def test_1(self):
# just need to install libcpptraj with openmp
# that's it
# export OMP_NUM_THREADS=1
# python ./test_openmp_0.py
# export OMP_NUM_THREADS=8
# python ./test_openmp_0.py
dslist = DatasetList()
dflist = DataFileList()
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
dslist.add("coords", "test_traj")
dslist[0].top = traj.top
for i in range(45):
dslist[0].load(traj.filename)
act = Analysis_Rms2d()
with Timer() as t:
act("crdset test_traj rmsout ./output/_test_2drms_CRDtest.openmp.dat",
dslist=dslist,
dflist=dflist)
# make sure to reproduce cpptraj to avoif false-impression :D
import numpy as np
matout = dslist[-1].get_full_matrix()
tmp = np.loadtxt("./data/test_openmp.Tc5b.n_threads_1.dat",
skiprows=1,
usecols=range(1, dslist[0].size + 1))
cpp_save = tmp.flatten()
# use decimal = 3 to mathc cpptraj's format here
assert_almost_equal(cpp_save, matout, decimal=3)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
itertraj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
for idx, (f0, f1) in enumerate(izip(traj, itertraj)):
assert_almost_equal(f0.xyz, f1.xyz)
assert idx == traj.n_frames - 1
def test_1(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
i = 0
for farray in traj.iterchunk(chunksize=4, stop=8):
i += 1
assert i == 2
i = 0
for farray in traj.iterchunk(chunksize=4):
i += 1
assert i == 3
i = 0
for farray in traj.iterchunk(chunksize=2):
i += 1
assert i == 5
i = 0
for farray in traj.iterchunk(start=3, chunksize=4, stop=8):
i += 1
assert i == 2
# action on chunk_iter
pt.calc_distance(
[traj.iterchunk(), traj.iterchunk(), traj[0]],
'@CA @CB',
top=traj.top)
rmsd0 = pt.rmsd(traj.iterchunk(3), ref=traj[-1], top=traj.top)
rmsd1 = pt.rmsd(traj, ref=-1)
assert_almost_equal(rmsd0, rmsd1)
def test_1(self):
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
i = 0
for farray in traj.iterchunk(chunksize=4, stop=8):
i += 1
assert i == 2
i = 0
for farray in traj.iterchunk(chunksize=4):
i += 1
assert i == 3
i = 0
for farray in traj.iterchunk(chunksize=2):
i += 1
assert i == 5
i = 0
for farray in traj.iterchunk(start=3, chunksize=4, stop=8):
i += 1
assert i == 2
# action on chunk_iter
pt.calc_distance(
[traj.iterchunk(), traj.iterchunk(), traj[0]],
'@CA @CB',
top=traj.top)
rmsd0 = pt.rmsd(traj.iterchunk(3), ref=traj[-1], top=traj.top)
rmsd1 = pt.rmsd(traj, ref=-1)
assert_almost_equal(rmsd0, rmsd1)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
itertraj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
for idx, (f0, f1) in enumerate(izip(traj, itertraj)):
assert_almost_equal(f0.xyz, f1.xyz)
assert idx == traj.n_frames - 1
def test_IterWithMask(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
farray = traj[:]
for frame in farray(mask='@CA'):
pass
f0 = traj[-1]
f0.strip(traj.top('!@CA'))
assert_almost_equal(f0.xyz, frame.xyz)
def test_IterWithMask(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = traj[:]
for frame in farray(mask='@CA'):
pass
f0 = traj[-1]
f0.strip(traj.top('!@CA'))
assert_almost_equal(f0.xyz, frame.xyz)
def test_IterWithMask(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = traj[:]
for frame in farray(mask='@CA'):
pass
f0 = traj[-1]
f0.strip(traj.top('!@CA'))
assert_almost_equal(f0.xyz, frame.xyz)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
top = traj.top
mlist = []
for atom in top:
mlist.append(atom.mass)
mlist = array('d', mlist)
assert_almost_equal(top.mass, mlist)
def test_1(self):
# why Trajectory is here? because I am lazy to move
mask = "@CA"
# creat Trajectory ( [:] )
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))[:]
traj.top
atm = traj.top(mask)
newtraj = traj[atm]
newtraj2 = traj[mask + ' :frame']
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
def test_1(self):
# why Trajectory is here? because I am lazy to move
mask = "@CA"
# creat Trajectory ( [:] )
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
top = traj.top
atm = traj.top(mask)
newtraj = traj[atm]
newtraj2 = traj[mask + ' :frame']
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
def test_2(self):
