def testBicyclicDecompositionForPolyringUsingAlkaneTricyclic(self):
# create testing molecule
smiles = 'C1CC2CCCC3C(C1)C23'
mol = Molecule().fromSMILES(smiles)
# extract polyring from the molecule
polyring = mol.getDisparateRings()[1][0]
bicyclicList, ringOccurancesDict = bicyclicDecompositionForPolyring(polyring)
# 1st test: number of cores
self.assertEqual(len(bicyclicList), 3)
# 2nd test: ringOccurancesDict
ringInCoreOccurances = sorted(ringOccurancesDict.values())
expectedRingInCoreOccurances = [2, 2, 2]
self.assertEqual(ringInCoreOccurances, expectedRingInCoreOccurances)
# 3rd test: size of each bicyclic core
bicyclicSizes = sorted([len(bicyclic.atoms) for bicyclic in bicyclicList])
expectedBicyclicSizes = [7, 7, 10]
self.assertEqual(bicyclicSizes, expectedBicyclicSizes)
# 4th test: bond info for members of each core
aromaticBondNumInBicyclics = []
for bicyclic in bicyclicList:
aromaticBondNum = len(findAromaticBondsFromSubMolecule(bicyclic))
aromaticBondNumInBicyclics.append(aromaticBondNum)
aromaticBondNumInBicyclics = sorted(aromaticBondNumInBicyclics)
expectedAromaticBondNumInBicyclics = [0, 0, 0]
self.assertEqual(aromaticBondNumInBicyclics, expectedAromaticBondNumInBicyclics)
def testAddPolyRingCorrectionThermoDataFromHeuristicUsingAlkaneTricyclic(self):
# create testing molecule
smiles = 'C1CC2CCCC3C(C1)C23'
mol = Molecule().fromSMILES(smiles)
# extract polyring from the molecule
polyring = mol.getDisparateRings()[1][0]
thermoData = ThermoData(
Tdata = ([300,400,500,600,800,1000,1500],"K"),
Cpdata = ([0.0,0.0,0.0,0.0,0.0,0.0,0.0],"J/(mol*K)"),
H298 = (0.0,"kJ/mol"),
S298 = (0.0,"J/(mol*K)"),
)
self.database._ThermoDatabase__addPolyRingCorrectionThermoDataFromHeuristic(
thermoData, polyring)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(thermoData)
ringGroupLabels = [ringGroup.label for ringGroup in ringGroups]
polycyclicGroupLabels = [polycyclicGroup.label for polycyclicGroup in polycyclicGroups]
self.assertIn('Cyclohexane', ringGroupLabels)
self.assertIn('Cyclopropane', ringGroupLabels)
self.assertIn('s2_6_6_ane', polycyclicGroupLabels)
self.assertIn('s2_3_6_ane', polycyclicGroupLabels)
def testAddPolyRingCorrectionThermoDataFromHeuristicUsingAlkaneTricyclic(
self):
# create testing molecule
smiles = 'C1CC2CCCC3C(C1)C23'
mol = Molecule().fromSMILES(smiles)
# extract polyring from the molecule
polyring = mol.getDisparateRings()[1][0]
thermoData = ThermoData(
Tdata=([300, 400, 500, 600, 800, 1000, 1500], "K"),
Cpdata=([0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "J/(mol*K)"),
H298=(0.0, "kJ/mol"),
S298=(0.0, "J/(mol*K)"),
)
self.database._ThermoDatabase__addPolyRingCorrectionThermoDataFromHeuristic(
thermoData, polyring)
ringGroups, polycyclicGroups = self.database.getRingGroupsFromComments(
thermoData)
ringGroupLabels = [ringGroup.label for ringGroup in ringGroups]
polycyclicGroupLabels = [
polycyclicGroup.label for polycyclicGroup in polycyclicGroups
]
self.assertIn('Cyclohexane', ringGroupLabels)
self.assertIn('Cyclopropane', ringGroupLabels)
self.assertIn('s2_6_6_ane', polycyclicGroupLabels)
self.assertIn('s2_3_6_ane', polycyclicGroupLabels)
def testBicyclicDecompositionForPolyringUsingAlkaneTricyclic(self):
# create testing molecule
smiles = 'C1CC2CCCC3C(C1)C23'
mol = Molecule().fromSMILES(smiles)
# extract polyring from the molecule
polyring = mol.getDisparateRings()[1][0]
bicyclicList, ringOccurancesDict = bicyclicDecompositionForPolyring(
polyring)
# 1st test: number of cores
self.assertEqual(len(bicyclicList), 3)
# 2nd test: ringOccurancesDict
ringInCoreOccurances = sorted(ringOccurancesDict.values())
expectedRingInCoreOccurances = [2, 2, 2]
self.assertEqual(ringInCoreOccurances, expectedRingInCoreOccurances)
# 3rd test: size of each bicyclic core
bicyclicSizes = sorted(
[len(bicyclic.atoms) for bicyclic in bicyclicList])
expectedBicyclicSizes = [7, 7, 10]
self.assertEqual(bicyclicSizes, expectedBicyclicSizes)
# 4th test: bond info for members of each core
aromaticBondNumInBicyclics = []
for bicyclic in bicyclicList:
aromaticBondNum = len(findAromaticBondsFromSubMolecule(bicyclic))
aromaticBondNumInBicyclics.append(aromaticBondNum)
aromaticBondNumInBicyclics = sorted(aromaticBondNumInBicyclics)
expectedAromaticBondNumInBicyclics = [0, 0, 0]
self.assertEqual(aromaticBondNumInBicyclics,
expectedAromaticBondNumInBicyclics)
def testAddRingCorrectionThermoDataFromTreeForExistingTricyclic(self):
# create testing molecule: C1CC2C3CCC(C3)C2C1
# this tricyclic molecule is already in polycyclic database
# so algorithm should give complete match: s2-3_5_5_5_ane
smiles = 'C1CC2C3CCC(C3)C2C1'
mol = Molecule().fromSMILES(smiles)
polyring = mol.getDisparateRings()[1][0]
poly_groups = self.database.groups['polycyclic']
_, matched_entry, _ = self.database._ThermoDatabase__addRingCorrectionThermoDataFromTree(None, poly_groups, mol, polyring)
self.assertEqual(matched_entry.label, 's2-3_5_5_5_ane')
def testAddRingCorrectionThermoDataFromTreeForExistingTricyclic(self):
# create testing molecule: C1CC2C3CCC(C3)C2C1
# this tricyclic molecule is already in polycyclic database
# so algorithm should give complete match: s2-3_5_5_5_ane
smiles = 'C1CC2C3CCC(C3)C2C1'
mol = Molecule().fromSMILES(smiles)
polyring = mol.getDisparateRings()[1][0]
poly_groups = self.database.groups['polycyclic']
_, matched_entry, _ = self.database._ThermoDatabase__addRingCorrectionThermoDataFromTree(
None, poly_groups, mol, polyring)
self.assertEqual(matched_entry.label, 's2-3_5_5_5_ane')
