Formating fixes to pass codevac

Removed some trailing white space. Already refactored three functions:

saturate_radicals
saturate_unfilled_valence
saturate_rng_bonds

from camel case to underscores as agreed upon for style.

Author: nyee

rmgpy/data/solvation.py

@@ -804,7 +804,7 @@ def estimateSoluteViaGroupAdditivity(self, molecule):
 
         # Now saturate radicals with H
         if sum([atom.radicalElectrons for atom in saturatedStruct.atoms]) > 0: # radical species
-            addedToRadicals = saturatedStruct.saturateRadicals()
+            addedToRadicals = saturatedStruct.saturate_radicals()
 
         # Saturated structure should now have no unpaired electrons, and only "expected" lone pairs
         # based on the valency

rmgpy/data/thermo.py

@@ -514,7 +514,7 @@ def splitBicyclicIntoSingleRings(bicyclic_submol):
     return [convertRingToSubMolecule(SSSR[0])[0],
                 convertRingToSubMolecule(SSSR[1])[0]]
 
-def saturateRingBonds(ring_submol):
+def saturate_ring_bonds(ring_submol):
     """
     Given a ring submolelcule (`Molecule`), makes a deep copy and converts non-single bonds 
     into single bonds, returns a new saturated submolecule (`Molecule`)
@@ -537,7 +537,7 @@ def saturateRingBonds(ring_submol):
                         bond_order = 1.5
                     mol0.addBond(Bond(atomsMapping[atom],atomsMapping[bondedAtom],order=bond_order))
 
-    mol0.saturateUnfilledValence()
+    mol0.saturate_unfilled_valence()
     mol0.updateAtomTypes()
     mol0.updateMultiplicity()
     mol0.updateConnectivityValues()
@@ -1404,7 +1404,7 @@ def estimateRadicalThermoViaHBI(self, molecule, stableThermoEstimator ):
 
         assert molecule.isRadical(), "Method only valid for radicals."
         saturatedStruct = molecule.copy(deep=True)
-        added = saturatedStruct.saturateRadicals()
+        added = saturatedStruct.saturate_radicals()
         saturatedStruct.props['saturated'] = True
 
         # Get thermo estimate for saturated form of structure
@@ -1680,7 +1680,7 @@ def __addPolyRingCorrectionThermoDataFromHeuristic(self, thermoData, polyring):
                     for aromaticBond in aromaticBonds:
                         aromaticBond.setOrderNum(1)
 
-                    submol.saturateUnfilledValence()
+                    submol.saturate_unfilled_valence()
                     submol.update
                     singleRingThermodata = self.__addRingCorrectionThermoDataFromTree(None, \
                                                 self.groups['ring'], submol, submol.atoms)[0]
@@ -1700,7 +1700,7 @@ def getBicyclicCorrectionThermoDataFromHeuristic(self, bicyclic):
         # saturate if the bicyclic has unsaturated bonds
         # otherwise return None
         bicyclic_submol = convertRingToSubMolecule(bicyclic)[0]
-        saturated_bicyclic_submol, alreadySaturated = saturateRingBonds(bicyclic_submol)
+        saturated_bicyclic_submol, alreadySaturated = saturate_ring_bonds(bicyclic_submol)
 
         if alreadySaturated:
             return None
@@ -1737,7 +1737,7 @@ def getBicyclicCorrectionThermoDataFromHeuristic(self, bicyclic):
                 for aromaticBond in aromaticBonds:
                     aromaticBond.setOrderNum(1)
 
-                submol.saturateUnfilledValence()
+                submol.saturate_unfilled_valence()
                 submol.update
                 single_ring_thermoData = self.__addRingCorrectionThermoDataFromTree(None,
                                             self.groups['ring'], submol, submol.atoms)[0]
@@ -1756,7 +1756,7 @@ def getBicyclicCorrectionThermoDataFromHeuristic(self, bicyclic):
                 for aromaticBond in aromaticBonds:
                     aromaticBond.setOrderNum(1)
 
