def kinetics_checkChildParentRelationships(self, family_name):
"""
This test checks that groups' parent-child relationships are correct in the database.
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, childNode in family.entries.iteritems():
#top nodes and product nodes don't have parents by definition, so they get an automatic pass:
if childNode in originalFamily.groups.top or childNode in originalFamily.forwardTemplate.products: continue
parentNode = childNode.parent
# 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):
ancestorNode = ancestorNode.parent
if isinstance(ancestorNode, 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))
def kinetics_checkChildParentRelationships(self, family_name):
"""
This test checks that groups' parent-child relationships are correct in the database.
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, childNode in family.entries.iteritems():
#top nodes and product nodes don't have parents by definition, so they get an automatic pass:
if childNode in originalFamily.groups.top or childNode in originalFamily.forwardTemplate.products:
continue
parentNode = childNode.parent
# 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):
ancestorNode = ancestorNode.parent
if isinstance(ancestorNode, 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))
def kinetics_checkSiblingsForParents(self, family_name):
"""
This test checks that siblings in a tree are not actually parent/child
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, node in family.entries.iteritems():
# Some families also construct a 2-level trees for the products
# (root with all entries down one level) We don't care about this
# tree as it is not used in searching, so we ignore products
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 written as a sibling of {2}, when it is actually a parent.".format(
family_name, child1, child2
),
)
nose.tools.assert_false(
family.matchNodeToChild(child2, child1),
"In family {0}, node {1} is written as a sibling of {2}, when it is actually a parent.".format(
family_name, child2, child1
),
)
def kinetics_checkSiblingsForParents(self, family_name):
"""
This test checks that siblings in a tree are not actually parent/child
"""
from rmgpy.data.base import Database
originalFamily = self.database.kinetics.families[family_name]
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, node in family.entries.iteritems():
#Some families also construct a 2-level trees for the products
#(root with all entries down one level) We don't care about this
#tree as it is not used in searching, so we ignore products
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 written as a sibling of {2}, when it is actually a parent."
.format(family_name, child1, child2))
nose.tools.assert_false(
family.matchNodeToChild(child2, child1),
"In family {0}, node {1} is written as a sibling of {2}, when it is actually a parent."
.format(family_name, child2, child1))