringType(contextual=True)
frequency_units = StringType(contextual=True)
standard = StringType(contextual=True)
temperature = StringType(contextual=True)
temperature_units = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
peaks = ListType(ModelType(NmrPeak))
compound = ModelType(Compound)
parsers = [NmrParser()]
[docs]class MeltingPoint(TemperatureModel):
solvent = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
compound = ModelType(Compound, contextual=True)
parsers = [MpParser()]
[docs]class GlassTransition(BaseModel):
"""A glass transition temperature."""
value = StringType()
units = StringType(contextual=True)
method = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
compound = ModelType(Compound)
parsers = [TgParser()]
[docs]class QuantumYield(BaseModel):
"""A quantum yield measurement."""
value = StringType()
units = StringType(contextual=True)
solvent = StringType(contextual=True)
type = StringType(contextual=True)
standard = StringType(contextual=True)
standard_value = StringType(contextual=True)
standard_solvent = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
temperature = StringType(contextual=True)
temperature_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
[docs]class FluorescenceLifetime(BaseModel):
"""A fluorescence lifetime measurement."""
value = StringType()
units = StringType(contextual=True)
solvent = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
temperature = StringType(contextual=True)
temperature_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
[docs]class ElectrochemicalPotential(BaseModel):
"""An oxidation or reduction potential, from cyclic voltammetry."""
value = StringType()
units = StringType(contextual=True)
type = StringType(contextual=True)
solvent = StringType(contextual=True)
concentration = StringType(contextual=True)
concentration_units = StringType(contextual=True)
temperature = StringType(contextual=True)
temperature_units = StringType(contextual=True)
apparatus = ModelType(Apparatus, contextual=True)
[docs]class NeelTemperature(TemperatureModel):
# expression = (I('T')+I('N')).add_action(merge)
expression = I('TN')
# specifier = I('TN')
specifier = StringType(parse_expression=expression, required=True, contextual=False, updatable=False)
compound = ModelType(Compound, required=False, contextual=False)
[docs]class CurieTemperature(TemperatureModel):
# expression = (I('T') + I('C')).add_action(merge)
expression = ((I('Curie') + R('^temperature(s)?$')) | R('T[Cc]\d?')).add_action(join)
specifier = StringType(parse_expression=expression, required=True, contextual=False, updatable=False)
compound = ModelType(Compound, required=False, contextual=False)
[docs]class InteratomicDistance(LengthModel):
specifier_expression = (R('^bond$') + R('^distance')).add_action(merge)
specifier = StringType(parse_expression=specifier_expression, required=False, contextual=True)
