def setUpClass(cls):
cls.ldr = stc.StructureLoader()
cls.s1 = cls.ldr.load_structure(cls.s1n)[0]
cls.s2 = cls.ldr.load_structure(cls.s2n)[0]
cls.s1.set_contact_map()
cls.s2.set_contact_map()
end = 10 if fast else None
s1ds = stc.AbstractDescriptor.create_descriptors(cls.s1)
s2ds = stc.AbstractDescriptor.create_descriptors(cls.s2)
cls.rdic1 = {}
cls.rdic2 = {}
for d1, d2 in zip(s1ds, s2ds):
try:
cls.rdic1[d1.central_element.central_monomer.ind] = d1
except AttributeError:
pass
try:
cls.rdic2[d2.central_element.central_monomer.ind] = d2
except AttributeError:
pass
cls.res = [(cpd.compdesc(d1, d2), d1, d2) for d1 in s1ds[:end]
for d2 in s2ds[:end] if None not in (d1, d2)]
if len(cls.res) == 0:
raise Warning("No results from compdesc.")
def test_pdbstring(self):
stg = self.struct.create_pdbstring()
self.struct.save_pdb('stc_test.pdb')
nstc = structure.StructureLoader().load_structure(
'test', path='stc_test.pdb')[0]
stg2 = nstc.create_pdbstring()
self.assertEqual(stg.read(), stg2.read())
def make_trajectorytest(strname):
"""Create and return a StructureTest testcase for a structures linked with dcd trajectories."""
sl = structure.StructureLoader()
class TrajectoryTest(unittest.TestCase):
name = strname
@classmethod
def setUpClass(cls):
cls.pdb_structure = sl.load_structure("mdm2",
path=dcd_data_dir +
cls.name + ".pdb")[0]
@testing(structure.Structure.link_dcd_file)
@testing(structure.Structure.disconnect_trajectory)
@testing(structure.Structure.next_frame)
@testing(structure.Structure.frame)
def test_linking_trajectory(self):
self.assertIsNone(self.pdb_structure.frame)
self.pdb_structure.link_dcd_file(dcd_data_dir + self.name + ".dcd")
fr = self.pdb_structure.frame
self.pdb_structure.next_frame()
self.assertEqual(fr + 1, self.pdb_structure.frame)
self.assertIsNotNone(self.pdb_structure.frame)
self.pdb_structure.disconnect_trajectory()
self.assertIsNone(self.pdb_structure.frame)
return TrajectoryTest
def w_load(app):
"""Creates structure loader and calls load_structure method with parameters given by user in dialog window."""
loader = structure.StructureLoader()
pdb_code = tkSimpleDialog.askstring("PyDesc", "Please enter a 4-char pdb code:", parent=app.root)
try:
loader.load_structure(pdb_code)
except:
tkMessageBox.showerror("Invalid code", "The code you entered is incorrect:" + pdb_code)
raise
def test_loader(self):
""" Test StructureLoader.load_structure. """
loader = structure.StructureLoader()
for name in self.structures:
with warnings.catch_warnings(record=True):
struct = loader.load_structure(name)
f = loader.handler.get_file(name)
pdb_models = Bio.PDB.PDBParser(QUIET=True).get_structure(name, f)
for s in struct:
self.assertIsInstance(s, structure.Structure)
self.assertEqual(len(struct), len(pdb_models))
def setUpClass(cls):
cls.s = structure.StructureLoader().load_structure(str_name)[0]
cls.s.set_contact_map(contacts.RcContact())
cls.ds = filter(
bool, structure.AbstractDescriptor.create_descriptors(cls.s))