def test_0(self):
# merge_coordinates
pass
# load 2 frames
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'), frame_slice=(0, 2))
# test mutable traj
coords = pt.tools.merge_coordinates(traj[:])
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
# test immutable traj
coords = pt.tools.merge_coordinates(traj)
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
# test tuple
coords = pt.tools.merge_coordinates((frame for frame in traj))
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
coords = pt.tools.merge_coordinates([f.copy() for f in traj])
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
def test_0(self):
# merge_coordinates
import numpy as np
# load 2 frames
traj = pt.iterload("./data/Tc5b.x",
"./data/Tc5b.top",
frame_slice=(0, 2))
# test mutable traj
coords = pt.tools.merge_coordinates(traj[:])
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj))
assert r0 == 0.
# test immutable traj
coords = pt.tools.merge_coordinates(traj)
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
# test tuple
coords = pt.tools.merge_coordinates((frame for frame in traj))
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
coords = pt.tools.merge_coordinates([f.copy() for f in traj])
r0 = pt.tools.rmsd(coords, pt.get_coordinates(traj), True)
assert r0 == 0.
def test_0(self):
import numpy as np
# load 2 frames
traj = pt.iterload("./data/Tc5b.x",
"./data/Tc5b.top",
frame_slice=(0, 2))
# test mutable traj
big_frame = pt.tools.merge_frames(traj[:])
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test immutable traj
big_frame = pt.tools.merge_frames(traj)
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test tuple
big_frame = pt.tools.merge_frames((frame for frame in traj))
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test list
big_frame = pt.tools.merge_frames([frame.copy() for frame in traj])
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
def test_0(self):
pass
# load 2 frames
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'), frame_slice=(0, 2))
# test mutable traj
big_frame = pt.tools.merge_frames(traj[:])
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test immutable traj
big_frame = pt.tools.merge_frames(traj)
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test tuple
big_frame = pt.tools.merge_frames((frame for frame in traj))
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test list
big_frame = pt.tools.merge_frames([frame.copy() for frame in traj])
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
def test_get_coordinates_trajectory():
'''mutable pytraj.Trajectory
'''
traj = pt.Trajectory(xyz=traj_tz2_ortho.xyz, top=traj_tz2_ortho.top)
# make a different copy since ``traj`` is mutable
traj2 = traj.copy()
# all coordinates
xyz = pt.get_coordinates(traj)
aa_eq(traj.xyz, xyz)
# given frames
xyz = pt.get_coordinates(traj, frame_indices=[0, 5])
aa_eq(traj[[0, 5]].xyz, xyz)
# given frames, autoimage=True
xyz = pt.get_coordinates(traj, frame_indices=[0, 5], autoimage=True)
aa_eq(traj2[[0, 5]].autoimage().xyz, xyz)
# given frames, autoimage=True, rmsfit=ref
ref = traj[-3]
pt.autoimage(ref, top=traj.top)
xyz = pt.get_coordinates(traj,
frame_indices=[0, 5],
autoimage=True,
rmsfit=ref)
aa_eq(traj2[[0, 5]].autoimage().superpose(ref=ref).xyz, xyz)
def test_0(self):
import numpy as np
# load 2 frames
traj = pt.iterload("./data/Tc5b.x",
"./data/Tc5b.top",
frame_slice=(0, 2))
# test mutable traj
big_frame = pt.tools.merge_frames(traj[:])
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test immutable traj
big_frame = pt.tools.merge_frames(traj)
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test tuple
big_frame = pt.tools.merge_frames((frame for frame in traj))
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
# test list
big_frame = pt.tools.merge_frames([frame.copy() for frame in traj])
assert pt.tools.rmsd(big_frame.xyz.flatten(),
pt.get_coordinates(traj).flatten()) < 1E-5
def test_1(self):
# merge_frames
import numpy as np
# load 2 frames
traj = pt.iterload("./data/Tc5b.x",
"./data/Tc5b.top",
frame_slice=(0, 2))
# test mutable traj
t0 = traj[:]
frame = pt.tools.merge_frames(t0)
r0 = pt.tools.rmsd(frame.xyz, pt.get_coordinates(traj), True)
assert r0 == 0.
