def test_traj_iteration():
from pyxmolpp2 import PdbFile, TrjtoolDatFile as DatFile, Trajectory
frame = PdbFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.pdb").frames()[0]
assert frame.atoms.size > 0
datfile1 = DatFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.dat")
datfile2 = DatFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00002.dat")
trj = Trajectory(frame)
trj.extend(datfile1)
trj.extend(datfile2)
assert trj.n_frames == datfile1.n_frames() + datfile2.n_frames()
n = 0
stride = 50
for f in trj[::stride]:
r = f.atoms[0].r
n += 1
assert trj.n_frames // stride == n
def test_pipes():
ref = PdbFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.pdb").frames()[0]
traj = Trajectory(ref)
traj.extend(
TrjtoolDatFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.dat"))
first_geom_center = XYZ(8.422286, 0.967190, -13.856332)
for frame in traj:
assert frame.coords.mean().distance(first_geom_center) < 0.001
break
del frame
for frame in traj | AngstromsToNanometers():
assert frame.coords.mean().distance(first_geom_center * 10) < 0.001
break
del frame
for frame in traj | Align(by=lambda a: True):
assert frame.coords.mean().distance(first_geom_center) < 0.001
del frame
for frame in traj[0:10] | Align(by=lambda a: True):
assert frame.coords.mean().distance(first_geom_center) < 0.001
del frame
for frame in traj[0:10] | Align(
by=lambda a: True) | AngstromsToNanometers():
assert frame.coords.mean().distance(first_geom_center * 10) < 0.001
del frame
def test_read_trjtool():
from pyxmolpp2 import PdbFile, TrjtoolDatFile
frame = PdbFile(os.environ["TEST_DATA_PATH"] + "/trjtool/GB1/run00001.pdb").frames()[0]
assert frame.atoms.size > 0
datfile = TrjtoolDatFile(os.environ["TEST_DATA_PATH"] + "/trjtool/GB1/run00001.dat")
assert datfile.n_frames() == 1000
assert datfile.n_atoms() == frame.atoms.size
datfile.advance(0)
datfile.read_frame(0, frame)
def test_tqdm():
from tqdm import tqdm
ref = PdbFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.pdb").frames()[0]
traj = Trajectory(ref)
traj.extend(
TrjtoolDatFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.dat"))
for _ in tqdm(traj):
pass
del _
for _ in tqdm(traj[::2]):
pass
del _
def test_unit_cell_scale():
ref = PdbFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00001.pdb").frames()[0]
traj = Trajectory(ref)
traj.extend(
TrjtoolDatFile(os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/run00002.dat"))
volumes = []
for frame in traj[::100] | ScaleUnitCell(
os.environ["TEST_DATA_PATH"] +
"/trjtool/GB1/summary/summary.VOLUME"):
volumes += [frame.cell.volume]
assert np.allclose(volumes, [
112190.6817, 111667.0223, 112060.3447, 112010.4530, 111899.7620,
112420.6936, 111794.6408, 112093.9081, 111655.2990, 111978.6604
])
def test_raise_file_is_empty():
from pyxmolpp2 import TrjtoolDatFile
import os
with pytest.raises(RuntimeError):
TrjtoolDatFile(os.devnull)
def test_raise_file_does_not_exists():
from pyxmolpp2 import TrjtoolDatFile
with pytest.raises(RuntimeError):
TrjtoolDatFile("does_not_exists.dat")