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_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/ala3.dcd", "./data/ala3.psf")
traj.save("./output/_save_charmm_to_amber.x", overwrite=True)
# test loading
trajamber = mdio.iterload("./output/_save_charmm_to_amber.x",
"./data/ala3.psf")
for i in range(traj.n_frames):
aa_eq(trajamber[i].xyz, traj[i].xyz, decimal=3)
def test_load_and_save_0(self):
traj = mdio.iterload(filename="./data/Tc5b.x",
top="./data/Tc5b.top")[:10]
indices = list(range(2, 3, 5)) + [3, 8, 9, 8]
mdio.write_traj(filename="./output/test_io_saved_.x",
traj=traj,
top="./data/Tc5b.top",
frame_indices=indices,
overwrite=True)
# check frames
traj2 = mdio.iterload(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
assert traj2.n_frames == len(indices)
def test_load_and_save_0(self):
traj = mdio.iterload(filename="./data/Tc5b.x",
top="./data/Tc5b.top")[:10]
indices = list(range(2, 3, 5)) + [3, 8, 9, 8]
mdio.write_traj(filename="./output/test_io_saved_.x",
traj=traj,
top="./data/Tc5b.top",
frame_indices=indices,
overwrite=True)
# check frames
traj2 = mdio.iterload(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
assert traj2.n_frames == len(indices)
def test_0(self):
# create TrajectoryIter (readonly)
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# convert to Trajectory
fa = traj[:]
# frame view
f0 = fa[0]
aa_eq(f0.xyz, fa[0].xyz)
# assign new values
f0[0, 0] = 1000.
assert f0[0, 0] == 1000.
aa_eq(f0.xyz, fa[0].xyz)
# sub-Trajectory view
fa1 = fa[2:8:2]
aa_eq(fa1.xyz, fa[2:8:2].xyz)
fa1[0, 0] = 200.
assert fa1[0, 0, 0] == 200.
assert fa[2, 0, 0] == 200.
aa_eq(fa1.xyz, fa[2:8:2].xyz)
# make sure we can make a copy
facp = fa.copy()
facp.xyz[0, 0, 0] = 501.
assert facp.xyz[0, 0, 0] == 501.
assert fa.xyz[0, 0, 0] != 501.
def main():
# require 'sanderapi' and 'parmed' packages in AmberTools15
# http://ambermd.org/#AmberTools
# more info about `sanderapi` in Amber15 manual
# http://ambermd.org/doc12/Amber15.pdf (page 341)
traj = io.iterload("../tests/data/Tc5b.x",
"../tests/data/Tc5b.top")
print(traj)
edict0 = pyca.energy_decomposition(parm="../tests/data/Tc5b.top",
traj=traj,
igb=8,
input_options=None)
print(edict0)
# edict1: use default igb=8
edict1 = pyca.energy_decomposition(traj=traj)
print(edict1)
aa_eq(edict0['tot'], edict1['tot'])
# update `input` and get minimal output
import sander
inp = sander.gas_input(6)
edict2 = pyca.energy_decomposition(traj, input_options=inp, mode='minimal')
print(edict2)
def test_0(self):
import numpy as np
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = traj[:]
for i in range(3):
fa.append_xyz(fa.xyz)
xyz = fa.xyz / 10.
fa.xyz = xyz
aa_eq(xyz, fa.xyz)
# try to build Trajectory from scratch
fa2 = Trajectory()
fa2.top = fa.top
fa2._allocate(fa.n_frames, fa.n_atoms)
fa2.xyz = fa.xyz[:]
aa_eq(fa2.xyz, fa.xyz)
# try to build Trajectory from scratch
fa2 = Trajectory(xyz=fa.xyz, top=fa.top)
aa_eq(fa2.xyz, fa.xyz)
# timing
xyz0 = np.empty((fa.n_frames, fa.n_atoms, 3))
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mdio.write_traj("test_1.pdb", traj[0], top=traj.top, overwrite=True)
mdio.write_traj("test_1.dcd", traj[0], top=traj.top, overwrite=True)
with TrajectoryWriter("./output/test_1", overwrite=True) as trajout:
trajout.write(traj[0])
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):
import numpy as np
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = traj[:]
for i in range(3):
fa.append_xyz(fa.xyz)
xyz = fa.xyz / 10.
