Change the way in which libraryOrder is handled for kinetics database.

Prior to this, libraryOrder listed all the libraries used in order of priority,
but did not indicate whether they are Seed mechs or reaction libraries.

Now, indicate this by setting libraryOrder as a list of tuples in the format
('library_label', LibraryType), where LibraryType is set to either 'Reaction Library'
or 'Seed'.  That way we can avoid trying to double generating reactions for the 'Seed'
library type (since they have already been added to the core).  This also gives us
more flexibility for treating the seeds and reaction libraries differently.

Author: connie

rmgpy/data/kinetics/__init__.py

@@ -62,7 +62,8 @@ def __init__(self):
         self.recommendedFamilies = {}
         self.families = {}
         self.libraries = {}
-        self.libraryOrder = []
+        self.libraryOrder = []     # a list of tuples in the format ('library_label', LibraryType),
+                                   # where LibraryType is set to either 'Reaction Library' or 'Seed'.  
         self.local_context = {
             'KineticsData': KineticsData,
             'Arrhenius': Arrhenius,
@@ -201,7 +202,7 @@ def loadLibraries(self, path, libraries=None):
         The `path` points to the folder of kinetics libraries in the database,
         and the libraries should be in files like :file:`<path>/<library>.py`.
         """
-        self.libraries = {}; self.libraryOrder = []
+        self.libraries = {}
 
         if libraries is not None:
             for library_name in libraries:
@@ -211,11 +212,12 @@ def loadLibraries(self, path, libraries=None):
                     library = KineticsLibrary(label=library_name)
                     library.load(library_file, self.local_context, self.global_context)
                     self.libraries[library.label] = library
-                    self.libraryOrder.append(library.label)
                 else:
                     raise IOError("Couldn't find kinetics library {0}".format(library_file))
-            assert (self.libraryOrder == libraries)
-        else:# load all the libraries you can find
+            # library order should've been set prior to this, with the given seed mechs and reaction libraries
+            assert (len(self.libraryOrder) == len(libraries))
+        else:# load all the libraries you can find (this cannot be activated in a normal RMG job.  Only activated when loading the database for other purposes)
+            self.libraryOrder = []
             for (root, dirs, files) in os.walk(os.path.join(path)):
                 for f in files:
                     name, ext = os.path.splitext(f)
@@ -226,7 +228,7 @@ def loadLibraries(self, path, libraries=None):
                         library = KineticsLibrary(label=label)
                         library.load(library_file, self.local_context, self.global_context)
                         self.libraries[library.label] = library
-                        self.libraryOrder.append(library.label)
+                        self.libraryOrder.append((library.label,'Reaction Library'))
 
     def save(self, path):
         """
@@ -348,8 +350,11 @@ def generateReactionsFromLibraries(self, reactants, products, **options):
         searches the depository.
         """
         reactionList = []
-        for label in self.libraryOrder:
-            reactionList.extend(self.generateReactionsFromLibrary(reactants, products, self.libraries[label], **options))
+        for label, libraryType in self.libraryOrder:
+            # Generate reactions from reaction libraries (no need to generate them from seeds)
+            if libraryType == "Reaction Library":
+                print 'generating reactions from library {0}'.format(label)
+                reactionList.extend(self.generateReactionsFromLibrary(reactants, products, self.libraries[label], **options))
         return reactionList
 
     def generateReactionsFromLibrary(self, reactants, products, library, **options):

rmgpy/data/rmg.py

@@ -139,17 +139,20 @@ def loadKinetics(self,
         `path` points to the top-level folder of the RMG kinetics database.
         """
         kineticsLibraries = []
-        if reactionLibraries is not None and seedMechanisms is not None:
-            kineticsLibraries.extend(seedMechanisms)
-            kineticsLibraries.extend(reactionLibraries)
-        elif reactionLibraries is not None and seedMechanisms is None:
-            kineticsLibraries.extend(reactionLibraries)
-        elif reactionLibraries is None and seedMechanisms is not None:
-            kineticsLibraries.extend(seedMechanisms)
-        else:
+        libraryOrder = []
+        if seedMechanisms is None and reactionLibraries is None:
             kineticsLibraries = None
-            
+        if seedMechanisms is not None:
+            for library in seedMechanisms:
+                kineticsLibraries.append(library)
+                libraryOrder.append((library,'Seed'))
+        if reactionLibraries is not None:
+            for library in reactionLibraries:
+                kineticsLibraries.append(library)
+                libraryOrder.append((library,'Reaction Library'))
+        
         self.kinetics = KineticsDatabase()
+        self.kinetics.libraryOrder = libraryOrder
         self.kinetics.load(path,
                            families=kineticsFamilies,
                            libraries=kineticsLibraries,