def test_load_samples(self):
traj = pt.load_sample_data()[:]
assert isinstance(traj, pt.Trajectory) == True
assert traj.top.n_atoms == 34
assert traj.shape == (1, 34, 3)
traj2 = pt.load_sample_data()
assert isinstance(traj2, pt.TrajectoryIterator) == True
assert traj2.top.n_atoms == 34
assert traj2.shape == (1, 34, 3)
aa_eq(traj.xyz, traj2.xyz)
def test_load_samples(self):
traj = pt.load_sample_data()[:]
assert isinstance(traj, pt.Trajectory) == True
assert traj.top.n_atoms == 34
assert traj.shape == (1, 34, 3)
traj2 = pt.load_sample_data()
assert isinstance(traj2, pt.TrajectoryIterator) == True
assert traj2.top.n_atoms == 34
assert traj2.shape == (1, 34, 3)
aa_eq(traj.xyz, traj2.xyz)
def test_join(self):
# need to create traj0, traj1 to keep lifetime of t0, t1
traj0 = pt.load_sample_data()
t0 = traj0.top
traj1 = pt.load_sample_data('tz2')
t1 = traj1.top
# +
t2 = t0 + t1 # mimic ParmEd
assert t2.n_atoms == t0.n_atoms + t1.n_atoms
t0 += t1
assert t0.n_atoms == t2.n_atoms
def test_join(self):
# need to create traj0, traj1 to keep lifetime of t0, t1
traj0 = pt.load_sample_data()
t0 = traj0.top
traj1 = pt.load_sample_data('tz2')
t1 = traj1.top
# +
t2 = t0 + t1 # mimic ParmEd
assert t2.n_atoms == t0.n_atoms + t1.n_atoms
t0 += t1
assert t0.n_atoms == t2.n_atoms
def get_remd_fn(txt):
"""
>>> fnlist, tn = get_remd_fn('remd_ala2')
"""
from pytraj import load_sample_data
traj = load_sample_data(txt)
return traj.filelist, traj.top.filename
def test_action_grid(self):
from pytraj.all_actions import grid
traj = pt.load_sample_data("tz2")[:]
traj.autoimage()
traj.rmsfit(mask=':1-13')
d = grid(traj, " 20 0.5 20 0.5 20 0.5 :WAT@O")
d = grid(traj(), " 20 0.5 20 0.5 20 0.5 :WAT@O", top=traj.top)
def get_remd_fn(txt):
"""
>>> fnlist, tn = get_remd_fn('remd_ala2')
"""
from pytraj import load_sample_data
traj = load_sample_data(txt)
return traj.filelist, traj.top.filename
def test_single_frame():
traj = pt.load_sample_data('tz2')
frame = pt.io.load_frame(traj.filename, traj.top.filename, 3)
aa_eq(traj[3].xyz, frame.xyz)
with pytest.raises(RuntimeError):
pt.io.load_frame('afddsfdsfa', traj.top.filename, 3)
with pytest.raises(RuntimeError):
pt.io.load_frame(filename='afddsfdsfa', top=traj.top.filename, index=3)
def test_loading(self):
traj = pt.load_sample_data('tz2')
traj[:]
traj[:3]
# load from a list of files
fname = traj.filename
t0 = pt.iterload([fname, fname],
traj.top,
frame_slice=[(0, 8, 2), ] * 2)
def test_single_frame(self):
traj = pt.load_sample_data('tz2')
frame = pt.io.load_frame(traj.filename, traj.top.filename, 3)
aa_eq(traj[3].xyz, frame.xyz)
self.assertRaises(
RuntimeError,
lambda: pt.io.load_frame('afddsfdsfa', traj.top.filename, 3))
self.assertRaises(
RuntimeError, lambda: pt.io.load_frame(
filename='afddsfdsfa', top=traj.top.filename, index=3))
def test_loading(self):
traj = pt.load_sample_data('tz2')
traj[:]
traj[:3]
# load from a list of files
fname = traj.filename
t0 = pt.iterload([fname, fname],
traj.top,
frame_slice=[
(0, 8, 2),
] * 2)
def get_fn(txt):
'''get absolute path for trajectory and topology samples. Legit text = 'ala3', 'tz2',
'rna'. Mostly for testing purpose.
Examples
--------
>>> # get trajectory file name
>>> fname = get_fn('tz2')[0]
>>> fname.split('/')[-1]
'tz2.ortho.nc'
'''
from pytraj import load_sample_data
traj = load_sample_data(txt)
return traj.filename, traj.top.filename
def get_fn(txt):
'''get absolute path for trajectory and topology samples. Legit text = 'ala3', 'tz2',
'rna'. Mostly for testing purpose.
Examples
--------
>>> # get trajectory file name
>>> fname = get_fn('tz2')[0]
>>> fname.split('/')[-1]
'tz2.ortho.nc'
'''
from pytraj import load_sample_data
traj = load_sample_data(txt)
return traj.filename, traj.top.filename
def set_xyz_not_same_n_atoms():
traj1 = pt.load_sample_data('ala3')
t0.xyz = traj1.xyz
# that stops travis
import pytraj as pt
from utils import fn
from memory_profiler import profile
traj = pt.load_sample_data('tz2')
# make fake large trajectory from 10 frames
for _ in range(9):
traj.load(traj.filelist)
@profile
def test_iterchunk(chunksize=100):
for chunk in traj.iterchunk(chunksize=chunksize):
pass
test_iterchunk(chunksize=100)
def append_2d():
traj1 = pt.load_sample_data('ala3')
t0.append_xyz(pt.tools.as_2darray(traj))
def setUp(self):
self.traj = pt.load_sample_data('tz2')
def test_velocity_and_force(self):
traj = pt.load_sample_data('ala3')
assert not traj[0].has_force(), 'does not have force'
assert not traj[0].has_velocity(), 'does not have force'
assert traj[0].force is None, 'force must be None'
assert traj[0].velocity is None, 'velocity is None'
def setUp(self):
self.traj = pt.load_sample_data('tz2')
# that stops travis
import os
import pytraj as pt
from numpy import max
from memory_profiler import profile, memory_usage
from glob import glob
traj0 = pt.load_sample_data('tz2')
# make fake large trajectory from 10 frames
for _ in range(9):
traj0.load(traj0.filelist)
tlist = [traj0, ]
if os.path.exists("./data/nogit/remd/myparm.parm7"):
tlist.append(pt.iterload(
glob("./data/nogit/remd/remd.x.*")[:10],
"./data/nogit/remd/myparm.parm7"))
for traj in tlist[:1]:
print(traj)
print(traj._estimated_GB)
@profile
def test_pairwise_rmsd():
pt.pairwise_rmsd(traj(stop=1000), mask='@CA')
@profile
def test_write():
pt.write_traj('test.nc',
traj,
def test_velocity_and_force(self):
traj = pt.load_sample_data('ala3')
assert not traj[0].has_force(), 'does not have force'
assert not traj[0].has_velocity(), 'does not have force'
assert traj[0].force is None, 'force must be None'
assert traj[0].velocity is None, 'velocity is None'
def set_xyz_not_same_n_atoms():
traj1 = pt.load_sample_data('ala3')
t0.xyz = traj1.xyz
def append_2d():
pt.load_sample_data('ala3')
def test_4_trajiter(self):
traj = pt.load_sample_data("tz2")
for idx, (f0, f1) in enumerate(zip(traj, traj)):
f0.rmsd(f1)
def append_2d():
pt.load_sample_data('ala3')
t0.append_xyz(pt.tools.as_2darray(traj))
def append_2d():
traj1 = pt.load_sample_data('ala3')