def generateThermoData(self, molecule):
"""
Determine the group additivity thermodynamic data for the given
`molecule`.
"""
thermoData = None
if sum([atom.radicalElectrons for atom in molecule.atoms]) > 0:
# 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('S')
saturatedStruct.addAtom(H)
saturatedStruct.addBond(atom, H, 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 = self.generateThermoData(saturatedStruct)
assert thermoData is not None, "Thermo data of saturated %s of molecule %s is None!" % (saturatedStruct, molecule)
# 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(atom, H)
saturatedStruct.removeAtom(H)
atom.incrementRadical()
saturatedStruct.updateConnectivityValues()
thermoData += self.__getThermoData(self.radicalDatabase, saturatedStruct, {'*':atom})
# Re-saturate
for H, bond in added[atom]:
saturatedStruct.addAtom(H)
saturatedStruct.addBond(atom, H, bond)
atom.decrementRadical()
# Subtract the enthalpy of the added hydrogens
for H, bond in added[atom]:
thermoData.H298 -= 52.103 * 4184
# Correct the entropy for the symmetry number
else:
# 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:
if thermoData is None:
thermoData = self.__getThermoData(self.groupDatabase, molecule, {'*':atom})
else:
thermoData += self.__getThermoData(self.groupDatabase, molecule, {'*':atom})
except KeyError:
print molecule
print molecule.toAdjacencyList()
raise
# Correct for gauche and 1,5- interactions
try:
thermoData += self.__getThermoData(self.gaucheDatabase, molecule, {'*':atom})
except KeyError: pass
try:
thermoData += self.__getThermoData(self.int15Database, molecule, {'*':atom})
except KeyError: pass
try:
thermoData += self.__getThermoData(self.otherDatabase, molecule, {'*':atom})
except KeyError: pass
# Do ring corrections separately because we only want to match
# each ring one time; this doesn't work yet
rings = molecule.getSmallestSetOfSmallestRings()
for ring in rings:
# Make a temporary structure containing only the atoms in the ring
ringStructure = Molecule()
for atom in ring: ringStructure.addAtom(atom)
for atom1 in ring:
for atom2 in ring:
if molecule.hasBond(atom1, atom2):
ringStructure.addBond(atom1, atom2, molecule.getBond(atom1, atom2))
# Get thermo correction for this ring
thermoData += self.__getThermoData(self.ringDatabase, ringStructure, {})
return thermoData
