def test_classifierVSselectors(self): """ make sure that the classifier returns the same results as its selectors """ bndClassifier = BondClassifier({ 'amide': AmideBondSelector(), 'cycle': CycleBondSelector(), 'leaf': LeafBondSelector(), 'peptide': PeptideBackBoneBondSelector(), }) #all the bonds in the molecule as a BondSet bnds = self.mol.allAtoms.bonds[0] #get the specified bonds as a BondSet localDict = {} localDict['amide'] = AmideBondSelector().select(bnds) localDict['cycle'] = CycleBondSelector().select(bnds) localDict['leaf'] = LeafBondSelector().select(bnds) localDict['peptide'] = PeptideBackBoneBondSelector().select(bnds) #make the classifier do the same thing resultDict = bndClassifier.classify(bnds) for k in resultDict.keys(): self.compareBondSets(localDict[k], resultDict[k])
def test_PeptideBackBoneBondSelector_select_all(self): """ test PetideBackBone select: all bonds """ ppbbSel = PeptideBackBoneBondSelector() ats = self.mol.allAtoms bnds = ats.bonds[0] resultBnds = ppbbSel.select(bnds) #print 'all_ppbbbonds:len(resultBnds)=', len(resultBnds) self.assertEqual(len(resultBnds) , 132)
def test_PeptideBackBoneBondSelector_select_none(self): """ test PetideBackBone select: no bonds """ ppbbSel = PeptideBackBoneBondSelector() ats = self.mol.allAtoms[4:8] bnds = ats.bonds[0] resultBnds = ppbbSel.select(bnds) #print 'no_ppbbbonds:len(resultBnds)=', len(resultBnds) self.assertEqual(len(resultBnds) , 0)
def test_PeptideBackBoneBondSelector_select_all(self): """ test PetideBackBone select: all bonds """ ppbbSel = PeptideBackBoneBondSelector() ats = self.mol.allAtoms bnds = ats.bonds[0] resultBnds = ppbbSel.select(bnds) #print 'all_ppbbbonds:len(resultBnds)=', len(resultBnds) self.assertEqual(len(resultBnds), 132)
def test_PeptideBackBoneBondSelector_select_none(self): """ test PetideBackBone select: no bonds """ ppbbSel = PeptideBackBoneBondSelector() ats = self.mol.allAtoms[4:8] bnds = ats.bonds[0] resultBnds = ppbbSel.select(bnds) #print 'no_ppbbbonds:len(resultBnds)=', len(resultBnds) self.assertEqual(len(resultBnds), 0)
def test_PeptideBackBoneBondSelector_select_some(self): """ test PetideBackBone select: some bonds """ ppbbSel = PeptideBackBoneBondSelector() ats = self.mol.allAtoms[:50] bnds = ats.bonds[0] resultBnds = ppbbSel.select(bnds) #print 'some_ppbbbonds:len(resultBnds)=', len(resultBnds) #self.assertEqual(len(resultBnds) , 22) self.assertEqual(len(resultBnds) , 17)
def test_PeptideBackBoneBondSelector_select_some(self): """ test PetideBackBone select: some bonds """ ppbbSel = PeptideBackBoneBondSelector() ats = self.mol.allAtoms[:50] bnds = ats.bonds[0] resultBnds = ppbbSel.select(bnds) #print 'some_ppbbbonds:len(resultBnds)=', len(resultBnds) #self.assertEqual(len(resultBnds) , 22) self.assertEqual(len(resultBnds), 17)
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_PeptideBackBoneBondSelector_constructor(self): """ test PetideBackBone constructor """ ppbbSel = PeptideBackBoneBondSelector() self.assertEqual(ppbbSel.__class__, PeptideBackBoneBondSelector)