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 visualize(self, show_ports=False):
"""Visualize the Compound using nglview. """
if run_from_ipython():
structure = self.to_parmed(show_ports)
return nglview.show_parmed(structure)
else:
raise RuntimeError('Visualization is only supported in Jupyter '
'Notebooks.')
def test_show_parmed():
import parmed as pmd
fn = nv.datafiles.PDB
parm = pmd.load_file(fn)
view = nv.show_parmed(parm)
ngl_traj = nv.ParmEdTrajectory(parm)
ngl_traj.only_save_1st_model = False
ngl_traj.get_structure_string()
def test_show_parmed():
import parmed as pmd
fn = nv.datafiles.PDB
parm = pmd.load_file(fn)
view = nv.show_parmed(parm)
ngl_traj = nv.ParmEdTrajectory(parm)
ngl_traj.only_save_1st_model = False
ngl_traj.get_structure_string()
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)
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)
def to_nglview_NGLWidget(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'parmed.Structure')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from nglview import show_parmed
from . import extract
tmp_item = extract(item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
tmp_item = show_parmed(tmp_item)
return tmp_item
def test_show_parmed():
import parmed as pmd
fn = nv.datafiles.PDB
parm = pmd.load_file(fn)
view = nv.show_parmed(parm)
def test_show_parmed():
import parmed as pmd
fn = nv.datafiles.PDB
parm = pmd.load_file(fn)
view = nv.show_parmed(parm)