from pytraj import iterframe_master as frame_iter
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
farray = traj[:]
count = 0
for frame in frame_iter(traj):
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
count = 0
for frame in frame_iter(farray):
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
def test_2(self):
from pytraj import iterframe_master as frame_iter
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = traj[:]
count = 0
for frame in frame_iter(traj):
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
count = 0
for frame in frame_iter(farray):
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
farray = traj[:]
traj0_CA = traj[:]
traj0_CA.strip("!@CA")
# test TrajectoryIterator
for idx, f0 in enumerate(traj(mask='@CA')):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
# test TrajectoryIterator with indices as mask
indices = traj.top("@CA").indices
for idx, f0 in enumerate(traj(mask=indices)):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
# test Trajectory
for idx, f0 in enumerate(farray(mask='@CA')):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
# test Trajectory with indices
for idx, f0 in enumerate(farray(mask=indices)):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
assert idx + 1 == traj0_CA.n_frames
def test_0(self):
traj = mdio.iterload("data/Tc5b.x", "data/Tc5b.top")
farray = traj[:]
traj0_CA = traj[:]
traj0_CA.strip("!@CA")
# test TrajectoryIterator
for idx, f0 in enumerate(traj(mask='@CA')):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
# test TrajectoryIterator with indices as mask
indices = traj.top("@CA").indices
for idx, f0 in enumerate(traj(mask=indices)):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
# test Trajectory
for idx, f0 in enumerate(farray(mask='@CA')):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
# test Trajectory with indices
for idx, f0 in enumerate(farray(mask=indices)):
f1 = traj0_CA[idx]
assert_almost_equal(f0.xyz, f1.xyz)
assert idx + 1 == traj0_CA.n_frames
def test_0(self):
dslist = CpptrajDatasetList()
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
calc_distance = adict['distance']
act = calc_distance
act.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act.setup(traj.top)
act.compute((traj.iterchunk(2), ))
assert dslist.size == 1
assert dslist[0].size == traj.n_frames
cppout = np.loadtxt(
fn('CAres2_CAres10.Tc5b.dat'), skiprows=1).transpose()[1]
assert_almost_equal(dslist[0][:], cppout)
act.compute((traj.iterchunk(chunksize=4, stop=8), ))
def test_0(self):
dslist = DatasetList()
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
calc_distance = adict['distance']
act = calc_distance
act.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act.check_topology(traj.top)
act.compute((traj.iterchunk(2), ))
assert dslist.size == 1
assert dslist[0].size == traj.n_frames
cppout = np.loadtxt("./data/CAres2_CAres10.Tc5b.dat",
skiprows=1).transpose()[1]
assert_almost_equal(dslist[0][:], cppout)
act.compute((traj.iterchunk(chunksize=4, stop=8), ))
def test_0(self):
dslist = DatasetList()
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
calc_distance = adict['distance']
act = calc_distance
act.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act.check_topology(traj.top)
act.compute((traj.iterchunk(2), ))
assert dslist.size == 1
assert dslist[0].size == traj.n_frames
cppout = np.loadtxt("./data/CAres2_CAres10.Tc5b.dat",
skiprows=1).transpose()[1]
assert_almost_equal(dslist[0][:], cppout)
act.compute((traj.iterchunk(chunksize=4, stop=8), ))
def test_0(self):
mask = "@CA"
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj.top
atm = traj.top(mask)
n_selected_atoms = atm.n_atoms
newtraj = traj[atm]
newtraj2 = traj[mask + ' :frame']
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
assert (newtraj.xyz.shape == (traj.n_frames, n_selected_atoms, 3))
# check if there is segmentation fault
i = 0
for frame in traj:
i += 1
def test_0(self):
mask = "@CA"
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
top = traj.top
atm = traj.top(mask)
n_selected_atoms = atm.n_atoms
