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)
