def testSubgraphIsomorphism(self):
# Simple test comparing C-C to C-C-C (no hydrogens)
mol = Molecule()
c1 = Atom(getElement(6))
c2 = c1.copy()
mol.addAtom(c1)
mol.addAtom(c2)
mol.addBond(Bond(c1, c2))
mol2 = Molecule()
c1 = c1.copy()
c2 = c1.copy()
c3 = c1.copy()
mol2.addAtom(c1)
mol2.addAtom(c2)
mol2.addAtom(c3)
mol2.addBond(Bond(c1, c2))
mol2.addBond(Bond(c2, c3))
self.assertTrue(self.vf3.isSubgraphIsomorphic(mol2, mol, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(mol, mol2, None))
# Ring membership is a semantic property of molecules,
# so straight chains are not considered sub graphs of rings
hexane = Molecule().fromSMILES("C1CCCCC1")
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexane, mol, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexane, mol2, None))
# Benzene and hexane, while technically sharing the same shape,
# differ in semantic information.
benzene = Molecule().fromSMILES("C1=CC=CC=C1")
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexane, benzene, None))
# Test sub graph isomorphism on rings
hexaneMinusH = hexane.copy(True)
hexaneMinusH.removeVertex(hexaneMinusH.vertices[6])
self.assertTrue(self.vf3.isSubgraphIsomorphic(hexane, hexaneMinusH, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexaneMinusH, hexane, None))
benzeneMinusH = benzene.copy(True)
benzeneMinusH.removeVertex(benzeneMinusH.vertices[6])
self.assertTrue(self.vf3.isSubgraphIsomorphic(benzene, benzeneMinusH, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(benzeneMinusH, hexane, None))
def testApplyActionLoseRadical(self):
"""
Test the Atom.applyAction() method for a LOSE_RADICAL action.
"""
action = ['LOSE_RADICAL', '*1', 1]
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons + 1)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionDecrementBond(self):
"""
Test the Atom.applyAction() method for a CHANGE_BOND action.
"""
action = ['CHANGE_BOND', '*1', -1, '*2']
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionLoseRadical(self):
"""
Test the Atom.applyAction() method for a LOSE_RADICAL action.
"""
action = ['LOSE_RADICAL', '*1', 1]
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons + 1)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionDecrementBond(self):
"""
Test the Atom.applyAction() method for a CHANGE_BOND action.
"""
action = ['CHANGE_BOND', '*1', -1, '*2']
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
class TestAtom(unittest.TestCase):
"""
Contains unit tests of the Atom class.
"""
def setUp(self):
"""
A method called before each unit test in this class.
"""
self.atom = Atom(element=getElement('C'), radicalElectrons=1, charge=0, label='*1', lonePairs=0)
def testMass(self):
"""
Test the Atom.mass property.
"""
self.assertTrue(self.atom.mass == self.atom.element.mass)
def testNumber(self):
"""
Test the Atom.number property.
"""
self.assertTrue(self.atom.number == self.atom.element.number)
def testSymbol(self):
"""
Test the Atom.symbol property.
"""
self.assertTrue(self.atom.symbol == self.atom.element.symbol)
def testIsHydrogen(self):
"""
Test the Atom.isHydrogen() method.
"""
for element in elementList:
atom = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
if element.symbol == 'H':
self.assertTrue(atom.isHydrogen())
else:
self.assertFalse(atom.isHydrogen())
def testIsNonHydrogen(self):
"""
Test the Atom.isNonHydrogen() method.
"""
for element in elementList:
atom = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
if element.symbol == 'H':
self.assertFalse(atom.isNonHydrogen())
else:
self.assertTrue(atom.isNonHydrogen())
def testIsCarbon(self):
"""
Test the Atom.isCarbon() method.
"""
for element in elementList:
atom = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
if element.symbol == 'C':
self.assertTrue(atom.isCarbon())
else:
self.assertFalse(atom.isCarbon())
def testIsOxygen(self):
"""
Test the Atom.isOxygen() method.
"""
for element in elementList:
atom = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=2)
if element.symbol == 'O':
self.assertTrue(atom.isOxygen())
else:
self.assertFalse(atom.isOxygen())
def testIncrementRadical(self):
"""
Test the Atom.incrementRadical() method.
"""
radicalElectrons = self.atom.radicalElectrons
self.atom.incrementRadical()
self.assertEqual(self.atom.radicalElectrons, radicalElectrons + 1)
def testDecrementRadical(self):
"""
Test the Atom.decrementRadical() method.