fa.xyz = xyz
aa_eq(xyz, fa.xyz)
# try to build Trajectory from scratch
fa2 = Trajectory()
fa2.top = fa.top
fa2._allocate(fa.n_frames, fa.n_atoms)
fa2.xyz = fa.xyz[:]
aa_eq(fa2.xyz, fa.xyz)
# try to build Trajectory from scratch
fa2 = Trajectory(xyz=fa.xyz, top=fa.top)
aa_eq(fa2.xyz, fa.xyz)
# timing
xyz0 = np.empty((fa.n_frames, fa.n_atoms, 3))
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
assert frame0._buffer2d[0, 0] == frame0[0, 0]
assert frame0._buffer2d[0, 1] == frame0[0, 1]
assert frame0._buffer2d[0, 2] == frame0[0, 2]
assert frame0._buffer2d[1, 0] == frame0[1, 0]
assert frame0._buffer2d[19, 0] == frame0[19, 0]
frame0._buffer2d[19, 0] = 1000.
# make sure changing _buffer2d will update frame0.xyz too
assert frame0._buffer2d[19, 0] == frame0[19, 0]
arr0 = np.asarray(frame0._buffer2d)
arr0[19] = [200, 300, 400.]
assert frame0._buffer2d[19, 0] == frame0[19, 0] == arr0[19, 0]
frame1 = frame0.copy()
frame1.strip(traj.top("!@CA"))
_f = pt.Frame(frame0, traj.top("@CA"))
CA_2 = _f[2, :]
aa_eq(CA_2, frame1[2, :])
assert frame0._buffer1d.shape == (912, )
assert frame0._buffer2d.shape == (304, 3)
assert frame0._buffer1d.is_c_contig() == True
frame0._buffer2d[1:3, 0] = array('d', [1., 2.])
aa_eq(frame0[1:3, 0], array('d', frame0._buffer2d[1:3, 0]))
aa_eq(frame0._buffer2d[1:3, 0], array('d', frame0._buffer2d[1:3, 0]))
def test_0(self):
import numpy as np
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = traj[:]
mask = ':1@CA :14@CB :15CA'
d0 = pt.calc_angle(traj, mask, dtype='dataset').to_ndarray()
d1 = pt.angle(traj, mask)
d2 = pt.angle(fa, mask)
aa_eq(d0, d1)
aa_eq(d0, d2)
Nsize = 10
arr = np.random.randint(0, 300, size=Nsize * 3).reshape(Nsize, 3)
d3 = pt.angle(fa, arr)
d4 = pt.angle(traj, arr)
d5 = pt.calc_angle(traj, arr)
d6 = pt.calc_angle(fa, arr)
d7 = pt.calc_angle([fa, traj], arr, n_frames=2 * fa.n_frames)
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:])
d8 = pt.angle(traj, mask, dtype='dataset')
d9 = pt.tools.dict_to_ndarray(pt.angle(traj, mask, dtype='dict'))
aa_eq(d0, d8.values)
aa_eq(d0, d9)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mdio.write_traj("test_1.pdb", traj[0], top=traj.top, overwrite=True)
mdio.write_traj("test_1.dcd", traj[0], top=traj.top, overwrite=True)
with TrajectoryWriter("./output/test_1", overwrite=True) as trajout:
trajout.write(traj[0])
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):
# create TrajectoryIter (readonly)
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# convert to Trajectory
fa = traj[:]
# frame view
f0 = fa[0]
aa_eq(f0.xyz, fa[0].xyz)
# assign new values
f0[0, 0] = 1000.
assert f0[0, 0] == 1000.
aa_eq(f0.xyz, fa[0].xyz)
# sub-Trajectory view
fa1 = fa[2:8:2]
aa_eq(fa1.xyz, fa[2:8:2].xyz)
fa1[0, 0] = 200.
assert fa1[0, 0, 0] == 200.
assert fa[2, 0, 0] == 200.
aa_eq(fa1.xyz, fa[2:8:2].xyz)
# make sure we can make a copy
facp = fa.copy()
facp.xyz[0, 0, 0] = 501.
assert facp.xyz[0, 0, 0] == 501.
assert fa.xyz[0, 0, 0] != 501.