newtraj = traj[atm]
newtraj2 = traj[mask + ' :frame']
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
assert_almost_equal(newtraj2.xyz.flatten(), newtraj.xyz.flatten())
assert (newtraj.xyz.shape == (traj.n_frames, n_selected_atoms, 3))
# check if there is segmentation fault
i = 0
for frame in traj:
i += 1
def get_frames_same_T():
# create a list of all remd trajs
flist = glob("../tests/data/Test_RemdTraj/rem.nc.*")
# make a list of TrajReadOnly instances
trajlist = []
for fh in flist:
topfile = "../tests/data/Test_RemdTraj/ala2.99sb.mbondi2.parm7"
# load trajectory and append to trajlist
trajlist.append(mdio.load(fh, topfile))
# make Trajectory instance that holds 492.2 T frames
# we need to reserve n_frames to hold the data
f4922 = Trajectory(n_frames=trajlist[0].n_frames)
assert f4922.n_frames == trajlist[0].n_frames
f4922.top = trajlist[0].top.copy()
# extract frames having T = 492.2
# use iteration for nested loops
for traj in trajlist:
for idx, frame in enumerate(traj):
if frame.temperature == 492.2:
# we don't use `append` method since we want to make sure
# frames are in the order of simulation time
f4922[idx] = frame
# make sure f4922 only hold frames having T = 492.2 K
arr0 = array(
'd',
[492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2])
assert f4922.temperatures == arr0
# make sure we reproduce cpptraj output
cpptraj = mdio.load("../tests/data/Test_RemdTraj/temp0.crd.492.20",
topfile)
print(f4922[5].coords[:10])
print(cpptraj[5].coords[:10])
for idx, framepy in enumerate(f4922):
assert_almost_equal(framepy.coords, cpptraj[idx].coords)
print("rmsd between pytraj Frame and cpptraj Frame = %s " %
framepy.rmsd(cpptraj[idx]))
# FIXME: `rmsd` do the fitting in the fly
# coords of frame would be changed
print("YES, we can reproduce cpptraj output")
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
frame = traj[0].copy()
frame.set_mass(traj.top)
arr0 = []
for f0 in traj:
f0.set_mass(traj.top)
arr0.append(frame.rmsd(f0, use_mass=True))
# load cpptraj output
rmsd_save = np.loadtxt("./data/rmsd_allatoms_to_1st.Tc5b.use_mass.dat",
skiprows=1)
rmsd_save = rmsd_save.transpose()
assert_almost_equal(arr0, rmsd_save[1])
def test_0(self):
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
frame = traj[0].copy()
frame.set_mass(traj.top)
arr0 = []
for f0 in traj:
f0.set_mass(traj.top)
arr0.append(frame.rmsd(f0, use_mass=True))
# load cpptraj output
rmsd_save = np.loadtxt(fn("rmsd_allatoms_to_1st.Tc5b.use_mass.dat"),
skiprows=1)
rmsd_save = rmsd_save.transpose()
assert_almost_equal(arr0, rmsd_save[1])
def test_1(self):
# just need to install libcpptraj with openmp
# that's it
# export OMP_NUM_THREADS=1
# python ./test_openmp_0.py
# export OMP_NUM_THREADS=8
# python ./test_openmp_0.py
dslist = DatasetList()
dflist = DataFileList()
trajin = "./data/Tc5b.x"
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
dslist.add(dtype="coords", name="test_traj")
dslist[0].top = traj.top
for i in range(45):
dslist[0].load(traj.filename)
act = Analysis_Rms2d()
@Timer()
def test_time():
act("crdset test_traj rmsout ./output/_test_2drms_CRDtest.openmp.dat",
dslist=dslist,
dflist=dflist)
test_time()
# make sure to reproduce cpptraj to avoif false-impression :D
import numpy as np
matout = dslist[-1].get_full_matrix()
tmp = np.loadtxt("./data/test_openmp.Tc5b.n_threads_1.dat",
skiprows=1,
usecols=range(1, dslist[0].size + 1))
cpp_save = tmp.flatten()
assert_almost_equal(cpp_save, matout, decimal=3)
def test_4(self):
from array import array
atm = AtomMask()
indices = array('i', range(100))
atm.add_selected_indices(indices)
assert_almost_equal(indices, atm.selected_indices())
assert_almost_equal(indices, atm.indices)
# test list
atm2 = AtomMask(list(indices))
assert_almost_equal(indices, atm2.indices)
# test range
range(100)
atm3 = AtomMask(range(100))
assert_almost_equal(indices, atm3.indices)
def test_4(self):
from array import array
atm = AtomMask()
indices = array('i', range(100))
atm.add_selected_indices(indices)
assert_almost_equal(indices, atm.selected_indices())
