def assert_build(ss_type, seq=seq):
cm = '{}:1-10'.format(ss_type)
traj = builder.build_protein(seq, [cm])
# traj.save('test.pdb', overwrite=True)
pdb_fn = get_fn('builder/ala10_{}.pdb'.format(ss_type))
saved_traj = pt.load(pdb_fn)
aa_eq(traj.xyz, saved_traj.xyz, decimal=3)
def test_add_struture_then_trajectory():
view = nv.show_structure_file('data/tz2.pdb')
traj = pt.datafiles.load_trpcage()
view.add_trajectory(traj)
view.frame = 3
coords = view.coordinates_dict[1].copy()
aa_eq(coords, traj[3].xyz)
def test_sander_struct():
fn = get_fn('4lzt_pawel/4lztabH.pdb')
tn = get_fn('4lzt_pawel/4lztab.parm7')
rst7 = get_fn('4lzt_pawel/4lztabH.rst7')
s_struct = SanderStruct(tn, rst7)
parm = pmd.load_file(tn, rst7)
aa_eq(parm.coordinates, s_struct.parm.coordinates)
def test_normal_pdb():
fn = get_fn('4lzt/4lzt.not_les.pdb')
tn = get_fn('4lzt/4lzt.parm7')
rst7 = get_fn('4lzt/4lzt.rst7')
pdb_input = pdb.input(fn)
symm = pdb_input.crystal_symmetry()
pdb_hc = pdb_input.construct_hierarchy()
phenix_coords_uc = expand_coord_to_unit_cell(pdb_hc.atoms().extract_xyz(),
symm)
indices_dict = get_indices_convert_dict(fn)
p2a_indices = indices_dict['p2a']
a2p_indices = indices_dict['a2p']
parm = pmd.load_file(tn, rst7)
a0 = reorder_coords_phenix_to_amber(phenix_coords_uc, p2a_indices)
# make sure phenix and amber read the same coordinates
aa_eq(pdb_input.atoms().extract_xyz(), parm.coordinates, decimal=2)
aa_eq(a0, parm.coordinates, decimal=2)
# make sure the a2p_indices and p2a_indices are identical for non-LES
indices_dict = get_indices_convert_dict_from_array(
pdb_input.atoms().extract_xyz(), parm.coordinates)
p2a_indices = indices_dict['p2a']
a2p_indices = indices_dict['a2p']
eq(a2p_indices, p2a_indices)
def test_nab_arna():
with tempfolder():
filename = 'nuc.pdb'
traj = builder.build_arna('AAAAAAAAAA')
nu = pt.nastruct(traj)
aa_eq(np.mean(nu.major[1]), [15.183,], decimal=3)
aa_eq(np.mean(nu.minor[1]), [18.804,], decimal=3)
def test_netcdf_trajectory():
command_refine = [
'phenix.refine',
get_fn('vAla3/vAla3.pdb'),
get_fn('vAla3/vAla3.cif'),
get_fn('vAla3/vAla3.mtz'),
'topology_file_name={}'.format(get_fn('vAla3/vAla3.prmtop')),
'coordinate_file_name={}'.format(get_fn('vAla3/vAla3.rst7')),
'use_amber=True', 'wxc_scale=0.025', '--overwrite',
'refinement.main.number_of_macro_cycles=1',
'amber.netcdf_trajectory_file_name=hello.nc'
]
n_frames = 59
parm = pmd.load_file(get_fn('vAla3/vAla3.prmtop'))
expected_boxes = np.array(n_frames * [
[30., 30., 30., 90., 90., 90.],
],
dtype='f8')
with tempfolder():
output = subprocess.check_output(command_refine)
traj = NetCDFTraj.open_old('hello.nc')
print(traj.coordinates.shape)
aa_eq(traj.box, expected_boxes)
assert traj.coordinates.shape == (n_frames, len(parm.atoms), 3)
def test_hausdorff(tmpdir):
# with tmpdir.as_cwd():
matrix = np.array([[1.0000, 2.2361, 3.0000, 4.1231],
[2.2361, 1.0000, 2.2361, 5.0000],
[3.0000, 2.2361, 1.0000, 4.1231],
[2.2361, 3.0000, 2.2361, 3.0000]])
aa_eq(pt.hausdorff(matrix), [[3.], [3.], [2.23609996]])
def test_coordinates_meta():
from mdtraj.testing import get_fn
fn, tn = [get_fn('frame0.pdb'),] * 2
trajs = [pt.load(fn, tn), md.load(fn, top=tn), pmd.load_file(tn, fn)]
N_FRAMES = trajs[0].n_frames
from MDAnalysis import Universe
u = Universe(tn, fn)
trajs.append(Universe(tn, fn))
views = [nv.show_pytraj(trajs[0]), nv.show_mdtraj(trajs[1]), nv.show_parmed(trajs[2])]
views.append(nv.show_mdanalysis(trajs[3]))
for index, (view, traj) in enumerate(zip(views, trajs)):
