Python group.GroupAtom类代码示例

    def testApplyActionLoseRadical(self):
        """
        Test the GroupAtom.applyAction() method for a LOSE_RADICAL action.
        """
        action = ['LOSE_RADICAL', '*1', 1]
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1', lonePairs=[0])
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.decrementRadical))
                for a in atomType.incrementRadical:
                    self.assertTrue(a in atom.atomType, "LOSE_RADICAL on {0} gave {1} not {2}".format(atomType, atom.atomType, atomType.decrementRadical))
                self.assertEqual(atom0.radicalElectrons, [r + 1 for r in atom.radicalElectrons])
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
                self.assertEqual(atom0.lonePairs, atom.lonePairs)
            except ActionError:
                self.assertEqual(len(atomType.decrementRadical), 0)

        #test when radicals unspecified
        group = Group().fromAdjacencyList("""
        1 R ux
        """) #ux causes a wildcare for radicals
        atom1 = group.atoms[0]
        atom1.applyAction(action)
        self.assertListEqual(atom1.radicalElectrons, [0,1,2,3])

 def testEquivalent(self):
     """
     Test the GroupAtom.equivalent() method.
     """
     for label1, atomType1 in atomTypes.iteritems():
         for label2, atomType2 in atomTypes.iteritems():
             atom1 = GroupAtom(atomType=[atomType1], radicalElectrons=[1], charge=[0], label="*1")
             atom2 = GroupAtom(atomType=[atomType2], radicalElectrons=[1], charge=[0], label="*1")
             if label1 == label2 or atomType2 in atomType1.generic or atomType1 in atomType2.generic:
                 self.assertTrue(atom1.equivalent(atom2), "{0!s} is not equivalent to {1!s}".format(atom1, atom2))
                 self.assertTrue(atom2.equivalent(atom1), "{0!s} is not equivalent to {1!s}".format(atom2, atom1))
             else:
                 self.assertFalse(atom1.equivalent(atom2), "{0!s} is equivalent to {1!s}".format(atom1, atom2))
                 self.assertFalse(atom2.equivalent(atom1), "{0!s} is equivalent to {1!s}".format(atom2, atom1))
         # Now see if charge and radical count are checked properly
         for charge in range(3):
             for radicals in range(2):
                 atom3 = GroupAtom(atomType=[atomType1], radicalElectrons=[radicals], charge=[charge], label="*1")
                 if radicals == 1 and charge == 0:
                     self.assertTrue(
                         atom1.equivalent(atom3), "{0!s} is not equivalent to {1!s}".format(atom1, atom3)
                     )
                     self.assertTrue(
                         atom1.equivalent(atom3), "{0!s} is not equivalent to {1!s}".format(atom3, atom1)
                     )
                 else:
                     self.assertFalse(atom1.equivalent(atom3), "{0!s} is equivalent to {1!s}".format(atom1, atom3))
                     self.assertFalse(atom1.equivalent(atom3), "{0!s} is equivalent to {1!s}".format(atom3, atom1))

 def testIsSpecificCaseOf(self):
     """
     Test the GroupAtom.isSpecificCaseOf() method.
     """
     for label1, atomType1 in atomTypes.iteritems():
         for label2, atomType2 in atomTypes.iteritems():
             atom1 = GroupAtom(atomType=[atomType1], radicalElectrons=[1], charge=[0], label="*1")
             atom2 = GroupAtom(atomType=[atomType2], radicalElectrons=[1], charge=[0], label="*1")
             # And make more generic types of these two atoms
             atom1gen = GroupAtom(atomType=[atomType1], radicalElectrons=[0, 1], charge=[0, 1], label="*1")
             atom2gen = GroupAtom(atomType=[atomType2], radicalElectrons=[0, 1], charge=[0, 1], label="*1")
             if label1 == label2 or atomType2 in atomType1.generic:
                 self.assertTrue(
                     atom1.isSpecificCaseOf(atom2), "{0!s} is not a specific case of {1!s}".format(atom1, atom2)
                 )
                 self.assertTrue(
                     atom1.isSpecificCaseOf(atom2gen),
                     "{0!s} is not a specific case of {1!s}".format(atom1, atom2gen),
                 )
                 self.assertFalse(
                     atom1gen.isSpecificCaseOf(atom2), "{0!s} is a specific case of {1!s}".format(atom1gen, atom2)
                 )
             else:
                 self.assertFalse(
                     atom1.isSpecificCaseOf(atom2), "{0!s} is a specific case of {1!s}".format(atom1, atom2)
                 )
                 self.assertFalse(
                     atom1.isSpecificCaseOf(atom2gen), "{0!s} is a specific case of {1!s}".format(atom1, atom2gen)
                 )
                 self.assertFalse(
                     atom1gen.isSpecificCaseOf(atom2), "{0!s} is a specific case of {1!s}".format(atom1gen, atom2)
                 )

