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Update the databasetest to be the same as RMG-Py's
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This fixes a problem with sibling test and adds the Cd test
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@nyee
nyee committed Jun 28, 2016
1 parent c1ef81e commit 2337eaf
Showing 1 changed file with 145 additions and 14 deletions.
159 changes: 145 additions & 14 deletions testing/databaseTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from copy import copy, deepcopy
from rmgpy.data.base import LogicOr
from rmgpy.molecule import Group
from rmgpy.molecule.atomtype import atomTypes

import nose
import nose.tools
Expand Down Expand Up @@ -60,6 +61,18 @@ def test_kinetics(self):
test.description = test_name
self.compat_func_name = test_name
yield test, family_name

test = lambda x: self.kinetics_checkSiblingsForParents(family_name)
test_name = "Kinetics family {0}: sibling relationships are correct?".format(family_name)
test.description = test_name
self.compat_func_name = test_name
yield test, family_name

test = lambda x: self.kinetics_checkCdAtomType(family_name)
test_name = "Kinetics family {0}: Cd, CS, CO, and Cdd atomtype used correctly?".format(family_name)
test.description = test_name
self.compat_func_name = test_name
yield test, family_name

test = lambda x: self.kinetics_checkReactantAndProductTemplate(family_name)
test_name = "Kinetics family {0}: reactant and product templates correctly defined?".format(family_name)
Expand Down Expand Up @@ -90,13 +103,13 @@ def test_thermo(self):
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkGroupsNonidentical(group_name, group)
test_name = "Thermo groups {0}: nodes are nonidentical?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkChildParentRelationships(group_name, group)
test_name = "Thermo groups {0}: parent-child relationships are correct?".format(group_name)
test.description = test_name
Expand All @@ -109,15 +122,20 @@ def test_thermo(self):
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)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

def test_solvation(self):
for group_name, group in self.database.solvation.groups.iteritems():
test = lambda x: self.general_checkNodesFoundInTree(group_name, group)
test_name = "Solvation groups {0}: nodes are in the tree with proper parents?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkGroupsNonidentical(group_name, group)
test_name = "Solvation groups {0}: nodes are nonidentical?".format(group_name)
test.description = test_name
Expand All @@ -135,21 +153,27 @@ def test_solvation(self):
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 = "Solvation groups {0}: Cd atomtype used correctly?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

def test_statmech(self):
for group_name, group in self.database.statmech.groups.iteritems():
test = lambda x: self.general_checkNodesFoundInTree(group_name, group)
test_name = "Statmech groups {0}: nodes are in the tree with proper parents?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkGroupsNonidentical(group_name, group)
test_name = "Statmech groups {0}: nodes are nonidentical?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkChildParentRelationships(group_name, group)
test_name = "Statmech groups {0}: parent-child relationships are correct?".format(group_name)
test.description = test_name
Expand All @@ -162,6 +186,12 @@ def test_statmech(self):
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkCdAtomType(group_name, group)
test_name = "Statmech groups {0}: Cd atomtype used correctly?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

def test_transport(self):
for group_name, group in self.database.transport.groups.iteritems():
test = lambda x: self.general_checkNodesFoundInTree(group_name, group)
Expand All @@ -175,7 +205,7 @@ def test_transport(self):
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

test = lambda x: self.general_checkChildParentRelationships(group_name, group)
test_name = "Transport groups {0}: parent-child relationships are correct?".format(group_name)
test.description = test_name
Expand All @@ -187,6 +217,12 @@ def test_transport(self):
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 = "Transport groups {0}: Cd, CS, CO, and Cdd atomtype used correctly?".format(group_name)
test.description = test_name
self.compat_func_name = test_name
yield test, group_name