view.frame = 3
nt.assert_equal(view.trajlist[0].n_frames, N_FRAMES)
nt.assert_equal(len(view.trajlist[0].get_coordinates_dict().keys()), N_FRAMES)
if index in [0, 1]:
# pytraj, mdtraj
if index == 0:
aa_eq(view.coordinates[0], traj.xyz[3], decimal=4)
else:
aa_eq(view.coordinates[0],10*traj.xyz[3], decimal=4)
view.coordinates = traj.xyz[2]
def test_non_LES_refinement_vAla3(use_amber):
command_refine = [
'phenix.refine',
get_fn('vAla3/vAla3.pdb'),
get_fn('vAla3/vAla3.cif'),
get_fn('vAla3/vAla3.mtz'),
'topology_file_name={}'.format(get_fn('vAla3/vAla3.prmtop')),
'coordinate_file_name={}'.format(get_fn('vAla3/vAla3.rst7')),
'use_amber={}'.format(use_amber), 'wxc_scale=0.025', '--overwrite',
'refinement.main.number_of_macro_cycles=1'
]
expected_r = {
# 'Start R-work': 0.0154, 'Start R-free': 0.0154,
'Final R-work': 0.0066,
'Final R-free': 0.0065
}
with tempfolder():
output = subprocess.check_output(command_refine)
for line in output.split('\n'):
if 'Final R-work' in line:
break
final_r_work = float(line.split()[3].strip(','))
final_r_free = float(line.split()[6])
aa_eq([
final_r_work,
], [
expected_r['Final R-work'],
], decimal=3)
aa_eq([
final_r_free,
], [
expected_r['Final R-free'],
], decimal=3)
def test_encode_and_decode():
xyz = np.arange(100).astype('f4')
shape = xyz.shape
b64_str = nv.encode_base64(xyz)
new_xyz = nv.decode_base64(b64_str, dtype='f4', shape=shape)
aa_eq(xyz, new_xyz)
def test_encode_and_decode():
xyz = np.arange(100).astype('f4')
shape = xyz.shape
b64_str = nv.encode_numpy(xyz)
new_xyz = nv.decode_base64(b64_str, dtype='f4', shape=shape)
aa_eq(xyz, new_xyz)
def test_add_struture_then_trajectory():
view = nv.show_structure_file(get_fn('tz2.pdb'))
view.loaded = True
traj = pt.datafiles.load_trpcage()
view.add_trajectory(traj)
view.frame = 3
coords = view.coordinates_dict[1].copy()
aa_eq(coords, traj[3].xyz)
view.loaded = False
view.add_trajectory(traj)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
# dummy
view._send_binary = False
view.coordinates_dict = {0: coords}
def test_add_struture_then_trajectory():
view = nv.show_structure_file(get_fn('tz2.pdb'))
view.loaded = True
traj = pt.datafiles.load_trpcage()
view.add_trajectory(traj)
view.frame = 3
coords = view._coordinates_dict[1].copy()
aa_eq(coords, traj[3].xyz)
view.loaded = False
view.add_trajectory(traj)
def test_show_htmd():
from htmd import Molecule
fn = nv.datafiles.PDB
traj = Molecule(fn)
view = nv.show_htmd(traj)
# trigger updating cooridnates
view.frame = 100
index = 0
view.frame = index
xyz_htmd = np.squeeze(traj.coords[:, :, index])
aa_eq(view._coordinates_dict[0], xyz_htmd)
def test_show_htmd():
from htmd import Molecule
fn = nv.datafiles.PDB
traj = Molecule(fn)
view = nv.show_htmd(traj)
# trigger updating cooridnates
view.frame = 100
index = 0
view.frame = index
xyz_htmd = np.squeeze(traj.coords[:, :, index])
aa_eq(view.coordinates_dict[0], xyz_htmd)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
# dummy
view._send_binary = False
view.coordinates_dict = {0: coords}
# increase coverage for IndexError: make index=1000 (which is larger than n_frames)
view._set_coordinates(1000)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
# dummy
view._send_binary = False
view.coordinates_dict = {0: coords}
# increase coverage for IndexError: make index=1000 (which is larger than n_frames)
view._set_coordinates(1000)
def test_converter_by_array():
fn = get_fn('4lzt_pawel/4lztabH.pdb')
tn = get_fn('4lzt_pawel/4lztab.parm7')
