def test_convert_to_dict_and_rebuild(self):
'''test_convert_to_dict_and_rebuild
'''
top = self.traj.top
d = top.to_dict()
new_top = pt.Topology()
MOLNUM = 0
for idx, (aname, atype, charge, mass, resid, resname,
mol_number) in enumerate(
zip(d['atom_name'], d['atom_type'], d['atom_charge'], d[
'atom_mass'], d['resid'], d['resname'], d[
'mol_number'])):
atom = pt.core.Atom(
name=aname, type=atype, charge=charge, mass=mass, resid=resid)
atom.set_mol(mol_number)
residue = pt.core.Residue(resname, resid)
new_top.add_atom(atom, residue)
if idx == 0:
new_top.start_new_mol()
if mol_number > MOLNUM:
new_top.start_new_mol()
MOLNUM += 1
new_top.add_bonds(d['bond_index'])
new_top.add_dihedrals(d['dihedral_index'])
new_top.box = Box(top.box.values)
assert_equal_topology(top, new_top, self.traj)
def test_comprehensive(self):
traj = pt.iterload("data/Test_RemdTraj/rem.nc.000",
"data/Test_RemdTraj/ala2.99sb.mbondi2.parm7")
# temperature
aa_eq(traj.temperatures, [300., 630.5, 630.5, 630.5, 630.5, 630.5,
630.5, 630.5, 492.2, 384.3])
# iterframe (already in doctest), just throwing raise to increase coverage score
self.assertRaises(ValueError, lambda: traj.iterframe(rmsfit='crazy'))
# raise
# memory error if load larger than 1GB for xyz
traj = pt.datafiles.load_tz2_ortho()
for _ in range(11):
traj._load(traj.filelist)
self.assertRaises(MemoryError, lambda: traj.xyz)
# can not find filename
self.assertRaises(ValueError, lambda: traj._load(None))
# has filename but does not have Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000", top=None))
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000"))
# empty Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000", top=pt.Topology()))
# weird Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator("data/Test_RemdTraj/rem.nc.000", top=pt.Frame))
def test_raise_construtor(self):
self.assertRaises(ValueError, lambda: pt.Trajectory(pt.trajectory))
# raise if filename is not string or list of string
empty_traj = pt.Trajectory()
empty_traj.top = pt.datafiles.load_tz2()[:].top
self.assertRaises(ValueError, lambda: empty_traj.load(pt.Trajectory))
# raise if empty Topology
xyz = np.arange(90).astype('f8').reshape(3, 10, 3)
self.assertRaises(ValueError, lambda: pt.Trajectory(xyz=xyz, top=pt.Topology()))
def test_comprehensive(self):
traj = pt.iterload(fn('Test_RemdTraj/rem.nc.000'),
fn('Test_RemdTraj/ala2.99sb.mbondi2.parm7'))
# temperature
aa_eq(traj.temperatures, [
300., 630.5, 630.5, 630.5, 630.5, 630.5, 630.5, 630.5, 492.2, 384.3
])
# iterframe (already in doctest), just throwing raise to increase coverage score
self.assertRaises(ValueError, lambda: traj.iterframe(rmsfit='crazy'))
# raise
# memory error if load larger than 1GB for xyz
traj = pt.datafiles.load_tz2_ortho()
for _ in range(2):
traj._load(traj.filelist)
with patch('pytraj.trajectory.trajectory_iterator.TrajectoryIterator._estimated_GB') as \
mem:
def mock_get(*args, **kwargs):
return 10000000
mem.__get__ = mock_get
self.assertRaises(MemoryError, lambda: traj.xyz)
# can not find filename
self.assertRaises(ValueError, lambda: traj._load(None))
# has filename but does not have Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000'),
top=None))
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000')))
# empty Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000'),
top=pt.Topology()))
# weird Topology
self.assertRaises(
ValueError,
lambda: pt.TrajectoryIterator(fn('Test_RemdTraj/rem.nc.000'),
top=pt.Frame))