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(fn('Tc5b.x'), fn('Tc5b.top'))
frame0 = traj[0]
assert frame0._buffer2d[0, 0] == frame0[0, 0]
assert frame0._buffer2d[0, 1] == frame0[0, 1]
assert frame0._buffer2d[0, 2] == frame0[0, 2]
assert frame0._buffer2d[1, 0] == frame0[1, 0]
assert frame0._buffer2d[19, 0] == frame0[19, 0]
frame0._buffer2d[19, 0] = 1000.
# make sure changing _buffer2d will update frame0.xyz too
assert frame0._buffer2d[19, 0] == frame0[19, 0]
arr0 = np.asarray(frame0._buffer2d)
arr0[19] = [200, 300, 400.]
assert frame0._buffer2d[19, 0] == frame0[19, 0] == arr0[19, 0]
frame1 = frame0.copy()
frame1.strip(traj.top("!@CA"))
_f = pt.Frame(frame0, traj.top("@CA"))
CA_2 = _f[2, :]
aa_eq(CA_2, frame1[2, :])
assert frame0._buffer1d.shape == (912, )
assert frame0._buffer2d.shape == (304, 3)
assert frame0._buffer1d.is_c_contig() == True
frame0._buffer2d[1:3, 0] = array('d', [1., 2.])
aa_eq(frame0[1:3, 0], array('d', frame0._buffer2d[1:3, 0]))
aa_eq(frame0._buffer2d[1:3, 0], array('d', frame0._buffer2d[1:3, 0]))
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_0(self):
import numpy as np
traj = mdio.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
fa = traj[:]
mask = ':1@CA :14@CB :15CA'
d0 = pt.calc_angle(traj, mask, dtype='dataset').to_ndarray()
d1 = pt.angle(traj, mask)
d2 = pt.angle(fa, mask)
aa_eq(d0, d1)
aa_eq(d0, d2)
Nsize = 10
arr = np.random.randint(0, 300, size=Nsize * 3).reshape(Nsize, 3)
d3 = pt.angle(fa, arr)
d4 = pt.angle(traj, arr)
d5 = pt.calc_angle(traj, arr)
d6 = pt.calc_angle(fa, arr)
d7 = pt.calc_angle([fa, traj], arr, n_frames=2 * fa.n_frames)
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:])
d8 = pt.angle(traj, mask, dtype='dataset')
d9 = pt.tools.dict_to_ndarray(pt.angle(traj, mask, dtype='dict'))
aa_eq(d0, d8.values)
aa_eq([d0], d9)
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")
indices = traj.top("@CA").indices
for frame in traj(mask=indices):
pass
for frame in traj(mask=[1, 5, 8, 10]):
pass
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")
indices = traj.top("@CA").indices
for frame in traj(mask=indices):
pass
for frame in traj(mask=[1, 5, 8, 10]):
pass
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
f0 = traj[0]
# creat new frame based on f0 and atommask
f1 = Frame(f0, traj.top('@CA'))
atm = AtomMask("")
traj.top.set_integer_mask(atm)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# +=
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 += 1.
aa_eq(f0.xyz, xyz + 1.)
# -=
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 -= 1.
aa_eq(f0.xyz, xyz - 1.)
# *=
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 *= 2.
aa_eq(f0.xyz, xyz * 2)
# /= single value
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 /= 2.
aa_eq(f0.xyz, xyz / 2)
# /= other Frame
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = traj[1].copy()
xyz1 = f1.xyz.copy()
f0 /= f1
aa_eq(f0.xyz, xyz / xyz1)
# +
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 + 1.
aa_eq(f1.xyz, xyz + 1.)
