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_CycleBondSelector_select_none(self):
"""
test CycleBondSelector select: no bonds
"""
cbSel = CycleBondSelector()
ats = self.mol.allAtoms[4:8]
bnds = ats.bonds[0]
resultBnds = cbSel.select(bnds)
#print 'no_cb_bonds:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds) , 0)
def test_CycleBondSelector_select_none(self):
"""
test CycleBondSelector select: no bonds
"""
cbSel = CycleBondSelector()
ats = self.mol.allAtoms[4:8]
bnds = ats.bonds[0]
resultBnds = cbSel.select(bnds)
#print 'no_cb_bonds:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 0)
def test_CycleBondSelector_select_all(self):
"""
test CycleBondSelector select: all bonds
"""
cbSel = CycleBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = cbSel.select(bnds)
#print 'all_cb_bonds:len(resultBnds)=', len(resultBnds)
#self.assertEqual(len(resultBnds) , 43)
#because of di-sulfide bridges:
#when increase RingFinder parameter "maxSize"
self.assertEqual(len(resultBnds) , 165)
def test_CycleBondSelector_select_all(self):
"""
test CycleBondSelector select: all bonds
"""
cbSel = CycleBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = cbSel.select(bnds)
#print 'all_cb_bonds:len(resultBnds)=', len(resultBnds)
#self.assertEqual(len(resultBnds) , 43)
#because of di-sulfide bridges:
#when increase RingFinder parameter "maxSize"
self.assertEqual(len(resultBnds), 165)
def test_CycleBondSelector_select_some(self):
"""
test CycleBondSelector select: some bonds
"""
cbSel = CycleBondSelector()
ats = self.mol.allAtoms[:50]
bnds = ats.bonds[0]
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_CycleBondSelector_constructor(self):
"""
test CycleBondSelector constructor
"""
cbSel = CycleBondSelector()
self.assertEqual(cbSel.__class__, CycleBondSelector)