Esempi in Python per Molecule.isAtomInCycle

Esempio n. 1

File: symmetryTest.py Progetto: ReactionMechanismGenerator/RMG-Py

    def testAtomSymmetryNumberEthanewithDeuteriumTritium(self):
        """
        Test the Molecule.calculateAtomSymmetryNumber() on CC(D)(T)

        This is meant to test whether chirality is accounted for, which
        should half the symmetry term.

        The total number is 1.5 because the methyl group contributes *3 and
        the chiral center contributes *0.5
        """
        molecule = Molecule().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 D u0 p0 c0 {1,S}
4 T u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}

""")
        symmetryNumber = 1
        for atom in molecule.atoms:
            if not molecule.isAtomInCycle(atom):
                symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
        self.assertAlmostEqual(symmetryNumber, 1.5)

Esempio n. 2

    def testAtomSymmetryNumberEthanewithDeuteriumTritium(self):
        """
        Test the Molecule.calculateAtomSymmetryNumber() on CC(D)(T)

        This is meant to test whether chirality is accounted for, which
        should half the symmetry term.

        The total number is 1.5 because the methyl group contributes *3 and
        the chiral center contributes *0.5
        """
        molecule = Molecule().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 D u0 p0 c0 {1,S}
4 T u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}

""")
        symmetryNumber = 1
        for atom in molecule.atoms:
            if not molecule.isAtomInCycle(atom):
                symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
        self.assertAlmostEqual(symmetryNumber, 1.5)

Esempio n. 3

File: moleculeTest.py Progetto: comocheng/RMG-Py

 def testIsInCycleCyclohexane(self):
     """
     Test the Molecule.isInCycle() method with ethane.
     """
     molecule = Molecule().fromInChI('InChI=1/C6H12/c1-2-4-6-5-3-1/h1-6H2')
     for atom in molecule.atoms:
         if atom.isHydrogen():
             self.assertFalse(molecule.isAtomInCycle(atom))
         elif atom.isCarbon():
             self.assertTrue(molecule.isAtomInCycle(atom))
     for atom1 in molecule.atoms:
         for atom2, bond in atom1.bonds.items():
             if atom1.isCarbon() and atom2.isCarbon():
                 self.assertTrue(molecule.isBondInCycle(bond))
             else:
                 self.assertFalse(molecule.isBondInCycle(bond))

Esempio n. 4

 def testIsInCycleCyclohexane(self):
     """
     Test the Molecule.isInCycle() method with ethane.
     """
     molecule = Molecule().fromInChI('InChI=1/C6H12/c1-2-4-6-5-3-1/h1-6H2')
     for atom in molecule.atoms:
         if atom.isHydrogen():
             self.assertFalse(molecule.isAtomInCycle(atom))
         elif atom.isCarbon():
             self.assertTrue(molecule.isAtomInCycle(atom))
     for atom1 in molecule.atoms:
         for atom2, bond in atom1.bonds.items():
             if atom1.isCarbon() and atom2.isCarbon():
                 self.assertTrue(molecule.isBondInCycle(bond))
             else:
                 self.assertFalse(molecule.isBondInCycle(bond))

Esempio n. 5

File: symmetryTest.py Progetto: ReactionMechanismGenerator/RMG-Py

 def testAtomSymmetryNumberEthane(self):
     """
     Test the Molecule.calculateAtomSymmetryNumber() on CC
     """
     molecule = Molecule().fromSMILES('CC')
     symmetryNumber = 1
     for atom in molecule.atoms:
         if not molecule.isAtomInCycle(atom):
             symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
     self.assertEqual(symmetryNumber, 9)

Esempio n. 6

File: symmetryTest.py Progetto: ReactionMechanismGenerator/RMG-Py

 def testAtomSymmetryNumberMethyl(self):
     """
     Test the Molecule.calculateAtomSymmetryNumber() on [CH3]
     """
     molecule = Molecule().fromSMILES('[CH3]')
     symmetryNumber = 1
     for atom in molecule.atoms:
         if not molecule.isAtomInCycle(atom):
             symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
     self.assertEqual(symmetryNumber, 6)

Esempio n. 7

File: symmetryTest.py Progetto: yplitw/RMG-Py

 def testAtomSymmetryNumberIsobutane(self):
     """
     Test the Molecule.calculateAtomSymmetryNumber() on CC(C)C
     """
     molecule = Molecule().fromSMILES('CC(C)C')
     symmetryNumber = 1
     for atom in molecule.atoms:
         if not molecule.isAtomInCycle(atom):
             symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
     self.assertEqual(symmetryNumber, 81)

Esempio n. 8

File: symmetryTest.py Progetto: yplitw/RMG-Py

 def testAtomSymmetryNumberMethyl(self):
     """
     Test the Molecule.calculateAtomSymmetryNumber() on [CH3]
     """
     molecule = Molecule().fromSMILES('[CH3]')
     symmetryNumber = 1
     for atom in molecule.atoms:
         if not molecule.isAtomInCycle(atom):
             symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
     self.assertEqual(symmetryNumber, 6)