# -
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 - 1.
aa_eq(f1.xyz, xyz - 1.)
# *
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 * 10.
aa_eq(f1.xyz, xyz * 10.)
# /
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 / 10.
aa_eq(f1.xyz, xyz / 10.)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# +=
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 += 1.
aa_eq(f0.xyz, xyz + 1.)
# -=
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 -= 1.
aa_eq(f0.xyz, xyz - 1.)
# *=
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 *= 2.
aa_eq(f0.xyz, xyz * 2)
# /= single value
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f0 /= 2.
aa_eq(f0.xyz, xyz / 2)
# /= other Frame
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = traj[1].copy()
xyz1 = f1.xyz.copy()
f0 /= f1
aa_eq(f0.xyz, xyz / xyz1)
# +
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 + 1.
aa_eq(f1.xyz, xyz + 1.)
# -
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 - 1.
aa_eq(f1.xyz, xyz - 1.)
# *
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 * 10.
aa_eq(f1.xyz, xyz * 10.)
# /
f0 = traj[0].copy()
xyz = f0.xyz.copy()
f1 = f0 / 10.
aa_eq(f1.xyz, xyz / 10.)
def test_0(self):
import numpy as np
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
f0 = traj[0]
arr0 = np.asarray(f0._buffer2d)
arr1 = np.asarray(f0)
aa_eq(arr0.flatten(), arr1.flatten())
arr0[0, 0] = 100.
aa_eq(arr0.flatten(), arr1.flatten())
aa_eq(arr0.flatten(), f0.xyz.flatten())
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 = 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_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
assert frame0.has_box() == False
box = frame0.box
assert frame0.box.type == 'nobox'
bview = frame0._boxview
bview[3:] = np.asarray([109.471220634, 109.471220634, 109.471220634])
bview[:3] = np.array([100, 100, 100], dtype='f8')
assert frame0.box.type == 'truncoct'
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
assert frame0.has_box() == False
box = frame0.box
assert frame0.box.type == 'nobox'
bview = frame0._boxview
bview[3:] = np.asarray([109.471220634, 109.471220634, 109.471220634])
bview[:3] = np.array([100, 100, 100], dtype='f8')
assert frame0.box.type == 'truncoct'
def test_0(self):
trajlist = []
N = 4
for i in range(N):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
trajlist.append(traj)
traj0 = trajlist[0]
mdio.write_traj("./output/test_savedtrajlist.x",
traj=trajlist,
top=traj.top,
overwrite=True)
# test loading
traj2 = mdio.iterload("./output/test_savedtrajlist.x", traj.top)
Nsize = int(traj2.n_frames / 4)
traj0_new = traj2[:Nsize]
for frame0, frame0_new in zip(traj0, traj0_new):
assert (frame0.rmsd(frame0_new) < 1E-3)
def test_0(self):
trajlist = []
N = 4
for i in range(N):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
trajlist.append(traj)
traj0 = trajlist[0]
mdio.write_traj("./output/test_savedtrajlist.x",
traj=trajlist,
top=traj.top,
overwrite=True)
# test loading
traj2 = mdio.iterload("./output/test_savedtrajlist.x", traj.top)
Nsize = int(traj2.n_frames / 4)
traj0_new = traj2[:Nsize]
for frame0, frame0_new in zip(traj0, traj0_new):
assert (frame0.rmsd(frame0_new) < 1E-3)
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_trajlist(self):
trajlist = []
N = 4
for i in range(N):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
trajlist.append(traj)
traj0 = trajlist[0]
with tempfolder():
pt.write_traj("test_savedtrajlist.x",
traj=trajlist,
top=traj.top,
overwrite=True)
# test loading
traj2 = pt.iterload("test_savedtrajlist.x", traj.top)
Nsize = int(traj2.n_frames / 4)
traj0_new = traj2[:Nsize]
for frame0, frame0_new in zip(traj0, traj0_new):
assert (frame0.rmsd(frame0_new) < 1E-3)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
if has_("numpy"):
import numpy as np
from numpy.testing import assert_almost_equal
arr0 = traj.xyz
aa_eq(arr0, traj[:, :, :].xyz)
# create Trajectory
farray = traj[:]
aa_eq(arr0, farray[:, :, :].xyz)
else:
pass
def test_4(self):
"""test write Trajectory"""
farray = pt.load("data/Tc5b.x",
"./data/Tc5b.top",
frame_indices=list(range(10)))
pt.write_traj("./output/test_write_output.x",
farray,
top=farray.top,
overwrite=True)
pt.write_traj("./output/test_pdb_1.dummyext",
farray[0],
top=farray.top,
overwrite=True)
# test 'save'
farray.save("./output/test_write_output_save_method.x", overwrite=True)
