def testAxisSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateAxisSymmetryNumber() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
def testAxisSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateAxisSymmetryNumber() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
def testGetResonanceHybrid(self):
"""
Tests that getResonanceHybrid returns an isomorphic structure
which has intermediate bond orders.
This check is for C=C[CH]CC which has another resonance structure,
[CH2]C=CC. When these structures are merged, the bond structure should be,
C~C~CC, where '~' is a hybrid bond of order 1.5.
"""
spec = Species().fromSMILES('C=C[CH]CC')
hybridMol = spec.getResonanceHybrid()
self.assertTrue(hybridMol.toSingleBonds().isIsomorphic(spec.molecule[0].toSingleBonds()))
# a rough check for intermediate bond orders
expected_orders = [1,1.5]
bonds = []
# ensure all bond orders are expected
for atom in hybridMol.atoms:
for atom2 in atom.bonds:
bond = hybridMol.getBond(atom,atom2)
self.assertTrue(any([bond.isOrder(otherOrder) for otherOrder in expected_orders]), 'Unexpected bond order {}'.format(bond.getOrderNum()))
bonds.append(bond)
# ensure all expected orders are present
for expected_order in expected_orders:
self.assertTrue(any([bond.isOrder(expected_order) for bond in bonds]),'No bond of order {} found'.format(expected_order))
def testGetResonanceHybrid(self):
"""
Tests that getResonanceHybrid returns an isomorphic structure
which has intermediate bond orders.
This check is for C=C[CH]CC which has another resonance structure,
[CH2]C=CC. When these structures are merged, the bond structure should be,
C~C~CC, where '~' is a hybrid bond of order 1.5.
"""
spec = Species().fromSMILES('C=C[CH]CC')
hybridMol = spec.getResonanceHybrid()
self.assertTrue(hybridMol.toSingleBonds().isIsomorphic(
spec.molecule[0].toSingleBonds()))
# a rough check for intermediate bond orders
expected_orders = [1, 1.5]
bonds = []
# ensure all bond orders are expected
for atom in hybridMol.atoms:
for atom2 in atom.bonds:
bond = hybridMol.getBond(atom, atom2)
self.assertTrue(
any([
bond.isOrder(otherOrder)
for otherOrder in expected_orders
]), 'Unexpected bond order {}'.format(bond.getOrderNum()))
bonds.append(bond)
# ensure all expected orders are present
for expected_order in expected_orders:
self.assertTrue(
any([bond.isOrder(expected_order) for bond in bonds]),
'No bond of order {} found'.format(expected_order))
def testDrawNonStandardBonds(self):
spec = Species().fromSMILES('[CH2]C=C[CH2]')
hybrid = spec.getResonanceHybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(hybrid, format='pdf')
self.assertIsInstance(surface, PDFSurface)
def testDrawNonStandardBonds(self):
spec = Species().fromSMILES('[CH2]C=C[CH2]')
hybrid = spec.getResonanceHybrid()
try:
from cairocffi import PDFSurface
except ImportError:
from cairo import PDFSurface
surface, cr, (xoff, yoff, width, height) = self.drawer.draw(hybrid, format='pdf')
self.assertIsInstance(surface, PDFSurface)
def testAtomSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
symmetryNumber = 1
for atom in molecule.atoms:
if not molecule.isAtomInCycle(atom):
symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
self.assertEqual(symmetryNumber, 2)
def testAtomSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
symmetryNumber = 1
for atom in molecule.atoms:
if not molecule.isAtomInCycle(atom):
symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
self.assertEqual(symmetryNumber, 2)
def testBondSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateBondSymmetryNumber() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
symmetryNumber = 1
for atom1 in molecule.atoms:
for atom2 in atom1.bonds:
if molecule.atoms.index(atom1) < molecule.atoms.index(atom2):
symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
self.assertEqual(symmetryNumber, 1)
def testBondSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateBondSymmetryNumber() on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
symmetryNumber = 1
for atom1 in molecule.atoms:
for atom2 in atom1.bonds:
if molecule.atoms.index(atom1) < molecule.atoms.index(atom2):
symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
self.assertEqual(symmetryNumber, 1)
def testEdgeCarbonAtomSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() for the edge carbons
on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
for atom in molecule.atoms:
if atom.symbol =='C':
number_carbon_bonds = sum([1 for bond in atom.bonds if bond.symbol=='C'])
if number_carbon_bonds == 1:
atom.label = 'edge'
symmetryNumber = calculateAtomSymmetryNumber(molecule, atom)
self.assertEqual(symmetryNumber, 1)
def testEdgeCarbonAtomSymmetryNumberAllyl(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() for the edge carbons
on [CH2]C=C
"""
spc = Species(molecule=[Molecule().fromSMILES('[CH2]C=C')])
molecule = spc.getResonanceHybrid()
for atom in molecule.atoms:
if atom.symbol =='C':
number_carbon_bonds = sum([1 for bond in atom.bonds if bond.symbol=='C'])
if number_carbon_bonds == 1:
atom.label = 'edge'
symmetryNumber = calculateAtomSymmetryNumber(molecule, atom)
self.assertEqual(symmetryNumber, 1)
def testMiddleCarbonAtomSymmetryNumberAllylUsingResonanceHybrid(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() for the middle carbon
on [CH2]C=C using the resonance hybrid structure
"""
molecule = Molecule().fromSMILES('[CH2]C=C')
species = Species(molecule=[molecule])
resonanceHybrid = species.getResonanceHybrid()
for atom in resonanceHybrid.atoms:
if atom.symbol == 'C':
number_carbon_bonds = sum([1 for bond in atom.bonds if bond.symbol=='C'])
if number_carbon_bonds == 2:
atom.label = 'center'
symmetryNumber = calculateAtomSymmetryNumber(resonanceHybrid, atom)
self.assertEqual(symmetryNumber, 2)
pass
def testMiddleCarbonAtomSymmetryNumberAllylUsingResonanceHybrid(self):
"""
Test the Molecule.calculateAtomSymmetryNumber() for the middle carbon
on [CH2]C=C using the resonance hybrid structure
"""
molecule = Molecule().fromSMILES('[CH2]C=C')
species = Species(molecule=[molecule])
resonanceHybrid = species.getResonanceHybrid()
for atom in resonanceHybrid.atoms:
if atom.symbol == 'C':
number_carbon_bonds = sum([1 for bond in atom.bonds if bond.symbol=='C'])
if number_carbon_bonds == 2:
atom.label = 'center'
symmetryNumber = calculateAtomSymmetryNumber(resonanceHybrid, atom)
self.assertEqual(symmetryNumber, 2)
pass