# test immutable traj
assert np.any(pt.tools.merge_frames(traj).xyz.flatten() ==
pt.get_coordinates(traj).flatten())
# tuple
assert np.any(pt.tools.merge_frames((
frame for frame in traj)).xyz.flatten() == pt.get_coordinates(
traj).flatten())
# list
assert np.any(pt.tools.merge_frames(
[frame for frame in traj]).xyz.flatten() == pt.get_coordinates(
traj).flatten())
# frame_iter: all atoms
assert np.any(pt.tools.merge_frames(traj()).xyz.flatten() ==
pt.get_coordinates(traj()).flatten())
def test_pieline(self):
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
fi = pt.pipe(traj, ['autoimage', ])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
fi = pt.pipe(traj, ['autoimage', ], frame_indices=[3, 5])
aa_eq(pt.get_coordinates(fi), traj[[3, 5]].autoimage().xyz)
def test_pieline(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
fi = pt.pipe(traj, ['autoimage', ])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
fi = pt.pipe(traj, ['autoimage', ], frame_indices=[3, 5])
aa_eq(pt.get_coordinates(fi), traj[[3, 5]].autoimage().xyz)
def test_closest_compared_to_cpptraj(self):
trajin = fn('tz2.ortho.nc')
parm = fn('tz2.ortho.parm7')
traj = pt.iterload(trajin, parm, frame_slice=[
(0, 2),
])
state = pt.load_cpptraj_state('''
parm {}
trajin {} 1 2
autoimage
closest 100 :1-13
createcrd mycrd'''.format(parm, trajin))
state.run()
fi, top = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100,
dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_issue807(self):
# files are provided by Chris Lee
traj = pt.iterload("./data/issue807/trunc.nc",
"./data/issue807/system.prmtop")
traj[0]
for frame in traj:
pass
traj[::2]
pt.radgyr(traj[[0, 3]])
pt.radgyr(traj, frame_indices=[0, 3])
pt.radgyr(traj())
traj[:3, '@O'].xyz
pt.get_coordinates((traj.iterframe(mask='@O')))
pt.radgyr(traj(mask='@O'))
for c in pt.iterchunk(traj, 4):
assert c[0].n_atoms == traj.top.n_atoms
def test_issue807(self):
# files are provided by Chris Lee
traj = pt.iterload("./data/issue807/trunc.nc",
"./data/issue807/system.prmtop")
traj[0]
for frame in traj:
pass
traj[::2]
pt.radgyr(traj[[0, 3]])
pt.radgyr(traj, frame_indices=[0, 3])
pt.radgyr(traj())
traj[:3, '@O'].xyz
pt.get_coordinates((traj.iterframe(mask='@O')))
pt.radgyr(traj(mask='@O'))
for c in pt.iterchunk(traj, 4):
assert c[0].n_atoms == traj.top.n_atoms
def test_comprehensive(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
# make sure we DO reproducing cpptraj output
f_saved = pt.iterload(fn("avg.Tc5b.pdb"), traj.top)[0]
# shorter
frame2 = mean_structure(traj)
aa_eq(frame2.xyz, f_saved.xyz, decimal=3)
frame3 = mean_structure(traj=traj)
aa_eq(frame3.xyz, f_saved.xyz, decimal=3)
# test list
frame4 = mean_structure(traj=[traj, traj[:3]], top=traj.top)
# test iter
frame5 = mean_structure(traj=traj(1, 8, 2), top=traj.top)
f5_saved = pt.iterload(fn("avg.Tc5b.frame_2_to_8_skip_2.pdb"),
traj.top)[0]
aa_eq(frame5.xyz, f5_saved.xyz, decimal=3)
# test iter CA
frame5 = mean_structure(traj[[0, 3, 7]], '@CA', top=traj.top)
# use atom_indices
ca_indices = pt.select('@CA', traj.top)
frame5_1 = mean_structure(traj[[0, 3, 7]], ca_indices, top=traj.top)
# test frame_indices
frame6 = mean_structure(traj, mask='@CA', frame_indices=[0, 3, 7])