rst7 = get_fn('4lzt_pawel/4lztabH.rst7')
pdb_input = pdb.input(fn)
parm = pmd.load_file(tn, rst7)
symm = pdb_input.crystal_symmetry()
# reorder
pdb_hc = pdb_input.construct_hierarchy()
phenix_coords_uc = expand_coord_to_unit_cell(pdb_hc.atoms().extract_xyz(),
symm)
indices_dict = get_indices_convert_dict_from_array(phenix_coords_uc,
parm.coordinates)
p2a_indices = indices_dict['p2a']
a2p_indices = indices_dict['a2p']
a0 = reorder_coords_phenix_to_amber(phenix_coords_uc, p2a_indices)
# make sure the original pdb and rst7 have the same coordinates
aa_eq(pdb_input.atoms().extract_xyz(), parm.coordinates, decimal=2)
# make sure reordered coordinates is equal to original coordinates
aa_eq(a0, parm.coordinates, decimal=2)
# raise KeyError if provide wrong coordinates
def make_sure_key_error_being_raised():
phenix_coords = flex.vec3_double([
[0., 2., 3.2], # should be [0., 2., 3.]
[4., 5., 6.],
[10., 12., 13.],
[7., 8., 9.]
])
amber_coords = np.array([[10., 12., 13.], [7., 8., 9], [4., 5., 6.],
[0., 2., 3.]])
get_indices_convert_dict_from_array(phenix_coords, amber_coords)
with pytest.raises(KeyError):
make_sure_key_error_being_raised()
def test_eneregy_and_force():
path = os.path.dirname(__file__)
prmtop = path + '/vAla3.prmtop'
rst7 = path + '/vAla3.rst7'
with mdgx.setup(prmtop, rst7) as context:
mdgx_energies, mdgx_forces = context.energy_forces()
pme_input = sander.pme_input()
parm = pmd.load_file(prmtop, rst7)
with sander.setup(prmtop, rst7, box=parm.box, mm_options=pme_input):
ene, sander_forces = sander.energy_forces()
sander_enegies = dict((att, getattr(ene, att)) for att in dir(ene) if not
att.startswith('_'))
print("")
print("potential energy")
print("sander_enegies")
print(sander_enegies['tot'])
print("mdgx_energies")
print(mdgx_energies['eptot'])
print("")
print('forces')
print('sander_forces, first 5 atoms')
print(sander_forces[:15])
print("")
print('mdgx_forces, first 5 atoms')
print(mdgx_forces.tolist()[:15])
aa_eq([sander_enegies['tot'],],
[mdgx_energies['eptot'],],
decimal=4)
def test_build_nuleic_acid():
builder = AmberBuilder()
builder.build_bdna('GGGGGG')
aa_eq(_compute_major_groove(builder), [17.24558067])
aa_eq(_compute_major_groove(builder.build_adna('GGGGGG')), [15.72079277])
# build_xxx will repalce old structure
aa_eq(_compute_major_groove(builder.build_arna('GGGGGG')), [15.18226528])
with tempfolder():
pdb_out = 'out.pdb'
builder.write_pdb(pdb_out)
with open(pdb_out) as fh:
assert "O2'" in fh.read()
def test_converter():
fn = get_fn('4lzt_pawel/4lztabH.pdb')
tn = get_fn('4lzt_pawel/4lztab.parm7')
rst7 = get_fn('4lzt_pawel/4lztabH.rst7')
pdb_input = pdb.input(fn)
parm = pmd.load_file(tn, rst7)
symm = pdb_input.crystal_symmetry()
pdb_hc = pdb_input.construct_hierarchy()
phenix_coords_uc = expand_coord_to_unit_cell(pdb_hc.atoms().extract_xyz(),
symm)
indices_dict = get_indices_convert_dict(fn)
p2a_indices = indices_dict['p2a']
a2p_indices = indices_dict['a2p']
# make sure two indices are not equal
with pytest.raises(AssertionError):
aa_eq(p2a_indices, a2p_indices)
a0 = reorder_coords_phenix_to_amber(phenix_coords_uc, p2a_indices)
aa_eq(pdb_input.atoms().extract_xyz(), parm.coordinates)
aa_eq(a0, parm.coordinates)
def test_trajectory_show_hide_sending_cooridnates():
view = NGLWidget()
traj0 = pt.datafiles.load_tz2()
traj1 = pt.datafiles.load_trpcage()
view.add_trajectory(nv.PyTrajTrajectory(traj0))
view.add_trajectory(nv.PyTrajTrajectory(traj1))
for traj in view._trajlist:
