def estimateThermoViaGroupAdditivityForSaturatedStructWithoutSymmetryCorrection(self, molecule):
"""
Return the set of thermodynamic parameters corresponding to a given
:class:`Molecule` object `molecule` by estimation using the group
additivity values. If no group additivity values are loaded, a
:class:`DatabaseError` is raised.
The entropy is not corrected for the symmetry of the molecule.
This should be done later by the calling function.
"""
assert not molecule.isRadical(), "This method is only for saturated non-radical species."
# For thermo estimation we need the atoms to already be sorted because we
# iterate over them; if the order changes during the iteration then we
# will probably not visit the right atoms, and so will get the thermo wrong
molecule.sortVertices()
# Create the ThermoData object
thermoData = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],"K"),
Cpdata = ([0.0,0.0,0.0,0.0,0.0,0.0,0.0],"J/(mol*K)"),
H298 = (0.0,"kJ/mol"),
S298 = (0.0,"J/(mol*K)"),
)
cyclic = molecule.isCyclic()
# Generate estimate of thermodynamics
for atom in molecule.atoms:
# Iterate over heavy (non-hydrogen) atoms
if atom.isNonHydrogen():
# Get initial thermo estimate from main group database
try:
self.__addGroupThermoData(thermoData, self.groups['group'], molecule, {'*':atom})
except KeyError:
logging.error("Couldn't find in main thermo database:")
logging.error(molecule)
logging.error(molecule.toAdjacencyList())
raise
# Correct for gauche and 1,5- interactions
if not cyclic:
try:
self.__addGroupThermoData(thermoData, self.groups['gauche'], molecule, {'*':atom})
except KeyError: pass
try:
self.__addGroupThermoData(thermoData, self.groups['int15'], molecule, {'*':atom})
except KeyError: pass
try:
self.__addGroupThermoData(thermoData, self.groups['other'], molecule, {'*':atom})
except KeyError: pass
# Do ring corrections separately because we only want to match
# each ring one time
if cyclic:
if molecule.getAllPolycyclicVertices():
# If the molecule has fused ring atoms, this implies that we are dealing
# with a polycyclic ring system, for which separate ring strain corrections may not
# be adequate. Therefore, we search the polycyclic thermo group corrections
# instead of adding single ring strain corrections within the molecule.
# For now, assume only one polycyclic RSC can be found per molecule
try:
self.__addGroupThermoData(thermoData, self.groups['polycyclic'], molecule, {})
except:
logging.error("Couldn't find in polycyclic ring database:")
logging.error(molecule)
logging.error(molecule.toAdjacencyList())
raise
else:
rings = molecule.getSmallestSetOfSmallestRings()
for ring in rings:
# Make a temporary structure containing only the atoms in the ring
# NB. if any of the ring corrections depend on ligands not in the ring, they will not be found!
try:
self.__addGroupThermoData(thermoData, self.groups['ring'], molecule, {})
except KeyError:
logging.error("Couldn't find in ring database:")
logging.error(ring)
logging.error(ring.toAdjacencyList())
raise
return thermoData
def estimateThermoViaGroupAdditivity(self, molecule):
"""
Return the set of thermodynamic parameters corresponding to a given
:class:`Molecule` object `molecule` by estimation using the group
additivity values. If no group additivity values are loaded, a
:class:`DatabaseError` is raised.