aa_eq(frame5.xyz, frame6.xyz, decimal=3)
aa_eq(frame5_1.xyz, frame6.xyz, decimal=3)
xyz_0 = pt.get_coordinates(traj(1, 8, 2))
xyz_1 = np.array([
frame.xyz.copy()
for frame in traj.iterframe(frame_indices=range(1, 8, 2))
])
aa_eq(xyz_0, xyz_1, decimal=3)
# test as traj
out_traj = mean_structure(traj,
mask='@CA',
frame_indices=[0, 3, 7],
dtype='traj')
assert isinstance(out_traj, Trajectory), 'must be Trajectory'
aa_eq(out_traj.xyz, frame6.xyz, decimal=3)
# raise if not trajectory, traj or frame
self.assertRaises(ValueError,
lambda: pt.mean_structure(traj, dtype='trajxyz'))
def test_get_coordinates_trajecotoryiterator():
'''immutable pytraj.TrajectoryIterator
'''
traj = traj_tz2_ortho.copy()
# all coordinates
xyz = pt.get_coordinates(traj)
aa_eq(traj.xyz, xyz)
# given frames
xyz = pt.get_coordinates(traj, frame_indices=[0, 5])
aa_eq(traj[[0, 5]].xyz, xyz)
# given frames, autoimage=True
xyz = pt.get_coordinates(traj, frame_indices=[0, 5], autoimage=True)
aa_eq(traj[[0, 5]].autoimage().xyz, xyz)
# given frames, autoimage=True, rmsfit=ref
ref = traj[-3]
pt.autoimage(ref, top=traj.top)
xyz = pt.get_coordinates(traj,
frame_indices=[0, 5],
autoimage=True,
rmsfit=ref)
aa_eq(traj[[0, 5]].autoimage().superpose(ref=ref).xyz, xyz)
xyz = pt.get_coordinates(traj,
frame_indices=range(3),
autoimage=True,
rmsfit=ref)
# with mask
xyz = pt.get_coordinates(traj, mask='@CA')
aa_eq(xyz, traj['@CA'].xyz)
# slow
fi = pt.pipe(traj, ['autoimage'])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
# raise
with pytest.raises(ValueError):
pt.get_coordinates(traj(), frame_indices=[0, 2])
def test_comprehensive(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# make sure we DO reproducing cpptraj output
f_saved = pt.iterload("./data/avg.Tc5b.pdb", traj.top)[0]
# shorter
frame2 = mean_structure(traj)
aa_eq(frame2.xyz, f_saved.xyz, decimal=3)
frame3 = mean_structure(traj=traj)
aa_eq(frame3.xyz, f_saved.xyz, decimal=3)
# test list
frame4 = mean_structure(traj=[traj, traj[:3]], top=traj.top)
# test iter
frame5 = mean_structure(traj=traj(1, 8, 2), top=traj.top)
f5_saved = pt.iterload("./data/avg.Tc5b.frame_2_to_8_skip_2.pdb",
traj.top)[0]
aa_eq(frame5.xyz, f5_saved.xyz, decimal=3)
# test iter CA
frame5 = mean_structure(traj[[0, 3, 7]], '@CA', top=traj.top)
# use atom_indices
ca_indices = pt.select('@CA', traj.top)
frame5_1 = mean_structure(traj[[0, 3, 7]], ca_indices, top=traj.top)
# test frame_indices
frame6 = mean_structure(traj, mask='@CA', frame_indices=[0, 3, 7])
aa_eq(frame5.xyz, frame6.xyz, decimal=3)
aa_eq(frame5_1.xyz, frame6.xyz, decimal=3)
xyz_0 = pt.get_coordinates(traj(1, 8, 2))
xyz_1 = np.array([frame.xyz.copy(
) for frame in traj.iterframe(frame_indices=range(1, 8, 2))])
aa_eq(xyz_0, xyz_1, decimal=3)
# test as traj
out_traj = mean_structure(traj,
mask='@CA',
frame_indices=[0, 3, 7],
dtype='traj')
assert isinstance(out_traj, Trajectory), 'must be Trajectory'
aa_eq(out_traj.xyz, frame6.xyz, decimal=3)
# raise if not trajectory, traj or frame
self.assertRaises(ValueError, lambda: pt.mean_structure(traj, dtype='trajxyz'))
def test_closest_compared_to_cpptraj(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