nt.assert_true(traj.shown)
view.frame = 1
def copy_coordinate_dict(view):
# make copy to avoid memory free
return dict((k, v.copy()) for k, v in view.coordinates_dict.items())
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide 0
view.hide([
0,
])
nt.assert_false(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
# update frame so view can update its coordinates
view.frame = 2
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
aa_eq(coordinates_dict[1], traj1[2].xyz)
# hide 0, 1
view.hide([0, 1])
nt.assert_false(view._trajlist[0].shown)
nt.assert_false(view._trajlist[1].shown)
view.frame = 3
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
nt.assert_equal(coordinates_dict[1].shape[0], 0)
# slicing, show only component 1
view[1].show()
view.frame = 0
nt.assert_false(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
aa_eq(coordinates_dict[1], traj1[0].xyz)
# show all
view[1].show()
view[0].show()
view.frame = 1
nt.assert_true(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide all
view[1].hide()
view[0].hide()
view.frame = 2
nt.assert_false(view._trajlist[0].shown)
nt.assert_false(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
nt.assert_equal(coordinates_dict[1].shape[0], 0)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
def test_something(self):
a = [1., 2., 4.]
b = [1.000000000001, 2., 4.]
aa_eq(a, b)
def test_nab_bdna():
with tempfolder():
traj = builder.build_bdna('AAAAAAAAAA')
nu = pt.nastruct(traj)
aa_eq(np.mean(nu.major[1]), [17.246,], decimal=3)
aa_eq(np.mean(nu.minor[1]), [11.459,], decimal=3)
def test_trajectory_show_hide_sending_cooridnates():
view = NGLWidget()
traj0 = pt.datafiles.load_tz2()
traj1 = pt.datafiles.load_trpcage()
view.add_trajectory(nv.PyTrajTrajectory(traj0))
view.add_trajectory(nv.PyTrajTrajectory(traj1))
for traj in view._trajlist:
assert traj.shown
view.frame = 1
def copy_coordinate_dict(view):
# make copy to avoid memory free
return {k: v.copy() for k, v in view._coordinates_dict.items()}
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide 0
view.hide([
0,
])
assert not view._trajlist[0].shown
assert view._trajlist[1].shown
# update frame so view can update its coordinates
view.frame = 2
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
aa_eq(coordinates_dict[1], traj1[2].xyz)
# hide 0, 1
view.hide([0, 1])
assert not view._trajlist[0].shown
assert not view._trajlist[1].shown
view.frame = 3
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
assert coordinates_dict[1].shape[0] == 0
# slicing, show only component 1
view[1].show()
view.frame = 0
assert not view._trajlist[0].shown
assert view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
aa_eq(coordinates_dict[1], traj1[0].xyz)
# show all
view[1].show()
view[0].show()
view.show(indices='all')
view.show(indices=[
0,
])
view.show(indices=[0, 1])
view.frame = 1
assert view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide all
view[1].hide()
view[0].hide()
view.frame = 2
assert not view._trajlist[0].shown
assert not view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
assert coordinates_dict[1].shape[0] == 0
(atom.id_str(), idx) for (idx, atom) in enumerate(pdb_inp.atoms()))
return {
'p2a': np.array([newids[atom.id_str()] for atom in pdb_inp.atoms()]),
'a2p':
np.array([oldids[atom.id_str()] for atom in pdb_hierarchy.atoms()])
}
if __name__ == '__main__':
import parmed as pmd
from numpy.testing import assert_almost_equal as aa_eq
root = './test_4lzt_les/'