Esempio n. 9

File: moleculeTest.py Progetto: comocheng/RMG-Py

 def testIsInCycleEthane(self):
     """
     Test the Molecule.isInCycle() method with ethane.
     """
     molecule = Molecule().fromSMILES('CC')
     for atom in molecule.atoms:
         self.assertFalse(molecule.isAtomInCycle(atom))
     for atom1 in molecule.atoms:
         for atom2, bond in atom1.bonds.items():
             self.assertFalse(molecule.isBondInCycle(bond))

Esempio n. 10

 def testIsInCycleEthane(self):
     """
     Test the Molecule.isInCycle() method with ethane.
     """
     molecule = Molecule().fromSMILES('CC')
     for atom in molecule.atoms:
         self.assertFalse(molecule.isAtomInCycle(atom))
     for atom1 in molecule.atoms:
         for atom2, bond in atom1.bonds.items():
             self.assertFalse(molecule.isBondInCycle(bond))

Esempio n. 11

File: symmetryTest.py Progetto: ReactionMechanismGenerator/RMG-Py

    def testAtomSymmetryNumberWithTwoChiralCenters(self):
        """
        Test the Molecule.calculateAtomSymmetryNumber() on [CH2]CC([CH2])C(C)C=C

        This is meant to test whether chirality is accounted for, which
        should half the symmetry term.

        The molecule has one methyl group (*3), two CH2dot groups (*2 each), and
        two chiral centers (*0.5), leading to a total atom symmetry number of 3
        """
        molecule = Molecule().fromAdjacencyList(
"""
multiplicity 3
1  C u1 p0 c0 {2,S} {3,S} {4,S}
2  H u0 p0 c0 {1,S}
3  H u0 p0 c0 {1,S}
4  C u0 p0 c0 {1,S} {5,S} {13,S} {14,S}
5  C u0 p0 c0 {4,S} {6,S} {9,S} {15,S}
6  C u1 p0 c0 {5,S} {7,S} {8,S}
7  H u0 p0 c0 {6,S}
8  H u0 p0 c0 {6,S}
9  C u0 p0 c0 {5,S} {10,S} {11,S} {16,S}
10 C u0 p0 c0 {9,S} {17,S} {18,S} {19,S}
11 C u0 p0 c0 {9,S} {12,D} {20,S}
12 C u0 p0 c0 {11,D} {21,S} {22,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
15 H u0 p0 c0 {5,S}
16 H u0 p0 c0 {9,S}
17 H u0 p0 c0 {10,S}
18 H u0 p0 c0 {10,S}
19 H u0 p0 c0 {10,S}
20 H u0 p0 c0 {11,S}
21 H u0 p0 c0 {12,S}
22 H u0 p0 c0 {12,S}
""")
        symmetryNumber = 1
        for atom in molecule.atoms:
            if not molecule.isAtomInCycle(atom):
                symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
        self.assertAlmostEqual(symmetryNumber, 3)

Esempio n. 12

File: symmetryTest.py Progetto: DrDew2/RMG-Py

    def testAtomSymmetryNumberWithTwoChiralCenters(self):
        """
        Test the Molecule.calculateAtomSymmetryNumber() on [CH2]CC([CH2])C(C)C=C

        This is meant to test whether chirality is accounted for, which
        should half the symmetry term.

        The molecule has one methyl group (*3), two CH2dot groups (*2 each), and
        two chiral centers (*0.5), leading to a total atom symmetry number of 3
        """
        molecule = Molecule().fromAdjacencyList(
"""
multiplicity 3
1  C u1 p0 c0 {2,S} {3,S} {4,S}
2  H u0 p0 c0 {1,S}
3  H u0 p0 c0 {1,S}
4  C u0 p0 c0 {1,S} {5,S} {13,S} {14,S}
5  C u0 p0 c0 {4,S} {6,S} {9,S} {15,S}
6  C u1 p0 c0 {5,S} {7,S} {8,S}
7  H u0 p0 c0 {6,S}
8  H u0 p0 c0 {6,S}
9  C u0 p0 c0 {5,S} {10,S} {11,S} {16,S}
10 C u0 p0 c0 {9,S} {17,S} {18,S} {19,S}
11 C u0 p0 c0 {9,S} {12,D} {20,S}
12 C u0 p0 c0 {11,D} {21,S} {22,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {4,S}
15 H u0 p0 c0 {5,S}
16 H u0 p0 c0 {9,S}
17 H u0 p0 c0 {10,S}
18 H u0 p0 c0 {10,S}
19 H u0 p0 c0 {10,S}
20 H u0 p0 c0 {11,S}
21 H u0 p0 c0 {12,S}
22 H u0 p0 c0 {12,S}
""")
        symmetryNumber = 1
        for atom in molecule.atoms:
            if not molecule.isAtomInCycle(atom):
                symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
        self.assertAlmostEqual(symmetryNumber, 3)