def test_load_and_save_0(self):
print "test_load_and_save"
# need to load to FrameArray to save
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")[:]
trajiter = mdio.iterload(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top",
chunk=100)
print trajiter
print traj.size
indices = range(20, 30, 5) + [103, 78, 90, 82]
print type(indices)
print indices
mdio.writetraj(filename="./output/test_io_saved_.x",
traj=traj[:],
top="./data/Tc5b.top",
indices=indices,
overwrite=True)
# check frames
traj2 = mdio.load(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
print "test_load_and_save_0"
print traj2.size
print traj2.is_empty()
print len(indices)
assert traj2.size == len(indices)
def test_iterload_1(self):
"""get FrameArray"""
print __doc__
for i in range(1):
print ""
print "loop number = %s-th" % i
genobj = iterload(filename="./data/md1_prod.Tc5b.x", top=Topology("./data/Tc5b.top"), chunk=50)
farray = genobj.next()
farray.warning = True
# create a view of farray[0]
frame0_0 = farray[0].copy()
print farray
assert farray.size == 50
print farray[0].n_atoms
assert farray[0].n_atoms == 304
print "next iteration"
farray = genobj.next()
frame0_1 = farray[0].copy()
print farray
assert farray.size == 50
print farray[0].n_atoms
assert farray[0].n_atoms == 304
print "make sure that we DID the iteration"
assert frame0_0.coords != frame0_1.coords
#print frame0_0[:10]
print frame0_1.coords[:10]
print frame0_0.coords[:10]
def test_iterload_0(self):
"""get single frame"""
genobj = iterload(filename="./data/md1_prod.Tc5b.x", top=Topology("./data/Tc5b.top"))
frame0 = genobj.next()
print frame0
print genobj.next()
print genobj.next()[0]
print genobj.next().n_atoms
def test_0(self):
# create FrameArray from Trajing_Single
# TODO : add more assert
traj = mdio.iterload("./data/md1_prod.Tc5b.x",
"./data/Tc5b.top",
chunk=100).next()
print traj
arr0 = traj[:, :, :]
print arr0.shape
print type(arr0)
def test_load_and_save_1(self):
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")
trajiter = mdio.iterload(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top",
chunk=100)
print trajiter
indices = range(20, 30, 5) + [103, 78, 90, 82]
mdio.writetraj(filename="./output/test_io_saved.pdb",
traj=traj,
top="./data/Tc5b.top",
fmt='pdbfile',
indices=indices,
overwrite=True)
# check frames
traj = mdio.load(filename="./output/test_io_saved.pdb",
top="./data/Tc5b.top")
assert traj.size == len(indices)
assert traj.top.n_atoms == 304