def test_1(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
trajectory_t0 = Trajectory(traj)
# __iter__
for f in trajectory_t0:
pass
f.xyz[0, 0] = 10.
assert f.xyz[0, 0] == 10.
assert trajectory_t0.xyz[-1, 0, 0] == 10.
# __getitem__
# make a new copy
trajectory_t0 = Trajectory(traj)
f0 = trajectory_t0[0]
f0.xyz[0, 0] = 200.
assert trajectory_t0.xyz[0, 0, 0] == 200.
# translate
# make a new copy
trajectory_t0 = Trajectory(traj)
t0 = traj[:]
pt.translate(trajectory_t0, 'x 1.2')
pt.translate(t0, 'x 1.2')
aa_eq(trajectory_t0.xyz, t0.xyz)
try:
pt.rmsd(t0, ref=0)
pt.rmsd(trajectory_t0, ref=0)
except ImportError:
pass
# test rmsfit
trajectory_t0.rmsfit(ref=0)
def test_transforming_trajectory(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
t0 = traj[:]
t0.transform([
'autoimage', 'center origin', 'rotate x 30', 'scale x 1.2',
'translate x 1.3'
])
t1 = traj[:].autoimage().center('origin').rotate('x 30').scale(
'x 1.2').translate('x 1.3')
aa_eq(t0.xyz, t1.xyz)
t2 = traj[:]
pt.transform(t2, [
'autoimage', 'center origin', 'rotate x 30', 'scale x 1.2',
'translate x 1.3'
])
aa_eq(t1.xyz, t2.xyz)
# another way
t3 = traj[:]
t3.autoimage().center('origin')
pt.rotate(t3, 'x 30')
pt.scale(t3, 'x 1.2')
pt.translate(t3, 'x 1.3')
aa_eq(t3.xyz, t2.xyz)
def test_transforming_trajectory(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
t0 = traj[:]
t0.transform(['autoimage', 'center origin', 'rotate x 30',
'scale x 1.2', 'translate x 1.3'])
t1 = traj[:].autoimage().center('origin').rotate('x 30').scale('x 1.2').translate('x 1.3')
aa_eq(t0.xyz, t1.xyz)
t2 = traj[:]
pt.transform(t2, ['autoimage', 'center origin', 'rotate x 30',
'scale x 1.2', 'translate x 1.3'])
aa_eq(t1.xyz, t2.xyz)
# another way
t3 = traj[:]
t3.autoimage().center('origin')
pt.rotate(t3, 'x 30')
pt.scale(t3, 'x 1.2')
pt.translate(t3, 'x 1.3')
aa_eq(t3.xyz, t2.xyz)
def test_1(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
trajectory_t0 = pt.trajectory.Trajectory(traj)
# __iter__
for f in trajectory_t0:
pass
f.xyz[0, 0] = 10.
assert f.xyz[0, 0] == 10.
assert trajectory_t0.xyz[-1, 0, 0] == 10.
# __getitem__
# make a new copy
trajectory_t0 = pt.trajectory.Trajectory(traj)
f0 = trajectory_t0[0]
f0.xyz[0, 0] = 200.
assert trajectory_t0.xyz[0, 0, 0] == 200.
# translate
# make a new copy
trajectory_t0 = pt.trajectory.Trajectory(traj)
t0 = traj[:]
pt.translate(trajectory_t0, 'x 1.2')
pt.translate(t0, 'x 1.2')
aa_eq(trajectory_t0.xyz, t0.xyz)
try:
import mdtraj as md
pt.rmsd(t0, ref=0)
pt.rmsd(trajectory_t0, ref=0)
except ImportError:
pass
# test rmsfit
trajectory_t0.rmsfit(ref=0)
def test_translate_regular():
# OK
for frame in traj(stop=400):
pt.translate(frame, '', top=traj.top)
def test_translate_regular():
# OK
for frame in traj(stop=400):
pt.translate(frame, '', top=traj.top)