Python GroupAtom.makeSampleAtom方法代码示例

# 需要导入模块: from rmgpy.molecule.group import GroupAtom [as 别名]
# 或者: from rmgpy.molecule.group.GroupAtom import makeSampleAtom [as 别名]

#.........这里部分代码省略.........
                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 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 testCopy(self):
        """
        Test the GroupAtom.copy() method.
        """
        atom = self.atom.copy()
        self.assertEqual(len(self.atom.atomType), len(atom.atomType))
        self.assertEqual(self.atom.atomType[0].label, atom.atomType[0].label)
        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 GroupAtom object can be successfully pickled and
        unpickled with no loss of information.
        """
        import cPickle
        atom = cPickle.loads(cPickle.dumps(self.atom))
        self.assertEqual(len(self.atom.atomType), len(atom.atomType))
        self.assertEqual(self.atom.atomType[0].label, atom.atomType[0].label)
        self.assertEqual(self.atom.radicalElectrons, atom.radicalElectrons)
        self.assertEqual(self.atom.charge, atom.charge)
        self.assertEqual(self.atom.label, atom.label)

    def testHasWildcards(self):
        """
        Tests the GroupAtom.hasWildcards() method
        """
        self.assertFalse(self.atom.hasWildcards())
        adjlist = """
1 *2 C     u0     {2,[D,T]} {3,S}
2 *3 C     u0     {1,[D,T]} {4,S}
3    C     ux     {1,S} {5,S}
4    C     u[0,1] {2,S}
5    [C,O] u0     {3,S}
"""
        group = Group().fromAdjacencyList(adjlist)
        for index, atom in enumerate(group.atoms):
            self.assertTrue(atom.hasWildcards(), 'GroupAtom with index {0} should have wildcards, but does not'.format(index))

    def testMakeSampleAtom(self):
        """
        Tests the GroupAtom.makeSampleAtom() method
        """
        newAtom = self.atom.makeSampleAtom()

        self.assertEquals(newAtom.element, elements.__dict__['C'])
        self.assertEquals(newAtom.radicalElectrons, 1)
        self.assertEquals(newAtom.charge, 0)