state = pt.load_cpptraj_state('''
autoimage
closest 100 :1-13
createcrd mycrd''', traj)
state.run()
fi, top = pt.closest(traj(autoimage=True), mask=':1-13', n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True), mask=':1-13', n_solvents=100, dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_modify_frame_use_Pipeline(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
dslist = CpptrajDatasetList()
dslist.add_new('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = ['autoimage', 'strip :WAT', 'createcrd mycrd', ]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj,
mask='!:WAT',
autoimage=True))
def test_closest(self):
# raise if not has solvent
traj0 = pt.iterload(fn('tz2.nc'),
fn('tz2.parm7'),
frame_slice=[(0, 2)])
self.assertRaises(RuntimeError, lambda: pt.closest(traj0))
traj = pt.iterload(fn('tz2.ortho.nc'),
fn('tz2.ortho.parm7'),
frame_slice=[(0, 2)])
fi, top = pt.closest(traj)
coords = []
for frame in fi:
coords.append(frame.xyz.copy())
assert isinstance(frame, pt.Frame), 'must be Frame'
# make a Trajectory
fi, top = pt.closest(traj)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(np.array(coords), t0.xyz)
# test write to disk
fi, top = pt.closest(traj)
pt.write_traj(outputname('fi.nc'), fi, top=top, overwrite=True)
# load back
t1 = pt.load(outputname('fi.nc'), top=top)
aa_eq(t0.xyz, t1.xyz)
# make sure n_sovent=10 (default)
n_solvents = 0
for mol in top.mols:
if mol.is_solvent():
n_solvents += 1
assert n_solvents == 10, 'must be 10 solvents'
fi, top = pt.closest(traj)
pt.write_traj(outputname('test.pdb'),
next(fi),
top=top,
overwrite=True)
def test_modify_frame_use_Pipeline(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
dslist = CpptrajDatasetList()
dslist.add('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = [
'autoimage',
'strip :WAT',
'createcrd mycrd',
]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_4(self):
# combined with get_coordinates
traj0 = pt.iterload("./data/tz2.truncoct.nc",
"./data/tz2.truncoct.parm7")
# test autoimage
traj1 = traj0[:]
xyz0 = pt.get_coordinates(traj0(autoimage=True))
traj1.autoimage()
xyz1 = traj1.xyz
# OK
assert rmsd_1darray(xyz0.flatten(), xyz1.flatten()) == 0.
# rmsfit
# reset traj1
traj1 = traj0[:]
# get new trajectory from traj0
traj2 = pt._load_from_frame_iter(traj0(rmsfit=(0, '@CA,C,N')))
traj1.rmsfit(ref=0, mask='@CA,C,N')
# take '@CA,C,N' xyz
xyz2 = traj2['@CA,C,N'].xyz
xyz1 = traj1['@CA,C,N'].xyz
# OK
assert rmsd_1darray(xyz1.flatten(), xyz2.flatten()) < 1E-10
# combine autoimage with rmsfit
# reset traj1
traj1 = traj0[:]
# get new trajectory from traj0
traj2 = pt._load_from_frame_iter(traj0(autoimage=True,
rmsfit=(0, '@CA,C,N')))
traj1.autoimage()
traj1.rmsfit(ref=0, mask='@CA,C,N')
# take '@CA,C,N' xyz
xyz2 = traj2['@CA,C,N'].xyz
xyz1 = traj1['@CA,C,N'].xyz
# PASSED
assert rmsd_1darray(xyz1.flatten(), xyz2.flatten()) < 1E-10
def test_4(self):
# combined with get_coordinates
traj0 = pt.iterload(fn('tz2.truncoct.nc'),
fn('tz2.truncoct.parm7'))
# test autoimage
traj1 = traj0[:]
xyz0 = pt.get_coordinates(traj0(autoimage=True))
traj1.autoimage()
xyz1 = traj1.xyz
# OK
assert rmsd_1darray(xyz0.flatten(), xyz1.flatten()) == 0.