fn, tn, rst7 = [
root + filename
for filename in ["4lztabH.pdb", "4lztab.parm7", "4lztabH.rst7"]
]
pdb_input = pdb.input(fn)
hi = pdb_input.construct_hierarchy()
parm = pmd.load_file(tn, rst7)
p2a_indices = get_indices_convert_dict(fn)['p2a']
a2p_indices = get_indices_convert_dict(fn)['a2p']
a0 = reorder_coords_phenix_to_amber(hi.atoms().extract_xyz(), p2a_indices)
print(a0.shape)
aa_eq(a0, parm.coordinates.flatten())
print("OK")
def test_trajectory_show_hide_sending_cooridnates():
view = NGLWidget()
traj0 = pt.datafiles.load_tz2()
traj1 = pt.datafiles.load_trpcage()
view.add_trajectory(nv.PyTrajTrajectory(traj0))
view.add_trajectory(nv.PyTrajTrajectory(traj1))
for traj in view._trajlist:
assert traj.shown
view.frame = 1
def copy_coordinate_dict(view):
# make copy to avoid memory free
return dict((k, v.copy()) for k, v in view.coordinates_dict.items())
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide 0
view.hide([0,])
assert not view._trajlist[0].shown
assert view._trajlist[1].shown
# update frame so view can update its coordinates
view.frame = 2
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
aa_eq(coordinates_dict[1], traj1[2].xyz)
# hide 0, 1
view.hide([0, 1])
assert not view._trajlist[0].shown
assert not view._trajlist[1].shown
view.frame = 3
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
assert coordinates_dict[1].shape[0] == 0
# slicing, show only component 1
view[1].show()
view.frame = 0
assert not view._trajlist[0].shown
assert view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
aa_eq(coordinates_dict[1], traj1[0].xyz)
# show all
view[1].show()
view[0].show()
view.show(indices='all')
view.show(indices=[0,])
view.show(indices=[0, 1])
view.frame = 1
assert view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide all
view[1].hide()
view[0].hide()
view.frame = 2
assert not view._trajlist[0].shown
assert not view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
assert coordinates_dict[1].shape[0] == 0
def test_trajectory_show_hide_sending_cooridnates():
view = NGLWidget()
traj0 = pt.datafiles.load_tz2()
traj1 = pt.datafiles.load_trpcage()
view.add_trajectory(nv.PyTrajTrajectory(traj0))
view.add_trajectory(nv.PyTrajTrajectory(traj1))
for traj in view._trajlist:
nt.assert_true(traj.shown)
view.frame = 1
def copy_coordinate_dict(view):
# make copy to avoid memory free
return dict((k, v.copy()) for k, v in view.coordinates_dict.items())
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide 0
view.hide([0,])
nt.assert_false(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
# update frame so view can update its coordinates
view.frame = 2
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
aa_eq(coordinates_dict[1], traj1[2].xyz)
# hide 0, 1
view.hide([0, 1])
nt.assert_false(view._trajlist[0].shown)
nt.assert_false(view._trajlist[1].shown)
view.frame = 3
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
nt.assert_equal(coordinates_dict[1].shape[0], 0)
# slicing, show only component 1
view[1].show()
view.frame = 0
nt.assert_false(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
aa_eq(coordinates_dict[1], traj1[0].xyz)
# show all
view[1].show()
view[0].show()
view.frame = 1
nt.assert_true(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide all
view[1].hide()
view[0].hide()
view.frame = 2
nt.assert_false(view._trajlist[0].shown)
nt.assert_false(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
nt.assert_equal(coordinates_dict[1].shape[0], 0)
