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_6(self):
traj = pt.iterload(tc5b_trajin, tc5b_top)
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_6(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_6(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_0(self):
cm = """
parm data/Tc5b.top
trajin data/Tc5b.x
distance d0 @2 @3
distance d1 @4 @7
corr d0 d1 out test.out
corr d0 out test2.out
"""
# exclude DatasetTopology (1st)
state = pt.datafiles.load_cpptraj_state(cm).run()
cout = state.data[1:]
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
dslist = pt.calc_distance(traj, ['@2 @3', '@4, @7'])
pout = pt.xcorr(dslist[0],
dslist[1])
# corr d0, d1
aa_eq(pout, cout[2])
# corr d0, d0
pout = pt.xcorr(dslist[0],
dslist[0])
aa_eq(pout, cout[3])
# autocorr d0, d0
pout = pt.acorr(dslist[0])
aa_eq(pout, cout[3])
def test_corr():
cm = """
parm {}
trajin {}
distance d0 @2 @3
distance d1 @4 @7
corr d0 d1 out test.out
corr d0 out test2.out
""".format(tc5b_top, tc5b_trajin)
with tempfolder():
# exclude DatasetTopology (1st)
state = pt.datafiles.load_cpptraj_state(cm).run()
cout = state.data[1:]
traj = pt.iterload(tc5b_trajin, tc5b_top)
dslist = pt.calc_distance(traj, ['@2 @3', '@4, @7'])
pout = pt.xcorr(dslist[0], dslist[1])
# corr d0, d1
aa_eq(pout, cout[2])
# corr d0, d0
pout = pt.xcorr(dslist[0], dslist[0])
aa_eq(pout, cout[4])
# autocorr d0, d0
pout = pt.acorr(dslist[0])
aa_eq(pout, cout[4])
def test_0(self):
cm = """
parm data/Tc5b.top
trajin data/Tc5b.x
distance d0 @2 @3
distance d1 @4 @7
corr d0 d1 out test.out
corr d0 out test2.out
"""
# exclude DatasetTopology (1st)
state = pt.datafiles.load_cpptraj_state(cm).run()
cout = state.data[1:]
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
dslist = pt.calc_distance(traj, ['@2 @3', '@4, @7'])
pout = pt.xcorr(dslist[0], dslist[1])
# corr d0, d1
aa_eq(pout, cout[2])
# corr d0, d0
pout = pt.xcorr(dslist[0], dslist[0])
aa_eq(pout, cout[3])
# autocorr d0, d0
pout = pt.acorr(dslist[0])
aa_eq(pout, cout[3])
def test_general(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = traj[:]
mask = ':1@CA :14@CB'
d0 = pt.calc_distance(traj, mask)
d1 = pt.distance(traj, mask)
d2 = pt.calc_distance(fa, mask)
aa_eq(d0, d1)
aa_eq(d0, d2)
Nsize = 12
arr = np.random.randint(0, 300, size=Nsize * 2).reshape(Nsize, 2)
d3 = pt.calc_distance(fa, arr)
d4 = pt.distance(traj, arr)
d5 = pt.calc_distance(traj, arr)
d6 = pt.calc_distance(fa, arr)
d7 = pt.calc_distance([fa, traj], arr, n_frames=2 * fa.n_frames)
d8 = pt.calc_distance([fa, traj],
arr,
n_frames=2 * fa.n_frames,
dtype='dataset')
aa_eq(d3, d4)
aa_eq(d3, d5)
aa_eq(d3, d6)
aa_eq(d3.T, d7.T[:fa.n_frames])
aa_eq(d3.T, d7.T[fa.n_frames:])
aa_eq(d7, d8.values)
# raise
self.assertRaises(ValueError, lambda: pt.dihedrals(traj, [[0, 3, 2]]))
def test_distances(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajin = pt.datafiles.tc5b_trajin + """
distance @CB @CA
distance @CA @H
"""
cout = pt.datafiles.load_cpptraj_output(trajin)[1:]
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
# compare to cpptraj output
aa_eq(dslist.flatten(), cout.values.flatten())
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_distances(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajin = pt.datafiles.tc5b_trajin + """
distance @CB @CA
distance @CA @H
"""
cout = pt.datafiles.load_cpptraj_output(trajin)[1:]
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
# compare to cpptraj output
aa_eq(dslist.flatten(), cout.values.flatten())
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_distances(self):
traj = pt.iterload(tc5b_trajin, tc5b_top)[:]
trajin = """
parm {}
trajin {}
distance @CB @CA
distance @CA @H
""".format(fn('Tc5b.parm7'), fn('Tc5b.x'))
cout = pt.datafiles.load_cpptraj_output(trajin)[1:]
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
# compare to cpptraj output
aa_eq(dslist.flatten(), cout.values.flatten())
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_run_5(self):
traj = pt.iterload(tc5b_trajin, tc5b_top)
mask_list = ('@CB @CA', '@CA @H')
dslist = CpptrajDatasetList()
actlist = ActionList()
for mask in mask_list:
actlist.add(CA.Action_Distance(), mask, traj.top, dslist=dslist)
actlist.compute(traj)
dslist2 = pt.calc_distance(traj, mask_list)
aa_eq(dslist.values, dslist2)
def test_run_5(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mask_list = ('@CB @CA', '@CA @H')
dslist = CpptrajDatasetList()
actlist = ActionList()
for mask in mask_list:
actlist.add(CA.Action_Distance(),
mask,
traj.top,
dslist=dslist)
actlist.compute(traj)
dslist2 = pt.calc_distance(traj, mask_list)
aa_eq(dslist.values, dslist2)