# rmsfit
# reset traj1
traj1 = traj0[:]
# get new trajectory from traj0
traj2 = pt.load_from_frame_iter(traj0(rmsfit=(0, '@CA,C,N')))
traj1.rmsfit(ref=0, mask='@CA,C,N')
# take '@CA,C,N' xyz
xyz2 = traj2['@CA,C,N'].xyz
xyz1 = traj1['@CA,C,N'].xyz
# OK
assert rmsd_1darray(xyz1.flatten(), xyz2.flatten()) < 1E-10
# combine autoimage with rmsfit
# reset traj1
traj1 = traj0[:]
# get new trajectory from traj0
traj2 = pt.load_from_frame_iter(traj0(autoimage=True,
rmsfit=(0, '@CA,C,N')))
traj1.autoimage()
traj1.rmsfit(ref=0, mask='@CA,C,N')
# take '@CA,C,N' xyz
xyz2 = traj2['@CA,C,N'].xyz
xyz1 = traj1['@CA,C,N'].xyz
# PASSED
assert rmsd_1darray(xyz1.flatten(), xyz2.flatten()) < 1E-10
def test_closest_compared_to_cpptraj(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
state = pt.load_cpptraj_state(
'''
autoimage
closest 100 :1-13
createcrd mycrd''', traj)
state.run()
fi, top = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100,
dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_closest(self):
# raise if not has solvent
traj0 = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
self.assertRaises(RuntimeError, lambda: pt.closest(traj0))
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
fi, top = pt.closest(traj)
coords = []
for frame in fi:
coords.append(frame.xyz.copy())
assert isinstance(frame, pt.Frame), 'must be Frame'
# make a Trajectory
fi, top = pt.closest(traj)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(np.array(coords), t0.xyz)
# test write to disk
fi, top = pt.closest(traj)
pt.write_traj('output/fi.nc', fi, top=top, overwrite=True)
# load back
t1 = pt.load('output/fi.nc', top=top)
aa_eq(t0.xyz, t1.xyz)
# make sure n_sovent=10 (default)
n_solvents = 0
for mol in top.mols:
if mol.is_solvent():
n_solvents += 1
assert n_solvents == 10, 'must be 10 solvents'
fi, top = pt.closest(traj)
pt.write_traj('output/test.pdb', next(fi), top=top, overwrite=True)
def test_1(self):
# merge_frames
import numpy as np
# load 2 frames
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'), frame_slice=(0, 2))
# test mutable traj
frame = pt.tools.merge_frames(traj[:])
r0 = pt.tools.rmsd(frame.xyz, pt.get_coordinates(traj), True)
assert r0 == 0.
#, True) test immutable traj
assert np.any(
pt.tools.merge_frames(traj).xyz.flatten() == pt.get_coordinates(
traj).flatten())
# tuple
assert np.any(
pt.tools.merge_frames(
(frame for frame in traj
)).xyz.flatten() == pt.get_coordinates(traj).flatten())
# list
assert np.any(
pt.tools.merge_frames([
frame for frame in traj
]).xyz.flatten() == pt.get_coordinates(traj).flatten())
# frame_iter: all atoms
assert np.any(
pt.tools.merge_frames(traj()).xyz.flatten() == pt.get_coordinates(
traj()).flatten())
# frame_iter: CA atoms
assert np.any(
pt.tools.merge_frames(traj(mask='@CA')).xyz.flatten() ==
pt.get_coordinates(traj(mask='@CA')).flatten())
def _get_coordinates(traj):
return pt.get_coordinates(traj, autoimage=True, rmsfit=(0, mask), mask=mask)
def _get_coordinates(traj):
return pt.get_coordinates(traj,
autoimage=True,
rmsfit=(0, '@CA'),
mask='@CA')
