def test_frame(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
frame = traj[0]
pt.to_pickle(frame, 'output/frame.pk')
frame0 = pt.read_pickle('output/frame.pk')
aa_eq(frame0.xyz, frame.xyz)
# test list of frames
fname = 'output/flist.pk'
pt.to_pickle([traj[0], traj[1]], fname)
f01 = pt.read_pickle(fname)
aa_eq(np.array([f.xyz for f in f01]), traj[[0, 1]].xyz)
def test_frame(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
frame = traj[0]
pt.to_pickle(frame, 'frame.pk')
frame0 = pt.read_pickle('frame.pk')
aa_eq(frame0.xyz, frame.xyz)
# test list of frames
fname = 'flist.pk'
pt.to_pickle([traj[0], traj[1]], fname)
f01 = pt.read_pickle(fname)
aa_eq(np.array([f.xyz for f in f01]), traj[[0, 1]].xyz)
def test_frame(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
frame = traj[0]
pt.to_pickle(frame, 'output/frame.pk')
frame0 = pt.read_pickle('output/frame.pk')
aa_eq(frame0.xyz, frame.xyz)
# test list of frames
fname = 'output/flist.pk'
pt.to_pickle([traj[0], traj[1]], fname)
f01 = pt.read_pickle(fname)
aa_eq(np.array([f.xyz for f in f01]), traj[[0, 1]].xyz)
def test_trajiter_with_actionlist(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
traj.autoimage().center('origin').superpose('@CA')
pk_fn = 'test.pk'
pt.to_pickle(traj, pk_fn)
traj2 = pt.read_pickle(pk_fn)
print(traj2._transform_commands)
aa_eq(traj.xyz, traj2.xyz)
def test_pickle_frame(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
f0 = traj[0]
print(f0.mass)
fn = 'f.pk'
pt.to_pickle(f0, fn)
f1 = pt.read_pickle(fn)
print(f1.mass)
def test_pickle_frame(self):
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
f0 = traj[0]
print(f0.mass)
fn = 'output/f.pk'
pt.to_pickle(f0, fn)
f1 = pt.read_pickle(fn)
print(f1.mass)
def test_pickle_frame(self):
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
f0 = traj[0]
print(f0.mass)
fn = 'output/f.pk'
pt.to_pickle(f0, fn)
f1 = pt.read_pickle(fn)
print(f1.mass)
def test_nupars(self):
pdb_fn = fn('Test_NAstruct/adh026.3.pdb')
traj = pt.iterload(pdb_fn, pdb_fn)
data = pt.nastruct(traj)
# default
text = '''
parm {}
trajin {}
nastruct groovecalc 3dna
'''.format(fn('Test_NAstruct/adh026.3.pdb'),
fn('Test_NAstruct/adh026.3.pdb'))
state = pt.load_cpptraj_state(text)
state.run()
for key in ['major', 'minor', 'twist']:
cpp_data = np.array(
[x.values for x in state.data if x.aspect == key])
# need to transpose to get shape=(n_frames, n_pairs)
cpp_data = cpp_data.T
aa_eq(data[key][1], cpp_data)
# TODO: assert
data._summary(np.mean, indices=None)
data._summary(np.mean, indices=[
1,
])
data._summary(np.mean, keys=['major', 'twist'], indices=[
1,
])
data._summary(np.mean, keys='major', indices=[
1,
])
data._summary(np.std, indices=[
1,
])
data._summary([np.std, np.mean], indices=[
1,
])
data._explain()
dir(data)
# pickle
pt.to_pickle(data, 'na.pk')
na2 = pt.read_pickle('na.pk')
for key in data.keys():
aa_eq(data[key][1], na2[key][1])
# raise
self.assertRaises(ValueError,
lambda: pt.nastruct(traj, dtype='ndarray'))
def test_pickle_progress_bar():
traj = pt.datafiles.load_tz2()
with tempfolder():
t2 = ProgressBarTrajectory(traj)
pt.to_pickle(t2, 'test.pk')
t3 = pt.read_pickle('test.pk')
data0 = pt.rmsd(traj)
data1 = pt.rmsd(t2)
data2 = pt.rmsd(t3)
aa_eq(data0, data1)
aa_eq(data0, data2)
def test_nupars(self):
fn = "./data/Test_NAstruct/adh026.3.pdb"
traj = pt.iterload(fn, fn)
data = pt.nastruct(traj)
# default
text = '''
parm "./data/Test_NAstruct/adh026.3.pdb"
trajin "./data/Test_NAstruct/adh026.3.pdb"
nastruct groovecalc 3dna
'''
state = pt.load_cpptraj_state(text)
state.run()
for key in ['major', 'minor', 'twist']:
cpp_data = np.array([x.values for x in state.data if x.aspect ==
key])
# need to transpose to get shape=(n_frames, n_pairs)
cpp_data = cpp_data.T
aa_eq(data[key][1], cpp_data)
# TODO: assert
data._summary(np.mean, indices=None)
data._summary(np.mean, indices=[1, ])
data._summary(np.mean, keys=['major', 'twist'], indices=[1, ])
data._summary(np.mean, keys='major', indices=[1, ])
data._summary(np.std, indices=[1, ])
data._summary([np.std, np.mean], indices=[1, ])
data._explain()
dir(data)
# pickle
pt.to_pickle(data, 'data/na.pk')
na2 = pt.read_pickle('data/na.pk')
for key in data.keys():
aa_eq(data[key][1], na2[key][1])
# raise
self.assertRaises(ValueError, lambda: pt.nastruct(traj, dtype='ndarray'))
def test_picle(self):
'''test_picle
'''
pt.to_pickle(self.traj.top, 'new_top.pk')
new_top = pt.read_pickle('new_top.pk')
assert_equal_topology(self.traj.top, new_top, self.traj)
def test_pickle_datasetlist(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'ds.pk')
dslist2 = pt.read_pickle('ds.pk')
aa_eq(dslist.values, dslist2.values)
def test_picle(self):
'''test_picle
'''
pt.to_pickle(self.traj.top, 'output/new_top.pk')
new_top = pt.read_pickle('output/new_top.pk')
assert_equal_topology(self.traj.top, new_top, self.traj)
def test_pickle_datasetlist(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'output/ds.pk')
dslist2 = pt.read_pickle('output/ds.pk')
aa_eq(dslist.values, dslist2.values)
def test_pickle_datasetlist(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'output/ds.pk')
dslist2 = pt.read_pickle('output/ds.pk')
aa_eq(dslist.values, dslist2.values)