"""
# For thermo estimation we need the atoms to already be sorted because we
# iterate over them; if the order changes during the iteration then we
# will probably not visit the right atoms, and so will get the thermo wrong
molecule.sortVertices()
# Create the ThermoData object
thermoData = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],"K"),
Cpdata = ([0.0,0.0,0.0,0.0,0.0,0.0,0.0],"J/(mol*K)"),
H298 = (0.0,"kJ/mol"),
S298 = (0.0,"J/(mol*K)"),
)
if molecule.getRadicalCount() > 0: # radical species
return self.estimateRadicalThermoViaHBI(molecule, self.estimateThermoViaGroupAdditivity )
else: # non-radical species
cyclic = molecule.isCyclic()
# Generate estimate of thermodynamics
for atom in molecule.atoms:
# Iterate over heavy (non-hydrogen) atoms
if atom.isNonHydrogen():
# Get initial thermo estimate from main group database
try:
self.__addGroupThermoData(thermoData, self.groups['group'], molecule, {'*':atom})
except KeyError:
logging.error("Couldn't find in main thermo database:")
logging.error(molecule)
logging.error(molecule.toAdjacencyList())
raise
# Correct for gauche and 1,5- interactions
if not cyclic:
try:
self.__addGroupThermoData(thermoData, self.groups['gauche'], molecule, {'*':atom})
except KeyError: pass
try:
self.__addGroupThermoData(thermoData, self.groups['int15'], molecule, {'*':atom})
except KeyError: pass
try:
self.__addGroupThermoData(thermoData, self.groups['other'], molecule, {'*':atom})
except KeyError: pass
# Do ring corrections separately because we only want to match
# each ring one time
if cyclic:
if molecule.getAllPolycyclicVertices():
# If the molecule has fused ring atoms, this implies that we are dealing
# with a polycyclic ring system, for which separate ring strain corrections may not
# be adequate. Therefore, we search the polycyclic thermo group corrections
# instead of adding single ring strain corrections within the molecule.
# For now, assume only one polycyclic RSC can be found per molecule
try:
self.__addGroupThermoData(thermoData, self.groups['polycyclic'], molecule, {})
except:
logging.error("Couldn't find in polycyclic ring database:")
logging.error(molecule)
logging.error(molecule.toAdjacencyList())
raise
else:
rings = molecule.getSmallestSetOfSmallestRings()
for ring in rings:
# Make a temporary structure containing only the atoms in the ring
# NB. if any of the ring corrections depend on ligands not in the ring, they will not be found!
try:
self.__addGroupThermoData(thermoData, self.groups['ring'], molecule, {})
except KeyError:
logging.error("Couldn't find in ring database:")
logging.error(ring)
logging.error(ring.toAdjacencyList())
raise
# Correct entropy for symmetry number
molecule.calculateSymmetryNumber()
thermoData.S298.value_si -= constants.R * math.log(molecule.symmetryNumber)
return thermoData
def estimateRadicalThermoViaHBI(self, molecule, stableThermoEstimator ):
"""
Estimate the thermodynamics of a radical by saturating it,
applying the provided stableThermoEstimator method on the saturated species,
then applying hydrogen bond increment corrections for the radical
site(s) and correcting for the symmetry.
The stableThermoEstimator should NOT have already corrected for the symmetry of the
stable saturated molecule, because we do not "uncorrect" it.
I.e. stableThermoEstimator should be a method that overestimates the entropy by R*ln(symmetry).
"""
#TODO: check the validity of the above statement for QMThermo and databases.
assert molecule.isRadical(), "Method only valid for radicals."
# Make a copy of the structure so we don't change the original
saturatedStruct = molecule.copy(deep=True)
# Saturate structure by replacing all radicals with bonds to
# hydrogen atoms
added = {}
for atom in saturatedStruct.atoms:
for i in range(atom.radicalElectrons):
H = Atom('H')
bond = Bond(atom, H, 'S')
saturatedStruct.addAtom(H)
saturatedStruct.addBond(bond)
if atom not in added:
added[atom] = []
added[atom].append([H, bond])
atom.decrementRadical()
# Update the atom types of the saturated structure (not sure why
# this is necessary, because saturating with H shouldn't be
# changing atom types, but it doesn't hurt anything and is not
# very expensive, so will do it anyway)
saturatedStruct.updateConnectivityValues()
saturatedStruct.sortVertices()
saturatedStruct.updateAtomTypes()
saturatedStruct.updateLonePairs()
saturatedStruct.multiplicity = 1
# Get thermo estimate for saturated form of structure
try:
thermoData = stableThermoEstimator(saturatedStruct)