 def testApplyActionDecrementBond(self):
     """
     Test the GroupAtom.applyAction() method for a CHANGE_BOND action.
     """
     action = ['CHANGE_BOND', '*1', -1, '*2']
     for label, atomType in atomTypes.iteritems():
         atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
         atom = atom0.copy()
         try:
             atom.applyAction(action)
             self.assertEqual(len(atom.atomType), len(atomType.decrementBond))
             for a in atomType.decrementBond:
                 self.assertTrue(a in atom.atomType)
             self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
             self.assertEqual(atom0.charge, atom.charge)
             self.assertEqual(atom0.label, atom.label)
         except ActionError:
             self.assertEqual(len(atomType.decrementBond), 0)

 def testApplyActionLoseRadical(self):
     """
     Test the GroupAtom.applyAction() method for a LOSE_RADICAL action.
     """
     action = ['LOSE_RADICAL', '*1', 1]
     for label, atomType in atomTypes.iteritems():
         atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
         atom = atom0.copy()
         try:
             atom.applyAction(action)
             self.assertEqual(len(atom.atomType), len(atomType.decrementRadical))
             for a in atomType.incrementRadical:
                 self.assertTrue(a in atom.atomType, "LOSE_RADICAL on {0} gave {1} not {2}".format(atomType, atom.atomType, atomType.decrementRadical))
             self.assertEqual(atom0.radicalElectrons, [r + 1 for r in atom.radicalElectrons])
             self.assertEqual(atom0.charge, atom.charge)
             self.assertEqual(atom0.label, atom.label)
         except ActionError:
             self.assertEqual(len(atomType.decrementRadical), 0)

 def testApplyActionFormBond(self):
     """
     Test the GroupAtom.applyAction() method for a FORM_BOND action.
     """
     action = ["FORM_BOND", "*1", "S", "*2"]
     for label, atomType in atomTypes.iteritems():
         atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label="*1")
         atom = atom0.copy()
         try:
             atom.applyAction(action)
             self.assertEqual(len(atom.atomType), len(atomType.formBond))
             for a in atomType.formBond:
                 self.assertTrue(a in atom.atomType)
             self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
             self.assertEqual(atom0.charge, atom.charge)
             self.assertEqual(atom0.label, atom.label)
         except ActionError:
             self.assertEqual(len(atomType.formBond), 0)

    def testApplyActionLosePair(self):
        """
        Test the GroupAtom.applyAction() method for a LOSE_PAIR action when lonePairs is either specified or not.
        """

        action = ['LOSE_PAIR', '*1', 1]

        # lonePairs specified:
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1', lonePairs=[1])
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.decrementLonePair))
                for a in atomType.decrementLonePair:
                    self.assertTrue(a in atom.atomType,
                                    "LOSE_PAIR on {0} gave {1} not {2}".format(atomType, atom.atomType,
                                                                                  atomType.decrementLonePair))
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
                self.assertEqual(atom0.lonePairs, [r + 1 for r in atom.lonePairs])
            except ActionError:
                self.assertEqual(len(atomType.decrementLonePair), 0)

        #lonePairs unspecified:
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.decrementLonePair))
                for a in atomType.decrementLonePair:
                    self.assertTrue(a in atom.atomType,
                                    "LOSE_PAIR on {0} gave {1} not {2}".format(atomType, atom.atomType,
                                                                               atomType.decrementLonePair))
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
                self.assertEqual([1,2,3,4], [r + 1 for r in atom.lonePairs])
            except ActionError:
                self.assertEqual(len(atomType.decrementLonePair), 0)

 def testApplyActionBreakBond(self):
     """
     Test the GroupAtom.applyAction() method for a BREAK_BOND action.
     """
     action = ['BREAK_BOND', '*1', 1, '*2']
     for label, atomType in atomTypes.iteritems():
         atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1', lonePairs=[0])
         atom = atom0.copy()
         try:
             atom.applyAction(action)
             self.assertEqual(len(atom.atomType), len(atomType.breakBond))
             for a in atomType.breakBond:
                 self.assertTrue(a in atom.atomType)
             self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
             self.assertEqual(atom0.charge, atom.charge)
             self.assertEqual(atom0.label, atom.label)
             self.assertEqual(atom0.label, atom.label)
             self.assertEqual(atom0.lonePairs, atom.lonePairs)
         except ActionError:
             self.assertEqual(len(atomType.breakBond), 0)