rij_label = R('^((X|Ac|Ag|Al|Am|Ar|As|At|Au|B|Ba|Be|Bh|Bi|Bk|Br|C|Ca|Cd|Ce|Cf|Cl|Cm|Cn|Co|Cr|Cs|Cu|Db|Ds|Dy|Er|Es|Eu|F|Fe|Fl|Fm|Fr|Ga|Gd|Ge|H|He|Hf|Hg|Ho|Hs|I|In|Ir|K|Kr|La|Li|Lr|Lu|Lv|Mc|Md|Mg|Mn|Mo|Mt|N|Na|Nb|Nd|Ne|Nh|Ni|No|Np|O|Og|Os|P|Pa|Pb|Pd|Pm|Po|Pr|Pt|Pu|Ra|Rb|Re|Rf|Rg|Rh|Rn|Ru|S|Sb|Sc|Se|Sg|Si|Sm|Sn|Sr|Ta|Tb|Tc|Te|Th|Ti|Tl|Tm|Ts|U|V|W|Xe|Y|Yb|Zn|Zr)\-?(X|Ac|Ag|Al|Am|Ar|As|At|Au|B|Ba|Be|Bh|Bi|Bk|Br|C|Ca|Cd|Ce|Cf|Cl|Cm|Cn|Co|Cr|Cs|Cu|Db|Ds|Dy|Er|Es|Eu|F|Fe|Fl|Fm|Fr|Ga|Gd|Ge|H|He|Hf|Hg|Ho|Hs|I|In|Ir|K|Kr|La|Li|Lr|Lu|Lv|Mc|Md|Mg|Mn|Mo|Mt|N|Na|Nb|Nd|Ne|Nh|Ni|No|Np|O|Og|Os|P|Pa|Pb|Pd|Pm|Po|Pr|Pt|Pu|Ra|Rb|Re|Rf|Rg|Rh|Rn|Ru|S|Sb|Sc|Se|Sg|Si|Sm|Sn|Sr|Ta|Tb|Tc|Te|Th|Ti|Tl|Tm|Ts|U|V|W|Xe|Y|Yb|Zn|Zr))$')
species = StringType(parse_expression=rij_label, required=True, contextual=False)
compound = ModelType(Compound, required=True, contextual=True)
another_label = StringType(parse_expression=R('^adgahg$'), required=False, contextual=False)
[docs]class CoordinationNumber(DimensionlessModel):
# something like NTi-O will not work with this, only work if there is space between the label and specifier
coordination_number_label = R('^((X|Ac|Ag|Al|Am|Ar|As|At|Au|B|Ba|Be|Bh|Bi|Bk|Br|C|Ca|Cd|Ce|Cf|Cl|Cm|Cn|Co|Cr|Cs|Cu|Db|Ds|Dy|Er|Es|Eu|F|Fe|Fl|Fm|Fr|Ga|Gd|Ge|H|He|Hf|Hg|Ho|Hs|I|In|Ir|K|Kr|La|Li|Lr|Lu|Lv|Mc|Md|Mg|Mn|Mo|Mt|N|Na|Nb|Nd|Ne|Nh|Ni|No|Np|O|Og|Os|P|Pa|Pb|Pd|Pm|Po|Pr|Pt|Pu|Ra|Rb|Re|Rf|Rg|Rh|Rn|Ru|S|Sb|Sc|Se|Sg|Si|Sm|Sn|Sr|Ta|Tb|Tc|Te|Th|Ti|Tl|Tm|Ts|U|V|W|Xe|Y|Yb|Zn|Zr)\-?(X|Ac|Ag|Al|Am|Ar|As|At|Au|B|Ba|Be|Bh|Bi|Bk|Br|C|Ca|Cd|Ce|Cf|Cl|Cm|Cn|Co|Cr|Cs|Cu|Db|Ds|Dy|Er|Es|Eu|F|Fe|Fl|Fm|Fr|Ga|Gd|Ge|H|He|Hf|Hg|Ho|Hs|I|In|Ir|K|Kr|La|Li|Lr|Lu|Lv|Mc|Md|Mg|Mn|Mo|Mt|N|Na|Nb|Nd|Ne|Nh|Ni|No|Np|O|Og|Os|P|Pa|Pb|Pd|Pm|Po|Pr|Pt|Pu|Ra|Rb|Re|Rf|Rg|Rh|Rn|Ru|S|Sb|Sc|Se|Sg|Si|Sm|Sn|Sr|Ta|Tb|Tc|Te|Th|Ti|Tl|Tm|Ts|U|V|W|Xe|Y|Yb|Zn|Zr))$')
# specifier = (R('^(N|n|k)$') | (I('Pair') + I('ij')).add_action(merge)
specifier_expression = R('^(N|n|k)$')
specifier = StringType(parse_expression=specifier_expression, required=True, contextual=True)
cn_label = StringType(parse_expression=coordination_number_label, required=True, contextual=True)
compound = ModelType(Compound, required=True, contextual=True)
[docs]class CNLabel(BaseModel):
# separate model to test automated parsing for stuff that are not quantities
coordination_number_label = R('^((X|Ac|Ag|Al|Am|Ar|As|At|Au|B|Ba|Be|Bh|Bi|Bk|Br|C|Ca|Cd|Ce|Cf|Cl|Cm|Cn|Co|Cr|Cs|Cu|Db|Ds|Dy|Er|Es|Eu|F|Fe|Fl|Fm|Fr|Ga|Gd|Ge|H|He|Hf|Hg|Ho|Hs|I|In|Ir|K|Kr|La|Li|Lr|Lu|Lv|Mc|Md|Mg|Mn|Mo|Mt|N|Na|Nb|Nd|Ne|Nh|Ni|No|Np|O|Og|Os|P|Pa|Pb|Pd|Pm|Po|Pr|Pt|Pu|Ra|Rb|Re|Rf|Rg|Rh|Rn|Ru|S|Sb|Sc|Se|Sg|Si|Sm|Sn|Sr|Ta|Tb|Tc|Te|Th|Ti|Tl|Tm|Ts|U|V|W|Xe|Y|Yb|Zn|Zr)\-?(X|Ac|Ag|Al|Am|Ar|As|At|Au|B|Ba|Be|Bh|Bi|Bk|Br|C|Ca|Cd|Ce|Cf|Cl|Cm|Cn|Co|Cr|Cs|Cu|Db|Ds|Dy|Er|Es|Eu|F|Fe|Fl|Fm|Fr|Ga|Gd|Ge|H|He|Hf|Hg|Ho|Hs|I|In|Ir|K|Kr|La|Li|Lr|Lu|Lv|Mc|Md|Mg|Mn|Mo|Mt|N|Na|Nb|Nd|Ne|Nh|Ni|No|Np|O|Og|Os|P|Pa|Pb|Pd|Pm|Po|Pr|Pt|Pu|Ra|Rb|Re|Rf|Rg|Rh|Rn|Ru|S|Sb|Sc|Se|Sg|Si|Sm|Sn|Sr|Ta|Tb|Tc|Te|Th|Ti|Tl|Tm|Ts|U|V|W|Xe|Y|Yb|Zn|Zr))$')
specifier = (I('Pair') + I('ij')).add_action(merge)
label_Juraj = StringType(parse_expression=coordination_number_label)
compound = ModelType(Compound, required=False)
parsers = [AutoSentenceParser(), AutoTableParser()]