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)