 def setUp(self):
     """
     A method called before each unit test in this class.
     """
     self.atom = GroupAtom(atomType=[atomTypes['Cd']], radicalElectrons=[1], charge=[0], label='*1')

class TestGroupAtom(unittest.TestCase):
    """
    Contains unit tests of the GroupAtom class.
    """

    def setUp(self):
        """
        A method called before each unit test in this class.
        """
        self.atom = GroupAtom(atomType=[atomTypes['Cd']], radicalElectrons=[1], charge=[0], label='*1')
    
    def testApplyActionBreakBond(self):
        """
        Test the GroupAtom.applyAction() method for a BREAK_BOND action.
        """
        action = ['BREAK_BOND', '*1', 1, '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.breakBond))
                for a in atomType.breakBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.breakBond), 0)
    
    def testApplyActionFormBond(self):
        """
        Test the GroupAtom.applyAction() method for a FORM_BOND action.
        """
        action = ['FORM_BOND', '*1', 1, '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.formBond))
                for a in atomType.formBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.formBond), 0)
    
    def testApplyActionIncrementBond(self):
        """
        Test the GroupAtom.applyAction() method for a CHANGE_BOND action.
        """
        action = ['CHANGE_BOND', '*1', 1, '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.incrementBond))
                for a in atomType.incrementBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.incrementBond), 0)
    
    def testApplyActionDecrementBond(self):
        """
        Test the GroupAtom.applyAction() method for a CHANGE_BOND action.
        """
        action = ['CHANGE_BOND', '*1', -1, '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.decrementBond))
                for a in atomType.decrementBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.decrementBond), 0)
    
    def testApplyActionGainRadical(self):
        """
        Test the GroupAtom.applyAction() method for a GAIN_RADICAL action.
        """
        action = ['GAIN_RADICAL', '*1', 1]
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.incrementRadical))
                for a in atomType.incrementRadical:
                    self.assertTrue(a in atom.atomType, "GAIN_RADICAL on {0} gave {1} not {2}".format(atomType, atom.atomType, atomType.incrementRadical))
#.........这里部分代码省略.........

class TestGroupAtom(unittest.TestCase):
    """
    Contains unit tests of the GroupAtom class.
    """

    def setUp(self):
        """
        A method called before each unit test in this class.
        """
        self.atom = GroupAtom(atomType=[atomTypes['Cd']], radicalElectrons=[1], charge=[0], label='*1')
    
    def testApplyActionBreakBond(self):
        """
        Test the GroupAtom.applyAction() method for a BREAK_BOND action.
        """
        action = ['BREAK_BOND', '*1', 'S', '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.breakBond))
                for a in atomType.breakBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.breakBond), 0)
    
    def testApplyActionFormBond(self):
        """
        Test the GroupAtom.applyAction() method for a FORM_BOND action.
        """
        action = ['FORM_BOND', '*1', 'S', '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.formBond))
                for a in atomType.formBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.formBond), 0)
    
    def testApplyActionIncrementBond(self):
        """
        Test the GroupAtom.applyAction() method for a CHANGE_BOND action.
        """
        action = ['CHANGE_BOND', '*1', 1, '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.incrementBond))
                for a in atomType.incrementBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.incrementBond), 0)
    
    def testApplyActionDecrementBond(self):
        """
        Test the GroupAtom.applyAction() method for a CHANGE_BOND action.
        """
        action = ['CHANGE_BOND', '*1', -1, '*2']
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.decrementBond))
                for a in atomType.decrementBond:
                    self.assertTrue(a in atom.atomType)
                self.assertEqual(atom0.radicalElectrons, atom.radicalElectrons)
                self.assertEqual(atom0.charge, atom.charge)
                self.assertEqual(atom0.label, atom.label)
            except ActionError:
                self.assertEqual(len(atomType.decrementBond), 0)
    
    def testApplyActionGainRadical(self):
        """
        Test the GroupAtom.applyAction() method for a GAIN_RADICAL action.
        """
        action = ['GAIN_RADICAL', '*1', 1]
        for label, atomType in atomTypes.iteritems():
            atom0 = GroupAtom(atomType=[atomType], radicalElectrons=[1], charge=[0], label='*1')
            atom = atom0.copy()
            try:
                atom.applyAction(action)
                self.assertEqual(len(atom.atomType), len(atomType.incrementRadical))
                for a in atomType.incrementRadical:
                    self.assertTrue(a in atom.atomType, "GAIN_RADICAL on {0} gave {1} not {2}".format(atomType, atom.atomType, atomType.incrementRadical))
#.........这里部分代码省略.........