Update lone pairs and multiplicity for qm calculation before HBI

The saturation of the radicals assigns the default value to
the lone pairs for the new hydrogen atoms (-100), and uses
the multiplicity for the radical molecule for the stable.

Without updating these attributes, the adjacency list
has an inconsistency and returns an error. This commit
should correct that issue.

Author: pierrelb

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)