def test_rings(self):
# benzene molecule
benzene = chemkit.Molecule("c1ccccc1", "smiles")
self.assertEqual(benzene.formula(), "C6H6")
self.assertEqual(benzene.ringCount(), 1)
ring = benzene.ring(0)
self.assertEqual(ring.size(), 6)
def test_name(self):
molecule = chemkit.Molecule()
atom = molecule.addAtom("C")
self.assertEqual(atom.name(), "Carbon")
atom.setAtomicNumber(8)
self.assertEqual(atom.name(), "Oxygen")
def test_symbol(self):
molecule = chemkit.Molecule()
atom = molecule.addAtom("C")
self.assertEqual(atom.symbol(), "C")
atom.setAtomicNumber(2)
self.assertEqual(atom.symbol(), "He")
def test_atoms(self):
molecule = chemkit.Molecule()
a = molecule.addAtom("C")
b = molecule.addAtom("C")
bond = molecule.addBond(a, b)
self.assertEqual(bond.atom(0), a)
self.assertEqual(bond.atom(1), b)
self.assertEqual(bond.atoms(), [a, b])
def test_formula(self):
# empty molecule
empty = chemkit.Molecule()
self.assertEqual(empty.formula(), "")
# ethanol molecule
ethanol = chemkit.Molecule()
C1 = ethanol.addAtom("C")
C2 = ethanol.addAtom("C")
O3 = ethanol.addAtom("O")
ethanol.addBond(C1, C2)
ethanol.addBond(C2, O3)
for atom in ethanol.atoms():
while (atom.formalCharge() < 0):
hydrogen = ethanol.addAtom("H")
ethanol.addBond(atom, hydrogen)
self.assertEqual(ethanol.formula(), "C2H6O")
def test_atom(self):
molecule = chemkit.Molecule()
C1 = molecule.addAtom("C")
self.assertEqual(C1.atomicNumber(), 6)
C2 = molecule.addAtom(6)
self.assertEqual(C2.atomicNumber(), 6)
C3 = molecule.addAtom(chemkit.Atom.Carbon)
self.assertEqual(C3.atomicNumber(), 6)
self.assertEqual(molecule.atomCount(), 3)
self.assertEqual(molecule.formula(), "C3")
def test_bond(self):
molecule = chemkit.Molecule()
self.assertEqual(molecule.bondCount(), 0)
C1 = molecule.addAtom("C")
C2 = molecule.addAtom("C")
C3 = molecule.addAtom("C")
C1_C2 = molecule.addBond(C1, C2)
self.assertEqual(molecule.bondCount(), 1)
C2_C3 = molecule.addBond(C2, C3, 2)
self.assertEqual(molecule.bondCount(), 2)
self.assertEqual(C2_C3.order(), 2)
def test_benzene_mmff(self):
molecule = chemkit.Molecule("c1ccccc1", "smiles")
self.assertEqual(molecule.formula(), "C6H6")
typer = chemkit.AtomTyper.create("mmff")
typer.setMolecule(molecule)
for atom in molecule.atoms():
if atom.symbol() == "C":
self.assertEqual(typer.type(atom), "37")
elif atom.symbol() == "H":
self.assertEqual(typer.type(atom), "5")
def test_length(self):
molecule = chemkit.Molecule()
a = molecule.addAtom("C")
a.setPosition(2, 0, 0)
b = molecule.addAtom("C")
b.setPosition(5, 0, 0)
bond = molecule.addBond(a, b)
self.assertEqual(round(bond.length()), 3)
b.setPosition(-2, 0, 0)
self.assertEqual(round(bond.length()), 4)
def test_order(self):
molecule = chemkit.Molecule()
a = molecule.addAtom("C")
b = molecule.addAtom("C")
bond = molecule.addBond(a, b)
self.assertEqual(bond.order(), 1)
self.assertEqual(bond.order(), chemkit.Bond.Single)
bond.setOrder(2)
self.assertEqual(bond.order(), 2)
self.assertEqual(bond.order(), chemkit.Bond.Double)
def test_assign_types(self):
molecule = chemkit.Molecule("CCO", "smiles")
self.assertEqual(molecule.formula(), "C2H6O")
for atom in molecule.atoms():
self.assertEqual(atom.type(), "")
chemkit.AtomTyper.assignAtomTypes(molecule, "element-name")
for atom in molecule.atoms():
if atom.symbol() == "C":
self.assertEqual(atom.type(), "Carbon")
elif atom.symbol() == "H":
self.assertEqual(atom.type(), "Hydrogen")
elif atom.symbol() == "O":
self.assertEqual(atom.type(), "Oxygen")