Merge pull request #167 from bbuesser/master

Add and modify calls for generateTransportData() and add updateLonePairs to fix adjacency lists generated by fromSMILES

Author: rwest

rmgpy/molecule/molecule.py

@@ -1048,7 +1048,7 @@ def fromRDKitMol(self, rdkitmol):
         """
         # Below are the declared variables for cythonizing the module
         cython.declare(i=cython.int)
-        cython.declare(radicalElectrons=cython.int, spinMultiplicity=cython.int, charge=cython.int)
+        cython.declare(radicalElectrons=cython.int, spinMultiplicity=cython.int, charge=cython.int, lonePairs=cython.int)
         cython.declare(atom=Atom, atom1=Atom, atom2=Atom, bond=Bond)
 
         self.vertices = []
@@ -1076,7 +1076,7 @@ def fromRDKitMol(self, rdkitmol):
             # Process charge
             charge = rdkitatom.GetFormalCharge()
 
-            atom = Atom(element, radicalElectrons, spinMultiplicity, charge)
+            atom = Atom(element, radicalElectrons, spinMultiplicity, charge, '', 0)
             self.vertices.append(atom)
 
             # Add bonds by iterating again through atoms
@@ -1098,6 +1098,7 @@ def fromRDKitMol(self, rdkitmol):
 
         # Set atom types and connectivity values
         self.updateConnectivityValues()
+        self.updateLonePairs()
         self.updateAtomTypes()
 
         return self
@@ -1790,4 +1791,25 @@ def getRadicalAtoms(self):
             if atom.radicalElectrons > 0:
                 radicalAtomsList.append(atom)
         return radicalAtomsList
+    
+    def updateLonePairs(self):
+        """
+        Iterate through the atoms in the structure and calcualte the
+        number of lone electron pairs, assumin a neutral molecule.
+        """
+        for atom1 in self.vertices:
+            order = 0
+            if not atom1.isHydrogen():
+                for atom2, bond12 in atom1.edges.items():
+                    if bond12.isSingle():
+                        order = order + 1
+                    if bond12.isDouble():
+                        order = order + 2
+                    if bond12.isTriple():
+                        order = order + 3
+                        
+                atom1.lonePairs = 4 - atom1.radicalElectrons - order
+        
+            else:
+                atom1.lonePairs = 0
 

rmgpy/rmg/main.py

@@ -335,9 +335,6 @@ def initialize(self, args):
             # DON'T generate any more reactions for the seed species at this time
             for seedMechanism in self.seedMechanisms:
                 self.reactionModel.addSeedMechanismToCore(seedMechanism, react=False)
-            
-            for spec in self.reactionModel.core.species:
-                spec.generateTransportData(self.database)
 
             # Reaction libraries: add species and reactions from reaction library to the edge so
             # that RMG can find them if their rates are large enough

rmgpy/rmg/model.py

@@ -1278,6 +1278,7 @@ def addSeedMechanismToCore(self, seedMechanism, react=False):
             r, isNew = self.makeNewReaction(rxn) # updates self.newSpeciesList and self.newReactionlist
         for spec in self.newSpeciesList:
             if spec.reactive: spec.generateThermoData(database, quantumMechanics=self.quantumMechanics)
+            spec.generateTransportData(database)
         for spec in self.newSpeciesList:
             self.addSpeciesToCore(spec)
 
@@ -1327,6 +1328,7 @@ def addReactionLibraryToEdge(self, reactionLibrary):
             if not isNew: logging.info("This library reaction was not new: {0}".format(rxn))
         for spec in self.newSpeciesList:
             if spec.reactive: spec.generateThermoData(database, quantumMechanics=self.quantumMechanics)
+            spec.generateTransportData(database)
         for spec in self.newSpeciesList:
             self.addSpeciesToEdge(spec)