Merge pull request #124 from ReactionMechanismGenerator/siblingTest

Make polycyclic pass sibling parent testing

Author: nyee

input/thermo/groups/polycyclic.py

@@ -8480,6 +8480,20 @@
 tree(
 """
 L1: PolycyclicRing
+    L2: s2-3_5_5_5_ane
+    L2: s2-3_5d1_5_5_ene
+    L2: s2-3f0_5_5_5_ane
+    L2: s2-3f1_6_5_5_ane
+    L2: s2-3_5_5_5d1_ene
+    L2: s3-3_5_6_5_ane
+    L2: s2-4f1_5_6_7_ane
+    L2: s2-4f2_5_6_8_ane
+    L2: s2-2f1_5_5_2_ane
+    L2: s2-3f1_5_5_6_ane
+    L2: s2-4f0_5_5_6_ane
+    L2: s2-4f1_5_5_7_ane
+    L2: s4-3f1_6_6_6_ane
+    L2: s3-3f1_6_5_6_ane
     L2: s1_3_3
         L3: s1_3_3_ane
         L3: s1_3_3_ene
@@ -8581,9 +8595,9 @@
     L2: s2_3_5
         L3: s2_3_5_ane
         L3: s2_3_5_ene
-            L4: s2_3_5_ene_1
-            L4: s2_3_5_ene_side
             L4: s2_3_5_ene_1_side
+            L4: s2_3_5_ene_1
+            L4: s2_3_5_ene_side 
     L2: s2_3_6
         L3: s2_3_6_ane
         L3: s2_3_6_ene
@@ -8811,20 +8825,6 @@
             L4: s4_6_8_ene_7
         L3: s4_6_8_diene
             L4: s4_6_8_diene_7_9
-    L2: s2-3_5_5_5_ane
-    L2: s2-3_5d1_5_5_ene
-    L2: s2-3f0_5_5_5_ane
-    L2: s2-3f1_6_5_5_ane
-    L2: s2-3_5_5_5d1_ene
-    L2: s3-3_5_6_5_ane
-    L2: s2-4f1_5_6_7_ane
-    L2: s2-4f2_5_6_8_ane
-    L2: s2-2f1_5_5_2_ane
-    L2: s2-3f1_5_5_6_ane
-    L2: s2-4f0_5_5_6_ane
-    L2: s2-4f1_5_5_7_ane
-    L2: s4-3f1_6_6_6_ane
-    L2: s3-3f1_6_5_6_ane
 """
 )
 

testing/databaseTest.py

@@ -116,12 +116,11 @@ def test_thermo(self):
             self.compat_func_name = test_name
             yield test, group_name
 
-            if group_name != 'polycyclic':
-                test = lambda x: self.general_checkSiblingsForParents(group_name, group)
-                test_name = "Thermo groups {0}: sibling relationships are correct?".format(group_name)
-                test.description = test_name
-                self.compat_func_name = test_name
-                yield test, group_name
+            test = lambda x: self.general_checkSiblingsForParents(group_name, group)
+            test_name = "Thermo groups {0}: sibling relationships are correct?".format(group_name)
+            test.description = test_name
+            self.compat_func_name = test_name
+            yield test, group_name
 
             test = lambda x: self.general_checkCdAtomType(group_name, group)
             test_name = "Thermo groups {0}: Cd atomtype used correctly?".format(group_name)
@@ -323,6 +322,9 @@ def kinetics_checkChildParentRelationships(self, family_name):
     def kinetics_checkSiblingsForParents(self, family_name):
         """
         This test checks that siblings in a tree are not actually parent/child
+
+        See general_checkSiblingsForParents comments for more detailed description
+        of the test.
         """
         from rmgpy.data.base import Database
         originalFamily = self.database.kinetics.families[family_name]
@@ -335,12 +337,8 @@ def kinetics_checkSiblingsForParents(self, family_name):
             if node in originalFamily.forwardTemplate.products: continue
             for index, child1 in enumerate(node.children):
                 for child2 in node.children[index+1:]:
-                    #Don't check a node against itself
-                    if child1 is child2: continue
                     nose.tools.assert_false(family.matchNodeToChild(child1, child2),
                                             "In family {0}, node {1} is a parent of {2}, but they are written as siblings.".format(family_name, child1, child2))
-                    nose.tools.assert_false(family.matchNodeToChild(child2, child1),
-                                            "In family {0}, node {1} is a parent of {2}, but they are written as siblings.".format(family_name, child2, child1))
 
     def kinetics_checkAdjlistsNonidentical(self, database):
         """
@@ -495,17 +493,27 @@ def general_checkChildParentRelationships(self, group_name, group):
 
     def general_checkSiblingsForParents(self, group_name, group):
         """
-        This test checks that siblings in a tree are not actually parent/child
+        This test checks that siblings in a tree are not actually parent/child.
+
+        For example in a tree:
+
+        L1. A
+            L2. B
+            L2. C
+
+        This tests that C is not a child of B, which would make C inaccessible because
+        we always match B first.
+
+        We do not check that B is not a child of C becausethat does not cause accessibility
+        problems and may actually be necessary in some trees. For example, in the polycyclic
+        thermo groups B might be a tricyclic and C a bicyclic parent. Currently there is no
+        way to writes a bicyclic group that excludes an analogous tricyclic.
         """
         for nodeName, node in group.entries.iteritems():
             for index, child1 in enumerate(node.children):
                 for child2 in node.children[index+1:]:
-                    #Don't check a node against itself
-                    if child1 is child2: continue
                     nose.tools.assert_false(group.matchNodeToChild(child1, child2),
                                             "In {0} group, node {1} is a parent of {2}, but they are written as siblings.".format(group_name, child1, child2))
-                    nose.tools.assert_false(group.matchNodeToChild(child2, child1),
-                                            "In {0} group, node {1} is a parent of {2}, but they are written as siblings.".format(group_name, child2, child1))
 
     def general_checkCdAtomType(self, group_name, group):
         """