Changed Ss and Sd to S2s and S2d

Author: alongd

documentation/source/users/rmg/database/thermo.rst

@@ -113,7 +113,7 @@ is organized in a hierarchical tree, and is defined at the bottom of the databas
 	        L3: Cb
 	            L4: Cb-H
 	            L4: Cb-Os
-	            L4: Cb-Ss
+	            L4: Cb-S2s
 	            L4: Cb-C
 	                L5: Cb-Cs
 	                L5: Cb-Cds

rmgpy/molecule/atomtypeTest.py

@@ -276,8 +276,8 @@ def testSulfurTypes(self):
         """
         Test that getAtomType() returns appropriate sulfur atom types.
         """
-        self.assertEqual(self.atomType(self.mol4, 8), 'Ss')
-        self.assertEqual(self.atomType(self.mol4, 10), 'Sd')
+        self.assertEqual(self.atomType(self.mol4, 8), 'S2s')
+        self.assertEqual(self.atomType(self.mol4, 10), 'S2d')
         self.assertEqual(self.atomType(self.mol21, 1), 'St')
 
     def testOtherTypes(self):

rmgpy/molecule/group.py

@@ -1383,7 +1383,7 @@ def createAndConnectAtom(self, atomtypes, connectingAtom, bondOrders):
 
     def addExplicitLigands(self):
         """
-        This function Od/Sd ligand to CO or CS atomtypes if they are not already there.
+        This function Od/S2d ligand to CO or CS atomtypes if they are not already there.
 
         Returns a 'True' if the group was modified otherwise returns 'False'
         """
@@ -1408,7 +1408,7 @@ def addExplicitLigands(self):
             if self.atoms[atomIndex].atomType[0] is atomTypes['CO']:
                 atomtypes = ['Od']
             elif self.atoms[atomIndex].atomType[0] is atomTypes['CS']:
-                atomtypes = ['Sd']
+                atomtypes = ['S2d']
             self.createAndConnectAtom(atomtypes, self.atoms[atomIndex], [2])
 
         return modified
@@ -1418,7 +1418,7 @@ def standardizeGroup(self):
         This function modifies groups to make them have a standard AdjList form.
 
         Currently it makes atomtypes as specific as possible and makes CO/CS atomtypes
-        have explicit Od/Sd ligands. Other functions can be added as necessary
+        have explicit Od/S2d ligands. Other functions can be added as necessary
 
         Returns a 'True' if the group was modified otherwise returns 'False'
         """

rmgpy/test_data/testing_database/kinetics/families/R_Addition_MultipleBond/groups.py

@@ -153,8 +153,8 @@
     label = "Sd_R",
     group = 
 """
-1 *1 Sd  u0 {2,D}
-2 *2 R!H u0 {1,D}
+1 *1 S2d  u0 {2,D}
+2 *2 R!H  u0 {1,D}
 """,
     kinetics = None,
 )
@@ -388,8 +388,8 @@
     label = "SsJ",
     group = 
 """
-1 *3 Ss u1 {2,S}
-2    R  u0 {1,S}
+1 *3 S2s u1 {2,S}
+2    R   u0 {1,S}
 """,
     kinetics = None,
 )