fix bug: check entry.item instead entry itself is LogicNode

also add an assertion test preventing child is same as parent

Author: KEHANG

testing/databaseTest.py

@@ -272,6 +272,7 @@ def kinetics_checkGroupsFoundInTree(self, family_name):
                 ascendParent = ascendParent.parent
                 nose.tools.assert_true(ascendParent is not None, "Group {group} in {family} family was found in the tree without a proper parent.".format(group=child, family=family_name))
                 nose.tools.assert_true(child in ascendParent.children, "Group {group} in {family} family was found in the tree without a proper parent.".format(group=nodeName, family=family_name))
+                nose.tools.assert_false(child is ascendParent, "Group {group} in {family} family is a parent to itself".format(group=nodeName, family=family_name))
 
     def kinetics_checkGroupsNonidentical(self, family_name):
         """
@@ -304,18 +305,21 @@ def kinetics_checkChildParentRelationships(self, family_name):
                 # This is a mistake in the database, but it should be caught by kinetics_checkGroupsFoundInTree
                 # so rather than report it twice or crash, we'll just silently carry on to the next node.
                 continue
+            elif parentNode in originalFamily.forwardTemplate.products:
+                #This is a product node made by training reactions which we do not need to check
+                continue
             # Check whether the node has proper parents unless it is the top reactant or product node
             # The parent should be more general than the child
             nose.tools.assert_true(family.matchNodeToChild(parentNode, childNode),
                             "In {family} family, group {parent} is not a proper parent of its child {child}.".format(family=family_name, parent=parentNode, child=nodeName))
 
             #check that parentNodes which are LogicOr do not have an ancestor that is a Group
             #If it does, then the childNode must also be a child of the ancestor
-            if isinstance(parentNode, LogicOr):
-                ancestorNode = childNode
-                while ancestorNode not in originalFamily.groups.top and isinstance(ancestorNode, LogicOr):
+            if isinstance(parentNode.item, LogicOr):
+                ancestorNode = parentNode
+                while ancestorNode not in originalFamily.groups.top and isinstance(ancestorNode.item, LogicOr):
                     ancestorNode = ancestorNode.parent
-                if isinstance(ancestorNode, Group):
+                if isinstance(ancestorNode.item, Group):
                     nose.tools.assert_true(family.matchNodeToChild(ancestorNode, childNode),
                                     "In {family} family, group {ancestor} is not a proper ancestor of its child {child}.".format(family=family_name, ancestor=ancestorNode, child=nodeName))
 
@@ -394,8 +398,6 @@ def kinetics_checkCdAtomType(self, family_name):
         family = self.database.kinetics.families[family_name]
         targetLabel=['Cd', 'CO', 'CS', 'Cdd']
         targetAtomTypes=[atomTypes[x] for x in targetLabel]
-        oxygen=[atomTypes['O']] + atomTypes['O'].specific
-        sulfur=[atomTypes['S']] + atomTypes['S'].specific
 
         #ignore product entries that get created from training reactions
         ignore=[]
@@ -426,8 +428,8 @@ def kinetics_checkCdAtomType(self, family_name):
                             #Ignore ligands that are not double bonded
                             if 'D' in bond.order:
                                 for ligAtomType in ligand.atomType:
-                                    if ligand.atomType[0] in oxygen: correctAtomList.append('CO')
-                                    elif ligand.atomType[0] in sulfur: correctAtomList.append('CS')
+                                    if ligand.atomType[0].isSpecificCaseOf(atomTypes['O']): correctAtomList.append('CO')
+                                    elif ligand.atomType[0].isSpecificCaseOf(atomTypes['S']): correctAtomList.append('CS')
 
                     #remove duplicates from correctAtom:
                     correctAtomList=list(set(correctAtomList))
@@ -451,6 +453,7 @@ def general_checkNodesFoundInTree(self, group_name, group):
                 ascendParent = ascendParent.parent
                 nose.tools.assert_true(ascendParent is not None, "Node {node} in {group} group was found in the tree without a proper parent.".format(node=child, group=group_name))
                 nose.tools.assert_true(child in ascendParent.children, "Node {node} in {group} group was found in the tree without a proper parent.".format(node=nodeName, group=group_name))
+                nose.tools.assert_false(child is ascendParent, "Node {node} in {group} is a parent to itself".format(node=nodeName, group=group_name))
 
     def general_checkGroupsNonidentical(self, group_name, group):
         """
@@ -483,11 +486,11 @@ def general_checkChildParentRelationships(self, group_name, group):
 
             #check that parentNodes which are LogicOr do not have an ancestor that is a Group
             #If it does, then the childNode must also be a child of the ancestor
-            if isinstance(parentNode, LogicOr):
-                ancestorNode = childNode
-                while ancestorNode not in group.top and isinstance(ancestorNode, LogicOr):
+            if isinstance(parentNode.item, LogicOr):
+                ancestorNode = parentNode
+                while ancestorNode not in group.top and isinstance(ancestorNode.item, LogicOr):
                     ancestorNode = ancestorNode.parent
-                if isinstance(ancestorNode, Group):
+                if isinstance(ancestorNode.item, Group):
                     nose.tools.assert_true(group.matchNodeToChild(ancestorNode, childNode),
                                     "In {group} group, node {ancestor} is not a proper ancestor of its child {child}.".format(group=group_name, ancestor=ancestorNode, child=nodeName))
 
@@ -522,8 +525,6 @@ def general_checkCdAtomType(self, group_name, group):
         """
         targetLabel=['Cd', 'CO', 'CS', 'Cdd']
         targetAtomTypes=[atomTypes[x] for x in targetLabel]
-        oxygen=[atomTypes['O']] + atomTypes['O'].specific
-        sulfur=[atomTypes['S']] + atomTypes['S'].specific
 
         for entryName, entry in group.entries.iteritems():
             if isinstance(entry.item, Group):
@@ -543,8 +544,8 @@ def general_checkCdAtomType(self, group_name, group):
                             #Ignore ligands that are not double bonded
                             if 'D' in bond.order:
                                 for ligAtomType in ligand.atomType:
-                                    if ligand.atomType[0] in oxygen: correctAtomList.append('CO')
-                                    elif ligand.atomType[0] in sulfur: correctAtomList.append('CS')
+                                    if ligand.atomType[0].isSpecificCaseOf(atomTypes['O']): correctAtomList.append('CO')
+                                    elif ligand.atomType[0].isSpecificCaseOf(atomTypes['S']): correctAtomList.append('CS')
 
                     #remove duplicates from correctAtom:
                     correctAtomList=list(set(correctAtomList))