Merge pull request #2 from connie/solvation-fix

Some more unit tests for solvation

Author: bslakman

rmgpy/data/solvationTest.py

@@ -100,9 +100,41 @@ def testLonePairSoluteGeneration(self):
 3 H u0 p0 c0 {1,S}
 """)
         species = Species(molecule=[molecule])
-	soluteData = self.database.getSoluteDataFromGroups(species)
+        soluteData = self.database.getSoluteDataFromGroups(species)
         self.assertTrue(soluteData is not None)
-
+        
+    @work_in_progress
+    def testSoluteDataGenerationAmmonia(self):
+        "Test we can obtain solute parameters via group additivity for ammonia"
+        molecule=Molecule().fromAdjacencyList(
+"""
+1 N u0 p1 c0 {2,S} {3,S} {4,S}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {1,S}
+""")
+        species = Species(molecule=[molecule])
+        soluteData = self.database.getSoluteDataFromGroups(species)
+        self.assertTrue(soluteData is not None)
+        
+    def testSoluteDataGenerationAmide(self):
+        "Test that we can obtain solute parameters via group additivity for an amide"        
+        molecule=Molecule().fromAdjacencyList(
+"""
+1  N u0 p1 {2,S} {3,S} {4,S}
+2   H   u0 {1,S}
+3   C u0 {1,S} {6,S} {7,S} {8,S}
+4   C  u0 {1,S} {5,D} {9,S}
+5   O  u0 p2 {4,D}
+6   H   u0 {3,S}
+7   H   u0 {3,S}
+8   H   u0 {3,S}
+9   H   u0 {4,S}
+""")
+        species = Species(molecule=[molecule])
+        soluteData = self.database.getSoluteDataFromGroups(species)
+        self.assertTrue(soluteData is not None)
+        
     def testRadicalandLonePairGeneration(self):
         """
         Test we can obtain solute parameters via group additivity for a molecule with both lone 
@@ -117,7 +149,7 @@ def testRadicalandLonePairGeneration(self):
 3 H u0 p0 c0 {2,S}
 """)
         species = Species(molecule=[molecule])
-	soluteData = self.database.getSoluteDataFromGroups(species)
+        soluteData = self.database.getSoluteDataFromGroups(species)
         self.assertTrue(soluteData is not None)
 
     def testCorrectionGeneration(self):

rmgpy/data/thermo.py

@@ -688,7 +688,7 @@ def getThermoDataFromLibraries(self, species, trainingSet=None):
             if thermoData is not None:
                 assert len(thermoData) == 3, "thermoData should be a tuple at this point"
                 if rmgpy.rmg.main.solvent is not None and trainingSet is None:
-                    thermoData[0].comment += 'Thermo library "corrected": ' + label
+                    thermoData[0].comment += 'Thermo library corrected for liquid phase: ' + label
                 else:
                     thermoData[0].comment += 'Thermo library: ' + label
                 return thermoData