# These are the actual tests, that don't start with a "test_" name:
def kinetics_checkCorrectNumberofNodesInRules(self, family_name):
Expand Down Expand Up @@ -277,7 +313,7 @@ def kinetics_checkChildParentRelationships(self, family_name):
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):
def kinetics_checkSiblingsForParents(self, family_name):
"""
This test checks that siblings in a tree are not actually parent/child
"""
Expand All @@ -286,17 +322,18 @@ def kinetics__checkSiblingsForParents(self, family_name):
family = Database()
family.entries = originalFamily.groups.entries
for nodeName, node in family.entries.iteritems():
#Some families also construct a 2-level trees (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 family.forwardTemplate.products: continue
#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 {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, 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 {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, 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_checkAdjlistsNonidentical(self, database):
"""
Expand Down Expand Up @@ -344,6 +381,59 @@ def kinetics_checkReactantAndProductTemplate(self, family_name):
for product_label in product_labels:
nose.tools.assert_false(reactant_label==product_label, "Reactant label {0} matches that of product label {1} in a non-reversible family template. Please rename product label.".format(reactant_label,product_label))

def kinetics_checkCdAtomType(self, family_name):
"""
This test checks that groups containing Cd, CO, CS and Cdd atomtypes are used
correctly according to their strict definitions
"""
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=[]
if not family.ownReverse:
for product in family.forwardTemplate.products:
ignore.append(product)
ignore.extend(product.children)
else: ignore=[]

for entryName, entry in family.groups.entries.iteritems():
#ignore products
if entry in ignore: continue
#ignore LogicOr groups
if isinstance(entry.item, Group):
for index, atom in enumerate(entry.item.atoms):
for atomtype1 in atom.atomType:
if atomtype1 in targetAtomTypes:
break
#If Cd not found in atomTypes, go to next atom
else: continue
#Create list of all the atomTypes that should be present in addition or instead of Cd
correctAtomList=[]
num_of_Dbonds=sum([1 if x.order[0] is 'D' and len(x.order)==1 else 0 for x in atom.bonds.values()])
if num_of_Dbonds == 2:
correctAtomList.append('Cdd')
elif num_of_Dbonds == 1:
for ligand, bond in atom.bonds.iteritems():
#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')

#remove duplicates from correctAtom:
correctAtomList=list(set(correctAtomList))
for correctAtom in correctAtomList:
nose.tools.assert_true(atomTypes[correctAtom] in atom.atomType,
"""In family {0}, node {1} is missing the atomtype {2} in atom {3} and may be misusing the atomtype Cd, CO, CS, or Cdd.
The following adjList may be have atoms in a different ordering than the input file:
{4}
""".format(family_name, entry, correctAtom, index+1, entry.item.toAdjacencyList()))


def general_checkNodesFoundInTree(self, group_name, group):
"""
This test checks whether nodes are found in the tree, with proper parents.
Expand Down Expand Up @@ -409,5 +499,46 @@ def general_checkSiblingsForParents(self, group_name, group):
"In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child1, child2))
nose.tools.assert_false(group.matchNodeToChild(child2, child1),
"In {0} group, node {1} is written as a sibling of {2}, when it is actually a parent.".format(group_name, child2, child1))

def general_checkCdAtomType(self, group_name, group):
"""
This test checks that groups containing Cd, CO, CS and Cdd atomtypes are used
correctly according to their strict definitions
"""
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):
for index, atom in enumerate(entry.item.atoms):
for atomtype1 in atom.atomType:
if atomtype1 in targetAtomTypes:
break
#If Cd not found in atomTypes, go to next atom
else: continue
#figure out what the correct atomType is
correctAtomList=[]
num_of_Dbonds=sum([1 if x.order[0] is 'D' and len(x.order)==1 else 0 for x in atom.bonds.values()])
if num_of_Dbonds == 2:
correctAtomList.append('Cdd')
elif num_of_Dbonds == 1:
for ligand, bond in atom.bonds.iteritems():
#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')

#remove duplicates from correctAtom:
correctAtomList=list(set(correctAtomList))
for correctAtom in correctAtomList:
nose.tools.assert_true(atomTypes[correctAtom] in atom.atomType,
"""In group {0}, node {1} is missing the atomtype {2} in atom {3} and may be misusing the atomtype Cd, CO, CS, or Cdd.
The following adjList may be have atoms in a different ordering than the input file:
{4}
""".format(group_name, entry, correctAtom, index+1, entry.item.toAdjacencyList()))

if __name__ == '__main__':
nose.run(argv=[__file__, '-v', '--nologcapture'], defaultTest=__name__)

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