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_traj_topology(self): traj = pt.TrajectoryIterator() assert traj.top.is_empty() == True traj.top = pt.load_topology(fn('Tc5b.top')) assert traj.top.is_empty() == False traj._load(fn('Tc5b.x')) # use toplogy traj = pt.TrajectoryIterator() assert traj.topology.is_empty() == True traj.topology = pt.load_topology(fn('Tc5b.top')) assert traj.topology.is_empty() == False traj._load(fn('Tc5b.x'))
def test_traj_topology(self): traj = pt.TrajectoryIterator() assert traj.top.is_empty() == True traj.top = pt.load_topology("./data/Tc5b.top") assert traj.top.is_empty() == False traj._load("./data/Tc5b.x") # use toplogy traj = pt.TrajectoryIterator() assert traj.topology.is_empty() == True traj.topology = pt.load_topology("./data/Tc5b.top") assert traj.topology.is_empty() == False traj._load("./data/Tc5b.x")
def test_indexing(self): traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top')) traj2 = pt.TrajectoryIterator() traj2.top = pt.load_topology(fn('Tc5b.top')) traj2._load(fn('Tc5b.x')) farray = traj2[[0, 9, 1]] assert farray.n_frames == 3 assert traj2[0].atom(0) == farray[0].atom(0) assert traj2[9].atom(0) == farray[1].atom(0) assert traj2[1].atom(0) == farray[2].atom(0) arr = np.asarray(traj2[0]._buffer1d[:]) frame0 = traj2[0] arr0 = np.asarray(frame0._buffer1d[:]) mat0 = np.asmatrix(arr0).reshape(304, 3) mat0[:, 0] = np.asmatrix(list(range(304))).reshape(304, 1) assert frame0[0, 0] == 0. assert frame0[1, 0] == 1. assert frame0[2, 0] == 2. # raise if size = 0 traj3 = pt.Trajectory() assert traj3.n_frames == 0, 'empty Trajectory, n_frames must be 0' self.assertRaises(IndexError, lambda: traj3[0]) self.assertRaises(IndexError, lambda: traj3.__setitem__(0, traj[3]))
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))
def test_iter_basic(self): traj = pt.TrajectoryIterator() traj.top = pt.load_topology(fn('Tc5b.top')) traj._load(fn('Tc5b.x')) for frame in traj: pass
def test_iter_basic(self): traj = pt.TrajectoryIterator() traj.top = pt.load_topology("./data/Tc5b.top") traj._load("./data/Tc5b.x") for frame in traj: pass