except AttributeError:
# Probably looking for thermo in a library
saturatedSpec = Species(molecule=[saturatedStruct])
thermoData = stableThermoEstimator(saturatedSpec)
if thermoData:
assert len(thermoData) == 3, "thermoData should be a tuple at this point: (thermoData, library, entry)"
thermoData = thermoData[0]
if thermoData is None:
# logging.info("Thermo data of saturated {0} of molecule {1} is None.".format(saturatedStruct, molecule))
return None
assert thermoData is not None, "Thermo data of saturated {0} of molecule {1} is None!".format(saturatedStruct, molecule)
# Correct entropy for symmetry number of radical structure
molecule.calculateSymmetryNumber()
thermoData.S298.value_si -= constants.R * math.log(molecule.symmetryNumber)
# For each radical site, get radical correction
# Only one radical site should be considered at a time; all others
# should be saturated with hydrogen atoms
for atom in added:
# Remove the added hydrogen atoms and bond and restore the radical
for H, bond in added[atom]:
saturatedStruct.removeBond(bond)
saturatedStruct.removeAtom(H)
atom.incrementRadical()
saturatedStruct.updateConnectivityValues()
try:
self.__addGroupThermoData(thermoData, self.groups['radical'], saturatedStruct, {'*':atom})
except KeyError:
logging.error("Couldn't find in radical thermo database:")
logging.error(molecule)
logging.error(molecule.toAdjacencyList())
raise
# Re-saturate
for H, bond in added[atom]:
saturatedStruct.addAtom(H)
saturatedStruct.addBond(bond)
atom.decrementRadical()
# Subtract the enthalpy of the added hydrogens
for H, bond in added[atom]:
thermoData.H298.value_si -= 52.103 * 4184
return thermoData
def estimateRadicalThermoViaHBI(self, molecule, stableThermoEstimator ):
"""
Estimate the thermodynamics of a radical by saturating it,
applying the provided stableThermoEstimator method on the saturated species,
then applying hydrogen bond increment corrections for the radical
site(s) and correcting for the symmetry.
"""
assert molecule.getRadicalCount() > 0, "Method only valid for radicals."
# Make a copy of the structure so we don't change the original
saturatedStruct = molecule.copy(deep=True)
# Saturate structure by replacing all radicals with bonds to
# hydrogen atoms
added = {}
for atom in saturatedStruct.atoms:
for i in range(atom.radicalElectrons):
H = Atom('H')
bond = Bond(atom, H, 'S')
saturatedStruct.addAtom(H)
saturatedStruct.addBond(bond)
if atom not in added:
added[atom] = []
added[atom].append([H, bond])
atom.decrementRadical()
# Update the atom types of the saturated structure (not sure why
# this is necessary, because saturating with H shouldn't be
# changing atom types, but it doesn't hurt anything and is not
# very expensive, so will do it anyway)
saturatedStruct.updateConnectivityValues()
saturatedStruct.sortVertices()
saturatedStruct.updateAtomTypes()
# Get thermo estimate for saturated form of structure
thermoData = stableThermoEstimator(saturatedStruct)
if thermoData is None:
logging.info("Thermo data of saturated {0} of molecule {1} is None.".format(saturatedStruct, molecule))
return None
assert thermoData is not None, "Thermo data of saturated {0} of molecule {1} is None!".format(saturatedStruct, molecule)
# Undo symmetry number correction for saturated structure
saturatedStruct.calculateSymmetryNumber()
thermoData.S298.value_si += constants.R * math.log(saturatedStruct.symmetryNumber)
# Correct entropy for symmetry number of radical structure
molecule.calculateSymmetryNumber()
thermoData.S298.value_si -= constants.R * math.log(molecule.symmetryNumber)
# For each radical site, get radical correction
# Only one radical site should be considered at a time; all others
# should be saturated with hydrogen atoms
for atom in added:
# Remove the added hydrogen atoms and bond and restore the radical
for H, bond in added[atom]:
saturatedStruct.removeBond(bond)
saturatedStruct.removeAtom(H)
atom.incrementRadical()
saturatedStruct.updateConnectivityValues()
try:
self.__addGroupThermoData(thermoData, self.groups['radical'], saturatedStruct, {'*':atom})
except KeyError:
logging.error("Couldn't find in radical thermo database:")
logging.error(molecule)
logging.error(molecule.toAdjacencyList())
raise
# Re-saturate
for H, bond in added[atom]:
saturatedStruct.addAtom(H)
saturatedStruct.addBond(bond)
atom.decrementRadical()
# Subtract the enthalpy of the added hydrogens
for H, bond in added[atom]:
thermoData.H298.value_si -= 52.103 * 4184
return thermoData
