Added getAllSpecies() method to Network class.

This method provides an easy way to get a list containing all of the species
that participate in the pressure-dependent reaction network, including all
isomers, reactant and product channels, and even bath gas species. This is
already useful in output file writing; I expect it to be useful in other
situations as well.

Author: jwallen

rmgpy/measure/network.py

@@ -126,6 +126,24 @@ def containsSpecies(self, species):
                 if rxn.products[0] == species and species in self.explored: return True
         return False
 
+    def getAllSpecies(self):
+        """
+        Return a list of all unique species in the network, including all
+        isomers, reactant and product channels, and bath gas species.
+        """
+        speciesList = []
+        for isomer in self.isomers:
+            if isomer not in speciesList: speciesList.append(isomer)
+        for reactants in self.reactants:
+            for spec in reactants:
+                if spec not in speciesList: speciesList.append(spec)
+        for products in self.products:
+            for spec in products:
+                if spec not in speciesList: speciesList.append(spec)
+        for spec in self.bathGas:
+            if spec not in speciesList: speciesList.append(spec)
+        return speciesList
+    
     def getEnergyGrains(self, Emin, Emax, dE=0.0, Ngrains=0):
         """
         Return an array of energy grains that have a minimum of `Emin`, a

rmgpy/measure/output.py

@@ -132,21 +132,7 @@ def writeNetworkSpecies(f, network):
     object`f`. All isomer, reactant, product, and bath gas species are
     automatically written one time each.
     """
-
-    # Get list of all species in network
-    speciesList = []
-    for isomer in network.isomers:
-        if isomer not in speciesList: speciesList.append(isomer)
-    for reactants in network.reactants:
-        for spec in reactants:
-            if spec not in speciesList: speciesList.append(spec)
-    for products in network.products:
-        for spec in products:
-            if spec not in speciesList: speciesList.append(spec)
-    for spec in network.bathGas:
-        if spec not in speciesList: speciesList.append(spec)
-
-    for spec in speciesList:
+    for spec in network.getAllSpecies():
         writeSpecies(f, spec)
 
 def writeSpecies(f, spec):