def test_GuanidiniumBondSelector_select_all(self):
"""
test GuanidiniumBond select: all bonds
"""
guanSel = GuanidiniumBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = guanSel.select(bnds)
#print 'all_guanidinium_bonds:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 6)
for b in resultBnds:
self.assertEqual(b.atom1.parent.type, 'ARG')
if b.atom1.element=='C':
self.assertEqual(b.atom1.name, 'CZ')
if b.atom1.element=='N':
self.assertEqual(b.atom1.name in ['NE','NH1','NH2'], True)
def test_GuanidiniumBondSelector_select_all(self):
"""
test GuanidiniumBond select: all bonds
"""
guanSel = GuanidiniumBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = guanSel.select(bnds)
#print 'all_guanidinium_bonds:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 6)
for b in resultBnds:
self.assertEqual(b.atom1.parent.type, 'ARG')
if b.atom1.element == 'C':
self.assertEqual(b.atom1.name, 'CZ')
if b.atom1.element == 'N':
self.assertEqual(b.atom1.name in ['NE', 'NH1', 'NH2'], True)
def test_GuanidiniumBondSelector_select_all(self):
"""
test GuanidiniumBond select: all bonds
"""
guanSel = GuanidiniumBondSelector()
ats = self.mol.allAtoms
bnds = ats.bonds[0]
resultBnds = guanSel.select(bnds)
# print 'all_guanidinium_bonds:len(resultBnds)=', len(resultBnds)
self.assertEqual(len(resultBnds), 6)
for b in resultBnds:
self.assertEqual(b.atom1.parent.type, "ARG")
if b.atom1.element == "C":
self.assertEqual(b.atom1.name, "CZ")
if b.atom1.element == "N":
self.assertEqual(b.atom1.name in ["NE", "NH1", "NH2"], True)
def setAutoFlexFields(res):
#process residues
if hasattr(res, 'setup'):
return
res.setup = 1
res.atoms.used = 0
res.atoms.bonds[0].possibleTors = 0
res.atoms.bonds[0].activeTors = 0
backbone_names = [
'C', 'N', 'O', 'HN', 'HN1', 'HN2', 'HA', 'H1', 'H2', 'H3', 'HO', 'H'
]
#includes CA
sidechain = res.atoms.get(lambda x: x.name not in backbone_names)
res.sideChain = sidechain
bondlist = res.bondlist = sidechain.bonds[0]
bondlist.leaf = 0
bondlist.possibleTors = 0
bondlist.activeTors = 0
rbs = RotatableBondSelector()
rotatables = rbs.select(bondlist)
for b in rotatables:
b.possibleTors = 1
b.activeTors = 1
amides = AmideBondSelector().select(bondlist)
for b in amides:
b.activeTors = 0
b.possibleTors = 1
guanidiniums = GuanidiniumBondSelector().select(bondlist)
for b in guanidiniums:
b.activeTors = 0
b.possibleTors = 1
leaves = LeafBondSelector().select(bondlist)
for b in leaves:
b.activeTors = 0
b.possibleTors = 0
res.torscount = len(bondlist.get(lambda x: x.activeTors == 1))
#this field is not used in AutoDock4
res.torsdof = res.torscount
res.torscount = len(bondlist.get(lambda x: x.activeTors == 1))
res.torsdof = res.torscount
caAtoms = res.atoms.get(lambda x: x.name == 'CA')
#get returns an AtomSet
if caAtoms: #this checks for len(caAtoms)
res.rootlist = caAtoms
else:
res.rootlist = AtomSet([res.atoms.get(lambda x: x._uniqIndex == 0)[0]])
res.sideChain = res.atoms
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