Merge pull request #219 from pierrelb/new-style-adjacency-list

Update lone pairs and multiplicities for radicals saturated for HBI

Author: rwest

rmgpy/data/solvation.py

@@ -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)

rmgpy/data/thermo.py

@@ -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)

rmgpy/rmg/model.py

@@ -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)