# reproduce result?
f0 = mdio.iterload("./output/test_write_output.x", "./data/Tc5b.top")
f1 = mdio.iterload("./output/test_write_output_save_method.x",
"./data/Tc5b.top")
aa_eq(f0[:, :, :].xyz, f1[:, :, :].xyz)
def test_0(self):
import numpy as np
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# 3 atoms x 2
arr = np.array([[12, 13, 15], [16, 17, 18]])
f0saved = traj[0].copy()
f0 = traj[0].copy()
f0.swap_atoms(arr)
aa_eq(f0saved[12], f0[16])
aa_eq(f0saved[13], f0[17])
aa_eq(f0saved[15], f0[18])
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
if has_("numpy"):
import numpy as np
from numpy.testing import assert_almost_equal
arr0 = traj.xyz
aa_eq(arr0, traj[:, :, :].xyz)
# create Trajectory
farray = traj[:]
aa_eq(arr0, farray[:, :, :].xyz)
else:
pass
def test_4(self):
"""test write Trajectory"""
farray = pt.load("data/Tc5b.x",
"./data/Tc5b.top",
frame_indices=list(range(10)))
pt.write_traj("./output/test_write_output.x",
farray,
top=farray.top,
overwrite=True)
pt.write_traj("./output/test_pdb_1.dummyext",
farray[0],
top=farray.top,
overwrite=True)
# test 'save'
farray.save("./output/test_write_output_save_method.x", overwrite=True)
# reproduce result?
f0 = mdio.iterload("./output/test_write_output.x", "./data/Tc5b.top")
f1 = mdio.iterload("./output/test_write_output_save_method.x",
"./data/Tc5b.top")
aa_eq(f0[:, :, :].xyz, f1[:, :, :].xyz)
def test_0(self):
traj = mdio.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
fa1 = traj[:]
# do inplace-autoimage for Trajectory
fa1.autoimage()
# fa2 will store frame when iterating `traj` (TrajectoryIterator)
fa2 = Trajectory()
fa2.top = traj.top.copy()
# frame_iter
for frame in traj(autoimage=True):
fa2.append(frame)
aa_eq(fa1.xyz, fa2.xyz)
# frame_iter with mask and autoimage
fa3 = fa2.copy()
# fa3 is a copy of autoimaged fa2. then we strip all but CA atoms
# just want to make sure we can use `mask`
fa3.strip("!@CA")
fa4 = Trajectory()
fa4.top = fa3.top.copy()
for frame in traj(mask='@CA', autoimage=True):
fa4.append(frame)
aa_eq(fa3.xyz, fa4.xyz)
# frame_iter with mask and autoimage, and rmsfit
# fa3 is a copy of autoimaged fa2. then we strip all but CA atoms
# just want to make sure we can use `mask`
fa3 = traj[:]
fa3.autoimage()
fa3.rmsfit(ref=5, mask='@CB')
fa3.strip("!@CA")
fa4 = Trajectory()
fa4.top = fa3.top.copy()
ref1 = traj[5].copy()
for frame in traj(mask='@CA', autoimage=True, rmsfit=(ref1, '@CB')):
fa4.append(frame)
aa_eq(fa3.xyz, fa4.xyz)
for f0, f1 in zip(fa3, fa4):
assert f0.rmsd_nofit(f1) < 1E-7
def test_0(self):
traj = mdio.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
fa1 = traj[:]
# do inplace-autoimage for Trajectory
fa1.autoimage()
# fa2 will store frame when iterating `traj` (TrajectoryIterator)
fa2 = Trajectory()
fa2.top = traj.top.copy()
# frame_iter
for frame in traj(autoimage=True):
fa2.append(frame)
aa_eq(fa1.xyz, fa2.xyz)
# frame_iter with mask and autoimage
fa3 = fa2.copy()
# fa3 is a copy of autoimaged fa2. then we strip all but CA atoms
# just want to make sure we can use `mask`
fa3.strip("!@CA")
fa4 = Trajectory()
fa4.top = fa3.top.copy()
for frame in traj(mask='@CA', autoimage=True):
