def test_subsequence(self):
"""Test setup of subsequence"""
mh = IMP.atom.read_pdb(self.get_input_file_name('chainA.pdb'),self.mdl)
sd = Subsequence(chain='A',residue_tuple=(100,125))
sd.add_range(chain='A',residue_tuple=(325,355))
sel = sd.get_selection(hier=mh,atom_type=IMP.atom.AtomType('CA'))
idxs = sorted([IMP.atom.get_residue(IMP.atom.Atom(h)).get_index()
for h in sel.get_selected_particles()])
self.assertEqual(idxs,list(range(100,126))+list(range(325,356)))
self.assertEqual(sd.__repr__(),'100-125.A_325-355.A')
def test_subsequence_data(self):
"""Test the SubsequenceData collection"""
ssd = SubsequenceData()
ssd.add_subsequence('helix',Subsequence(molecule='m1',
residue_tuple=(55,58)))
ssd.add_subsequence('helix',Subsequence(molecule='m2',
residue_tuple=(195,208)))
beta = Subsequence(molecule='m1',residue_tuple=(5,10))
beta.add_range(molecule='m2',residue_tuple=(95,100))
ssd.add_subsequence('beta',beta)
self.assertEqual(len(ssd['helix']),2)
self.assertEqual(len(ssd['beta']),1)
self.assertEqual(ssd['helix'][0].__repr__(),
'55-58.m1')
self.assertEqual(ssd['helix'][1].__repr__(),
'195-208.m2')
self.assertEqual(ssd['beta'][0].__repr__(),
'5-10.m1_95-100.m2')
def test_subsequence(self):
"""Test setup of subsequence"""
mh = IMP.atom.read_pdb(self.get_input_file_name('chainA.pdb'),
self.mdl)
sd = Subsequence(chain='A', residue_tuple=(100, 125))
sd.add_range(chain='A', residue_tuple=(325, 355))
sel = sd.get_selection(hier=mh, atom_type=IMP.atom.AtomType('CA'))
idxs = sorted([
IMP.atom.get_residue(IMP.atom.Atom(h)).get_index()
for h in sel.get_selected_particles()
])
self.assertEqual(idxs, list(range(100, 126)) + list(range(325, 356)))
self.assertEqual(sd.__repr__(), '100-125.A_325-355.A')
def test_subsequence_data(self):
"""Test the SubsequenceData collection"""
ssd = SubsequenceData()
ssd.add_subsequence('helix',
Subsequence(molecule='m1', residue_tuple=(55, 58)))
ssd.add_subsequence(
'helix', Subsequence(molecule='m2', residue_tuple=(195, 208)))
beta = Subsequence(molecule='m1', residue_tuple=(5, 10))
beta.add_range(molecule='m2', residue_tuple=(95, 100))
ssd.add_subsequence('beta', beta)
self.assertEqual(len(ssd['helix']), 2)
self.assertEqual(len(ssd['beta']), 1)
self.assertEqual(ssd['helix'][0].__repr__(), '55-58.m1')
self.assertEqual(ssd['helix'][1].__repr__(), '195-208.m2')
self.assertEqual(ssd['beta'][0].__repr__(), '5-10.m1_95-100.m2')