assert_almost_equal(indices, atm.indices)
# test list
atm2 = AtomMask(list(indices))
assert_almost_equal(indices, atm2.indices)
# test range
r100 = range(100)
atm3 = AtomMask(range(100))
assert_almost_equal(indices, atm3.indices)
def test_1(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
top2 = traj.top.copy()
for frame in traj(mask='@CA'):
pass
top2.strip("!@CA")
assert frame.n_atoms == top2.n_atoms
for frame in traj():
pass
assert frame.n_atoms == traj[0].n_atoms
for frame in traj[:](mask='@CA'):
pass
f0 = traj[-1]
f0.strip(traj.top('!@CA'))
assert_almost_equal(f0.xyz, frame.xyz)
assert frame.n_atoms == top2.n_atoms
for frame in traj[:]():
pass
assert frame.n_atoms == traj[0].n_atoms
def test_0(self):
flist = glob("./data/Test_RemdTraj/rem.nc.*")
trajlist = []
for fh in flist:
topfile = "./data/Test_RemdTraj/ala2.99sb.mbondi2.parm7"
trajlist.append(mdio.iterload(fh, topfile))
Tset = set([])
f4922 = Trajectory()
f4922._allocate(trajlist[0].n_frames, trajlist[0].n_atoms)
f4922.top = trajlist[0].top.copy()
for traj in trajlist:
for idx, frame in enumerate(traj):
if frame.temperature == 492.2:
f4922[idx] = frame
# make sure we reproduce cpptraj output
cpptraj = mdio.iterload("./data/Test_RemdTraj/temp0.crd.492.20",
topfile)
for idx, framepy in enumerate(f4922):
assert_almost_equal(framepy.xyz, cpptraj[idx].xyz, decimal=3)
def test_0(self):
flist = glob("./data/Test_RemdTraj/rem.nc.*")
trajlist = []
for fh in flist:
topfile = "./data/Test_RemdTraj/ala2.99sb.mbondi2.parm7"
trajlist.append(mdio.iterload(fh, topfile))
Tset = set([])
f4922 = Trajectory()
f4922._allocate(trajlist[0].n_frames, trajlist[0].n_atoms)
f4922.top = trajlist[0].top.copy()
for traj in trajlist:
for idx, frame in enumerate(traj):
if frame.temperature == 492.2:
f4922[idx] = frame
# make sure we reproduce cpptraj output
cpptraj = mdio.iterload("./data/Test_RemdTraj/temp0.crd.492.20",
topfile)
for idx, framepy in enumerate(f4922):
assert_almost_equal(framepy.xyz, cpptraj[idx].xyz, decimal=3)
def test_1(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
top2 = traj.top.copy()
for frame in traj(mask='@CA'):
pass
top2.strip("!@CA")
assert frame.n_atoms == top2.n_atoms
for frame in traj():
pass
assert frame.n_atoms == traj[0].n_atoms
for frame in traj[:](mask='@CA'):
pass
f0 = traj[-1]
f0.strip(traj.top('!@CA'))
assert_almost_equal(f0.xyz, frame.xyz)
assert frame.n_atoms == top2.n_atoms
for frame in traj[:]():
pass
assert frame.n_atoms == traj[0].n_atoms
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = traj[:]
xyz_save = farray[0].xyz.copy()
farray[9].xyz[:] = farray[0].xyz
assert_almost_equal(farray[9].xyz, farray[0].xyz)
assert_almost_equal(farray[9].xyz, xyz_save.flatten())
f0 = Frame(traj.n_atoms)
f0.xyz[:] = farray[0].xyz
f1 = Frame()
f1.append_xyz(farray[0].xyz)
assert_almost_equal(f1.xyz, farray[0].xyz)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = traj[:]
xyz_save = farray[0].xyz.copy()
farray[9].xyz[:] = farray[0].xyz
assert_almost_equal(farray[9].xyz, farray[0].xyz)
assert_almost_equal(farray[9].xyz, xyz_save.flatten())
f0 = Frame(traj.n_atoms)
f0.xyz[:] = farray[0].xyz
f1 = Frame()
f1.append_xyz(farray[0].xyz)
assert_almost_equal(f1.xyz, farray[0].xyz)
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
farray = traj[:]
xyz_save = farray[0].xyz.copy()
farray[9].xyz[:] = farray[0].xyz
assert_almost_equal(farray[9].xyz, farray[0].xyz)
assert_almost_equal(farray[9].xyz, xyz_save.flatten())
f0 = Frame(traj.n_atoms)
f0.xyz[:] = farray[0].xyz
f1 = Frame()
f1.append_xyz(farray[0].xyz)
assert_almost_equal(f1.xyz, farray[0].xyz)
def test_3(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
count = 0
for frame in traj.iterframe():
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
count = 0
for frame in traj.iterframe(2, 8, 2):
count += 1
assert count == 3
assert_almost_equal(frame.xyz, traj[6].xyz)
count = 0
for frame in traj[:].iterframe():
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
def test_3(self):
from pytraj import iterframe_master as frame_iter
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