-                submol.saturateUnfilledValence()
+                submol.saturate_unfilled_valence()
                 submol.update
                 single_ring_thermoData = self.__addRingCorrectionThermoDataFromTree(None,
                                             self.groups['ring'], submol, submol.atoms)[0]

rmgpy/data/thermoTest.py

@@ -1201,8 +1201,8 @@ def testSplitBicyclicIntoSingleRings1(self):
         single_ring_submol_a, single_ring_submol_b = sorted(single_ring_submols,
                                 key=lambda submol: len(submol.atoms))
 
-        single_ring_submol_a.saturateUnfilledValence()
-        single_ring_submol_b.saturateUnfilledValence()
+        single_ring_submol_a.saturate_unfilled_valence()
+        single_ring_submol_b.saturate_unfilled_valence()
 
         expected_submol_a = Molecule().fromSMILES('C1=CC1')
         expected_submol_a.updateConnectivityValues()
@@ -1231,8 +1231,8 @@ def testSplitBicyclicIntoSingleRings2(self):
         single_ring_submol_a, single_ring_submol_b = sorted(single_ring_submols,
                                 key=lambda submol: len(submol.atoms))
 
-        single_ring_submol_a.saturateUnfilledValence()
-        single_ring_submol_b.saturateUnfilledValence()
+        single_ring_submol_a.saturate_unfilled_valence()
+        single_ring_submol_b.saturate_unfilled_valence()
 
         expected_submol_a = Molecule().fromSMILES('C1=CC1')
         expected_submol_a.updateConnectivityValues()
@@ -1251,7 +1251,7 @@ def testSaturateRingBonds1(self):
         mol = Molecule().fromSMILES(smiles)
         ring_submol = convertRingToSubMolecule(mol.getDisparateRings()[1][0])[0]
 
-        saturated_ring_submol, alreadySaturated = saturateRingBonds(ring_submol)
+        saturated_ring_submol, alreadySaturated = saturate_ring_bonds(ring_submol)
 
         expected_saturated_ring_submol = Molecule().fromSMILES('C1CCC2C1C2')
 
@@ -1272,7 +1272,7 @@ def testSaturateRingBonds2(self):
         mol = spe.molecule[1]
         ring_submol = convertRingToSubMolecule(mol.getDisparateRings()[1][0])[0]
 
-        saturated_ring_submol, alreadySaturated = saturateRingBonds(ring_submol)
+        saturated_ring_submol, alreadySaturated = saturate_ring_bonds(ring_submol)
 
         expected_spe = Species().fromSMILES('C1=CC=C2CCCCC2=C1')
         expected_spe.generateResonanceIsomers()
@@ -1295,7 +1295,7 @@ def testSaturateRingBonds3(self):
         mol = spe.molecule[1]
         ring_submol = convertRingToSubMolecule(mol.getDisparateRings()[1][0])[0]
 
-        saturated_ring_submol, alreadySaturated = saturateRingBonds(ring_submol)
+        saturated_ring_submol, alreadySaturated = saturate_ring_bonds(ring_submol)
 
         expected_spe = Species().fromSMILES('C1=CC=C2CCCCC2=C1')
         expected_spe.generateResonanceIsomers()

rmgpy/data/transport.py

@@ -450,7 +450,7 @@ def estimateCriticalPropertiesViaGroupAdditivity(self, molecule):
 
             # Saturate structure by replacing all radicals with bonds to
             # hydrogen atoms
-            added = saturatedStruct.saturateRadicals()
+            saturatedStruct.saturate_radicals()
 