"""
radicalElectrons = self.atom.radicalElectrons
self.atom.decrementRadical()
self.assertEqual(self.atom.radicalElectrons, radicalElectrons - 1)
def testApplyActionBreakBond(self):
"""
Test the Atom.applyAction() method for a BREAK_BOND action.
"""
action = ['BREAK_BOND', '*1', 'S', '*2']
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionFormBond(self):
"""
Test the Atom.applyAction() method for a FORM_BOND action.
"""
action = ['FORM_BOND', '*1', 'S', '*2']
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionIncrementBond(self):
"""
Test the Atom.applyAction() method for a CHANGE_BOND action.
"""
action = ['CHANGE_BOND', '*1', 1, '*2']
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionDecrementBond(self):
"""
Test the Atom.applyAction() method for a CHANGE_BOND action.
"""
action = ['CHANGE_BOND', '*1', -1, '*2']
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionGainRadical(self):
"""
Test the Atom.applyAction() method for a GAIN_RADICAL action.
"""
action = ['GAIN_RADICAL', '*1', 1]
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons - 1)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionLoseRadical(self):
"""
Test the Atom.applyAction() method for a LOSE_RADICAL action.
"""
action = ['LOSE_RADICAL', '*1', 1]
for element in elementList:
atom0 = Atom(element=element, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons + 1)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testEquivalent(self):
"""
Test the Atom.equivalent() method.
"""
for index1, element1 in enumerate(elementList[0:10]):
for index2, element2 in enumerate(elementList[0:10]):
atom1 = Atom(element=element1, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom2 = Atom(element=element2, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
if index1 == index2:
self.assertTrue(atom1.equivalent(atom2))
self.assertTrue(atom2.equivalent(atom1))
else:
self.assertFalse(atom1.equivalent(atom2))
self.assertFalse(atom2.equivalent(atom1))
def testIsSpecificCaseOf(self):
"""
Test the Atom.isSpecificCaseOf() method.
"""
for index1, element1 in enumerate(elementList[0:10]):
for index2, element2 in enumerate(elementList[0:10]):
atom1 = Atom(element=element1, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
atom2 = Atom(element=element2, radicalElectrons=1, charge=0, label='*1', lonePairs=0)
if index1 == index2:
self.assertTrue(atom1.isSpecificCaseOf(atom2))
else:
self.assertFalse(atom1.isSpecificCaseOf(atom2))
def testCopy(self):
"""
Test the Atom.copy() method.
"""
atom = self.atom.copy()
self.assertEqual(self.atom.element.symbol, atom.element.symbol)
self.assertEqual(self.atom.atomType, atom.atomType)
self.assertEqual(self.atom.radicalElectrons, atom.radicalElectrons)
self.assertEqual(self.atom.charge, atom.charge)
self.assertEqual(self.atom.label, atom.label)
def testPickle(self):
"""
Test that a Atom object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
atom = cPickle.loads(cPickle.dumps(self.atom))
self.assertEqual(self.atom.element.symbol, atom.element.symbol)
self.assertEqual(self.atom.atomType, atom.atomType)
self.assertEqual(self.atom.radicalElectrons, atom.radicalElectrons)
self.assertEqual(self.atom.charge, atom.charge)
self.assertEqual(self.atom.label, atom.label)
class TestAtom(unittest.TestCase):
"""
Contains unit tests of the Atom class.
"""
def setUp(self):
"""
A method called before each unit test in this class.
"""
self.atom = Atom(element=getElement('C'),
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
def testMass(self):
"""
Test the Atom.mass property.
"""
self.assertTrue(self.atom.mass == self.atom.element.mass)
def testNumber(self):
"""
Test the Atom.number property.
"""
self.assertTrue(self.atom.number == self.atom.element.number)
def testSymbol(self):
"""
Test the Atom.symbol property.
"""
self.assertTrue(self.atom.symbol == self.atom.element.symbol)
def testIsHydrogen(self):
"""
Test the Atom.isHydrogen() method.
"""
for element in elementList:
atom = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
if element.symbol == 'H':
self.assertTrue(atom.isHydrogen())
else:
self.assertFalse(atom.isHydrogen())
def testIsNonHydrogen(self):
"""
Test the Atom.isNonHydrogen() method.
"""
for element in elementList:
atom = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
if element.symbol == 'H':
self.assertFalse(atom.isNonHydrogen())
else:
self.assertTrue(atom.isNonHydrogen())
def testIsCarbon(self):
"""
Test the Atom.isCarbon() method.