count = 0
for frame in traj.iterframe():
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
count = 0
for frame in traj.iterframe(2, 8, 2):
count += 1
assert count == 3
assert_almost_equal(frame.xyz, traj[6].xyz)
count = 0
for frame in traj[:].iterframe():
count += 1
assert_almost_equal(frame.xyz, traj[-1].xyz)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = traj[:]
for i, f0 in enumerate(traj):
for j, x in enumerate(f0.xyz):
if np.all(np.abs(x - 5.707) < 1E-3):
pass
for frame in traj.iterframe():
pass
for frame0 in farray.iterframe():
pass
i = 0
for frame0 in farray.iterframe(start=0, step=1):
i += 1
assert_almost_equal(traj[-1].xyz, frame0.xyz)
start, stop, step = 2, 8, 4
indices = list(range(start, stop, step))
for idx, frame0, f in zip(indices, farray.iterframe(start, stop, step),
traj[indices]):
aa_eq(frame0.xyz, f.xyz)
assert_almost_equal(traj[6].xyz, frame0.xyz)
for frame0 in farray.iterframe(start=2, step=2):
pass
assert_almost_equal(traj[8].xyz, frame0.xyz)
arr0 = traj[6][0]
for frame0 in traj.iterframe(start=2, step=4, stop=8):
pass
for frame0 in traj.iterframe(start=2, step=4, stop=8):
pass
assert_almost_equal(traj[6].xyz, frame0.xyz)
for frame0 in traj.iterframe(start=2, step=2):
pass
assert_almost_equal(traj[8].xyz, frame0.xyz)
count = 0
for frame0 in traj.iterframe(start=2):
count += 1
assert_almost_equal(traj[-1].xyz, frame0.xyz)
count = 0
for frame0 in traj.iterframe(start=2, stop=7):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
for frame0 in traj.iterframe():
pass
assert_almost_equal(traj[-1].xyz, frame0.xyz)
for frame0 in farray.iterframe():
pass
assert_almost_equal(traj[-1].xyz, frame0.xyz)
for frame0 in traj():
pass
assert_almost_equal(traj[-1].xyz, frame0.xyz)
for frame0 in farray():
pass
assert_almost_equal(farray[-1].xyz, frame0.xyz)
count = 0
for frame0 in traj(start=2, stop=7):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
count = 0
for frame0 in farray(start=2, stop=7):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
count = 0
for frame0 in farray(2, 7, 1):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
count = 0
for frame0 in farray(2, 7, 2):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
farray = traj[:]
for i, f0 in enumerate(traj):
for j, x in enumerate(f0.xyz):
if np.all(np.abs(x - 5.707) < 1E-3):
pass
for frame in traj.iterframe():
pass
for frame0 in farray.iterframe():
pass
i = 0
for frame0 in farray.iterframe(start=0, step=1):
i += 1
assert_almost_equal(traj[-1].xyz, frame0.xyz)
start, stop, step = 2, 8, 4
indices = list(range(start, stop, step))
for idx, frame0, f in zip(indices, farray.iterframe(start, stop, step),
traj[indices]):
aa_eq(frame0.xyz, f.xyz)
assert_almost_equal(traj[6].xyz, frame0.xyz)
for frame0 in farray.iterframe(start=2, step=2):
pass
assert_almost_equal(traj[8].xyz, frame0.xyz)
traj[6][0]
for frame0 in traj.iterframe(start=2, step=4, stop=8):
pass
for frame0 in traj.iterframe(start=2, step=4, stop=8):
pass
assert_almost_equal(traj[6].xyz, frame0.xyz)
for frame0 in traj.iterframe(start=2, step=2):
pass
assert_almost_equal(traj[8].xyz, frame0.xyz)
count = 0
for frame0 in traj.iterframe(start=2):
count += 1
assert_almost_equal(traj[-1].xyz, frame0.xyz)
count = 0
for frame0 in traj.iterframe(start=2, stop=7):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
for frame0 in traj.iterframe():
pass
assert_almost_equal(traj[-1].xyz, frame0.xyz)
for frame0 in farray.iterframe():
pass
assert_almost_equal(traj[-1].xyz, frame0.xyz)
for frame0 in traj():
pass
assert_almost_equal(traj[-1].xyz, frame0.xyz)
for frame0 in farray():
pass
assert_almost_equal(farray[-1].xyz, frame0.xyz)
count = 0
for frame0 in traj(start=2, stop=7):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
count = 0
for frame0 in farray(start=2, stop=7):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
count = 0
for frame0 in farray(2, 7, 1):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
count = 0
for frame0 in farray(2, 7, 2):
count += 1
assert_almost_equal(traj[6].xyz, frame0.xyz)