             # Get critical point contribution estimates for saturated form of structure
             criticalPoint = self.estimateCriticalPropertiesViaGroupAdditivity(saturatedStruct)

rmgpy/molecule/atomtypeTest.py

@@ -453,7 +453,7 @@ def testSulfurTypes(self):
         self.assertEqual(self.atomType(self.mol23, 1), 'S4sc')
         self.assertEqual(self.atomType(self.mol25, 2), 'S4d')
         self.assertEqual(self.atomType(self.mol26, 1), 'S4dc')
-        #self.assertEqual(self.atomType(self.mol27, 0), 'S4b') # RMG correctly can't represent heteroatoms in aromatics. See RMG-Py issue #982 
+        #self.assertEqual(self.atomType(self.mol27, 0), 'S4b') # RMG correctly can't represent heteroatoms in aromatics. See RMG-Py issue #982
         self.assertEqual(self.atomType(self.mol28, 1), 'S4dd')
         self.assertEqual(self.atomType(self.mol38, 1), 'S4dd')
         self.assertEqual(self.atomType(self.mol28, 4), 'S4t')

rmgpy/molecule/molecule.py

@@ -1657,7 +1657,7 @@ def getNetCharge(self):
             charge += atom.charge
         return charge
 
-    def saturateUnfilledValence(self, update = True):
+    def saturate_unfilled_valence(self, update = True):
         """
         Saturate the molecule by adding H atoms to any unfilled valence
         """
@@ -1666,7 +1666,7 @@ def saturateUnfilledValence(self, update = True):
         saturator.saturate(self.atoms)
         if update: self.update()
 
-    def saturateRadicals(self):
+    def saturate_radicals(self):
         """
         Saturate the molecule by replacing all radicals with bonds to hydrogen atoms.  Changes self molecule object.  
         """

rmgpy/molecule/moleculeTest.py

@@ -1468,7 +1468,7 @@ def testSaturateAromaticRadical(self):
 17 H u0 p0 c0 {6,S}
 """)
         saturated_molecule = indenyl.copy(deep=True)
-        saturated_molecule.saturateRadicals()
+        saturated_molecule.saturate_radicals()
         self.assertTrue(saturated_molecule.isIsomorphic(indene))
 
     def testMalformedAugmentedInChI(self):
@@ -2158,7 +2158,7 @@ def testSaturateUnfilleValence(self):
             if atom.isHydrogen(): hydrogens +=1
         self.assertEquals(hydrogens, 0)
 
-        test.saturateUnfilledValence()
+        test.saturate_unfilled_valence()
 
         hydrogens = 0
         for atom in test.atoms:
@@ -2177,7 +2177,7 @@ def testSaturateUnfilleValence(self):
             if atom.isHydrogen(): hydrogens +=1
         self.assertEquals(hydrogens, 0)
 
-        test.saturateUnfilledValence()
+        test.saturate_unfilled_valence()
 
         hydrogens = 0
         for atom in test.atoms:

rmgpy/test_data/testing_database/thermo/groups/gauche.py

@@ -9,7 +9,7 @@
 entry(
     index = 0,
     label = "CsOsCdSs",
-    group = 
+    group =
 """
 1 * [Cs,O2s,Cd,S2s] u0
 """,
@@ -20,7 +20,7 @@
         S298 = (0,'cal/(mol*K)'),
     ),
     shortDesc = u"""""",
-    longDesc = 
+    longDesc =
 u"""
 
 """,
@@ -29,7 +29,7 @@
 entry(
     index = 1,
     label = "Cs(RRRR)",
-    group = 
+    group =
 """
 1 * Cs u0
 """,

rmgpy/tools/uncertainty.py

@@ -38,7 +38,7 @@ def retrieveSaturatedSpeciesFromList(species, speciesList):
     molecule = species.molecule[0]
     assert molecule.isRadical(), "Method only valid for radicals."
     saturatedStruct = molecule.copy(deep=True)
-    saturatedStruct.saturateRadicals()
+    saturatedStruct.saturate_radicals()
     for otherSpecies in speciesList:
         if otherSpecies.isIsomorphic(saturatedStruct):
             return otherSpecies