fa4.append(frame)
aa_eq(fa3.xyz, fa4.xyz)
# frame_iter with mask and autoimage, and rmsfit
# fa3 is a copy of autoimaged fa2. then we strip all but CA atoms
# just want to make sure we can use `mask`
fa3 = traj[:]
fa3.autoimage()
fa3.rmsfit(ref=5, mask='@CB')
fa3.strip("!@CA")
fa4 = Trajectory()
fa4.top = fa3.top.copy()
ref1 = traj[5].copy()
for frame in traj(mask='@CA', autoimage=True, rmsfit=(ref1, '@CB')):
fa4.append(frame)
aa_eq(fa3.xyz, fa4.xyz)
for f0, f1 in zip(fa3, fa4):
assert f0.rmsd_nofit(f1) < 1E-7
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("../tests/data/Tc5b.x",
"../tests/data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `optionsl` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_0(self):
from pytraj import DatasetList
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
from pytraj.all_actions import calc_multidihedral
command = "resrange 2-19 phi psi"
d0 = calc_multidihedral(traj, command)
d1 = calc_multidihedral(traj, command)
assert isinstance(d0, DatasetList) == True
assert (len(d0.keys()) == len(d1.keys()))
d3 = calc_multidihedral(traj)
import numpy as np
d0np = calc_multidihedral(traj, command, dtype='ndarray')
self.assertIsInstance(d0np, np.ndarray)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
start, stop, stride = 0, 8, 2
indices = list(range(start, stop, stride))
flist = []
count = 0
for i, frame in enumerate(traj[:stop + 1]):
count += 1
if i in indices:
flist.append(frame)
if i > stop:
traj.end_traj()
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):
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):
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):
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):
from pytraj import DatasetList
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
from pytraj.all_actions import calc_multidihedral
command = "resrange 2-19 phi psi"
d0 = calc_multidihedral(traj, command)
d1 = calc_multidihedral(traj, command)
assert isinstance(d0, DatasetList) == True
assert (len(d0.keys()) == len(d1.keys()))
d3 = calc_multidihedral(traj)
import numpy as np
d0np = calc_multidihedral(traj, command, dtype='ndarray')
self.assertIsInstance(d0np, np.ndarray)
def test_1(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
act = adict['distance']
dslist = DatasetList()
act.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act.check_topology(traj.top)
for frame in traj.iterframe(stop=5):
act.compute(frame)
dslist = DatasetList()
act2 = adict['distance']
act2.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act2.check_topology(traj.top)
act2.compute(traj.iterframe(stop=5))
assert act2.n_frames == 5
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_1(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
act = adict['distance']
dslist = DatasetList()
act.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act.check_topology(traj.top)
for frame in traj.iterframe(stop=5):
act.compute(frame)
dslist = DatasetList()
act2 = adict['distance']
act2.read_input(":2@CA :10@CA", traj.top, dslist=dslist)
act2.check_topology(traj.top)
act2.compute(traj.iterframe(stop=5))
assert act2.n_frames == 5