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Update lone pairs and multiplicities for radicals saturated for HBI #219

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Merged
merged 2 commits into from
May 28, 2014
Merged

Update lone pairs and multiplicities for radicals saturated for HBI #219

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76d34b7
Update lone pairs and multiplicity for qm calculation before HBI
pierrelb May 27, 2014
ba319ef
Update lone pairs and multiplicity for solvation corrections
pierrelb May 27, 2014
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2 changes: 2 additions & 0 deletions rmgpy/data/solvation.py
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Expand Up @@ -643,6 +643,8 @@ def estimateSoluteViaGroupAdditivity(self, molecule):
saturatedStruct.updateConnectivityValues()
saturatedStruct.sortVertices()
saturatedStruct.updateAtomTypes()
saturatedStruct.updateLonePairs()
saturatedStruct.multiplicity = saturatedStruct.getRadicalCount() + 1

# Get solute descriptor estimates for saturated form of structure
soluteData = self.estimateSoluteViaGroupAdditivity(saturatedStruct)
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2 changes: 2 additions & 0 deletions rmgpy/data/thermo.py
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Expand Up @@ -819,6 +819,8 @@ def estimateRadicalThermoViaHBI(self, molecule, stableThermoEstimator ):
saturatedStruct.updateConnectivityValues()
saturatedStruct.sortVertices()
saturatedStruct.updateAtomTypes()
saturatedStruct.updateLonePairs()
saturatedStruct.multiplicity = saturatedStruct.getRadicalCount() + 1

# Get thermo estimate for saturated form of structure
thermoData = stableThermoEstimator(saturatedStruct)
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1 change: 0 additions & 1 deletion rmgpy/rmg/model.py
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Expand Up @@ -129,7 +129,6 @@ def generateThermoData(self, database, thermoClass=NASA, quantumMechanics=None):
thermo = []
for molecule in self.molecule:
molecule.clearLabeledAtoms()
molecule.updateAtomTypes()
tdata = database.thermo.estimateRadicalThermoViaHBI(molecule, quantumMechanics.getThermoData)
if tdata is not None:
thermo.append(tdata)
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