"""
for element in elementList:
atom = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
if element.symbol == 'C':
self.assertTrue(atom.isCarbon())
else:
self.assertFalse(atom.isCarbon())
def testIsOxygen(self):
"""
Test the Atom.isOxygen() method.
"""
for element in elementList:
atom = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=2)
if element.symbol == 'O':
self.assertTrue(atom.isOxygen())
else:
self.assertFalse(atom.isOxygen())
def testIncrementRadical(self):
"""
Test the Atom.incrementRadical() method.
"""
radicalElectrons = self.atom.radicalElectrons
self.atom.incrementRadical()
self.assertEqual(self.atom.radicalElectrons, radicalElectrons + 1)
def testDecrementRadical(self):
"""
Test the Atom.decrementRadical() method.
"""
radicalElectrons = self.atom.radicalElectrons
self.atom.decrementRadical()
self.assertEqual(self.atom.radicalElectrons, radicalElectrons - 1)
def testApplyActionBreakBond(self):
"""
Test the Atom.applyAction() method for a BREAK_BOND action.
"""
action = ['BREAK_BOND', '*1', 'S', '*2']
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionFormBond(self):
"""
Test the Atom.applyAction() method for a FORM_BOND action.
"""
action = ['FORM_BOND', '*1', 'S', '*2']
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionIncrementBond(self):
"""
Test the Atom.applyAction() method for a CHANGE_BOND action.
"""
action = ['CHANGE_BOND', '*1', 1, '*2']
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionDecrementBond(self):
"""
Test the Atom.applyAction() method for a CHANGE_BOND action.
"""
action = ['CHANGE_BOND', '*1', -1, '*2']
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionGainRadical(self):
"""
Test the Atom.applyAction() method for a GAIN_RADICAL action.
"""
action = ['GAIN_RADICAL', '*1', 1]
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons - 1)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testApplyActionLoseRadical(self):
"""
Test the Atom.applyAction() method for a LOSE_RADICAL action.
"""
action = ['LOSE_RADICAL', '*1', 1]
for element in elementList:
atom0 = Atom(element=element,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom = atom0.copy()
atom.applyAction(action)
self.assertEqual(atom0.element, atom.element)
self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons + 1)
self.assertEqual(atom0.charge, atom.charge)
self.assertEqual(atom0.label, atom.label)
def testEquivalent(self):
"""
Test the Atom.equivalent() method.
"""
for index1, element1 in enumerate(elementList[0:10]):
for index2, element2 in enumerate(elementList[0:10]):
atom1 = Atom(element=element1,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom2 = Atom(element=element2,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
if index1 == index2:
self.assertTrue(atom1.equivalent(atom2))
self.assertTrue(atom2.equivalent(atom1))
else:
self.assertFalse(atom1.equivalent(atom2))
self.assertFalse(atom2.equivalent(atom1))
def testIsSpecificCaseOf(self):
"""
Test the Atom.isSpecificCaseOf() method.
"""
for index1, element1 in enumerate(elementList[0:10]):
for index2, element2 in enumerate(elementList[0:10]):
atom1 = Atom(element=element1,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
atom2 = Atom(element=element2,
radicalElectrons=1,
charge=0,
label='*1',
lonePairs=0)
if index1 == index2:
self.assertTrue(atom1.isSpecificCaseOf(atom2))
else:
self.assertFalse(atom1.isSpecificCaseOf(atom2))
def testCopy(self):
"""
Test the Atom.copy() method.
"""
atom = self.atom.copy()
self.assertEqual(self.atom.element.symbol, atom.element.symbol)
self.assertEqual(self.atom.atomType, atom.atomType)
self.assertEqual(self.atom.radicalElectrons, atom.radicalElectrons)
self.assertEqual(self.atom.charge, atom.charge)
self.assertEqual(self.atom.label, atom.label)
def testPickle(self):
"""
Test that a Atom object can be successfully pickled and
unpickled with no loss of information.
"""
import cPickle
atom = cPickle.loads(cPickle.dumps(self.atom))
self.assertEqual(self.atom.element.symbol, atom.element.symbol)
self.assertEqual(self.atom.atomType, atom.atomType)
self.assertEqual(self.atom.radicalElectrons, atom.radicalElectrons)
self.assertEqual(self.atom.charge, atom.charge)
self.assertEqual(self.atom.label, atom.label)