def test_BondOrderBondSelector_select_all(self): """ test BondOrder select: all bonds """ bobSel = BondOrderBondSelector() ats = self.mol.allAtoms bnds = ats.bonds[0] resultBnds = bobSel.select(bnds) #print 'all_cb_bonds:len(resultBnds)=', len(resultBnds) self.assertEqual(len(resultBnds) , 341)
def test_BondOrderBondSelector_select_all(self): """ test BondOrder select: all bonds """ bobSel = BondOrderBondSelector() ats = self.mol.allAtoms bnds = ats.bonds[0] resultBnds = bobSel.select(bnds) #print 'all_cb_bonds:len(resultBnds)=', len(resultBnds) self.assertEqual(len(resultBnds), 341)
def test_BondOrderBondSelector_select_some(self): """ test BondOrder select: some bonds """ bobSel = BondOrderBondSelector() ats = self.mol.allAtoms[:50] bnds = ats.bonds[0] resultBnds = bobSel.select(bnds) #print 'some_cb_bonds:len(resultBnds)=', len(resultBnds) #self.assertEqual(len(resultBnds) , 43) self.assertEqual(len(resultBnds) , 44)
def test_BondOrderBondSelector_select_none(self): """ test BondOrder select: no bonds """ bobSel = BondOrderBondSelector() ats = self.mol.allAtoms[4:8] bnds = ats.bonds[0] resultBnds = bobSel.select(bnds) #print 'no_cb_bonds:len(resultBnds)=', len(resultBnds) #self.assertEqual(len(resultBnds) , 2) self.assertEqual(len(resultBnds) , 3)
def test_BondOrderBondSelector_select_some(self): """ test BondOrder select: some bonds """ bobSel = BondOrderBondSelector() ats = self.mol.allAtoms[:50] bnds = ats.bonds[0] resultBnds = bobSel.select(bnds) #print 'some_cb_bonds:len(resultBnds)=', len(resultBnds) #self.assertEqual(len(resultBnds) , 43) self.assertEqual(len(resultBnds), 44)
def test_BondOrderBondSelector_select_none(self): """ test BondOrder select: no bonds """ bobSel = BondOrderBondSelector() ats = self.mol.allAtoms[4:8] bnds = ats.bonds[0] resultBnds = bobSel.select(bnds) #print 'no_cb_bonds:len(resultBnds)=', len(resultBnds) #self.assertEqual(len(resultBnds) , 2) self.assertEqual(len(resultBnds), 3)
def __init__(self, tolerance=0.01, detectAll=True): self.detect_all_cycles = detectAll self.d = { 'amide': AmideBondSelector(), 'ppbb': PeptideBackBoneBondSelector(), 'leaf': LeafBondSelector(), 'cycle': CycleBondSelector(), 'rotatable': RotatableBondSelector(), 'bondOrder2': BondOrderBondSelector(2), 'hydrogenRotators': HydrogenRotatorBondSelector(), 'guanidinium': GuanidiniumBondSelector(), 'aromatic': AromaticCycleBondSelector2() } BondClassifier.__init__(self, self.d) #used to detect colinear atoms #if dist1+dist2<dist13+0.1 self.tolerance = 0.01
def test_BondOrderBondSelector(self): """ test BondOrder constructor """ bobSel = BondOrderBondSelector() self.assertEqual(bobSel.__class__, BondOrderBondSelector)