def test_Kollman_calc_addCharges(self):
"""
KollmanChargeCalculator addCharges to each atom, giving expected total
"""
atlen = len(self.mol.allAtoms)
k_calc = KollmanChargeCalculator()
k_calc.addCharges(self.mol.allAtoms)
k_ats = self.mol.allAtoms.get(lambda x: x.chargeSet == 'Kollman')
self.assertEquals(atlen, len(k_ats))
total_charge = Numeric.add.reduce(self.mol.allAtoms.charge)
self.assertAlmostEquals(total_charge, -19.554, 4)
def test_Kollman_calc_addCharges(self):
"""
KollmanChargeCalculator addCharges to each atom, giving expected total
"""
atlen = len(self.mol.allAtoms)
k_calc = KollmanChargeCalculator()
k_calc.addCharges(self.mol.allAtoms)
k_ats = self.mol.allAtoms.get(lambda x: x.chargeSet=='Kollman')
self.assertEquals(atlen, len(k_ats))
total_charge = Numeric.add.reduce(self.mol.allAtoms.charge)
self.assertAlmostEquals(total_charge, -19.554, 4)
def test_Kollman_calc_from_bug(self):
"""
test KollmanChargeCalculator can add charges to 1a30
"""
mol = Read("Data/1a30.pdb")[0]
atlen = len(mol.allAtoms)
k_calc = KollmanChargeCalculator()
k_calc.addCharges(mol.allAtoms)
k_ats = mol.allAtoms.get(lambda x: x.chargeSet == 'Kollman')
self.assertEquals(atlen, len(k_ats))
total_charge = Numeric.add.reduce(mol.allAtoms.charge)
self.assertAlmostEquals(total_charge, 5.7060, 4)
def test_Kollman_calc_from_bug(self):
"""
test KollmanChargeCalculator can add charges to 1a30
"""
mol = Read("Data/1a30.pdb")[0]
atlen = len(mol.allAtoms)
k_calc = KollmanChargeCalculator()
k_calc.addCharges(mol.allAtoms)
k_ats = mol.allAtoms.get(lambda x: x.chargeSet=='Kollman')
self.assertEquals(atlen, len(k_ats))
total_charge = Numeric.add.reduce(mol.allAtoms.charge)
self.assertAlmostEquals(total_charge, 5.7060, 4)
def test_kollman_calc_constructor(self):
"""
instantiate an KollmanChargeCalculator
"""
k_calc = KollmanChargeCalculator()
self.assertEquals(k_calc.__class__, KollmanChargeCalculator)
