def test_HydrogenRotatorBondSelector_select_all(self):
"""
test HydrogenRotator select: all bonds
"""
HRSel = HydrogenRotatorBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = HRSel.select(bnds)
#print 'all_hydrogenrotators:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds) , 18)
def test_HydrogenRotatorBondSelector_select_none(self):
"""
test HydrogenRotator select: no bonds
"""
HRSel = HydrogenRotatorBondSelector()
ats = self.mol.allAtoms[2:6]
bnds = ats.bonds[0]
resultBnds = HRSel.select(bnds)
#print 'no_hydrogenrotators:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds) , 0)
def test_HydrogenRotatorBondSelector_select_some(self):
"""
test HydrogenRotator select: some bonds
"""
HRSel = HydrogenRotatorBondSelector()
ats = self.mol.chains.residues[:8].atoms
bnds = ats.bonds[0]
resultBnds = HRSel.select(bnds)
#print 'some_hydrogenrotators:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds) , 4)
def test_HydrogenRotatorBondSelector_select_all(self):
"""
test HydrogenRotator select: all bonds
"""
HRSel = HydrogenRotatorBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = HRSel.select(bnds)
#print 'all_hydrogenrotators:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 18)
def test_HydrogenRotatorBondSelector_select_some(self):
"""
test HydrogenRotator select: some bonds
"""
HRSel = HydrogenRotatorBondSelector()
ats = self.mol.chains.residues[:8].atoms
bnds = ats.bonds[0]
resultBnds = HRSel.select(bnds)
#print 'some_hydrogenrotators:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 4)
def test_HydrogenRotatorBondSelector_select_none(self):
"""
test HydrogenRotator select: no bonds
"""
HRSel = HydrogenRotatorBondSelector()
ats = self.mol.allAtoms[2:6]
bnds = ats.bonds[0]
resultBnds = HRSel.select(bnds)
#print 'no_hydrogenrotators:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 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_HydrogenRotatorBondSelector_constructor(self):
"""
test HydrogenRotator constructor
"""
hrBndSel = HydrogenRotatorBondSelector()
self.assertEqual(hrBndSel.__class__, HydrogenRotatorBondSelector)
