def test_component_for_duck_typing():
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
view.add_component(get_fn('tz2.pdb'))
view.add_component(get_fn('tz2_2.pdb.gz'))
view.add_trajectory(nv.PyTrajTrajectory(traj))
view.component_0.add_representation('cartoon')
c0 = view[0]
c1 = view[1]
assert hasattr(view, 'component_0')
assert hasattr(view, 'component_1')
assert hasattr(view, 'trajectory_0')
assert hasattr(view.trajectory_0, 'n_frames')
assert hasattr(view.trajectory_0, 'get_coordinates')
assert hasattr(view.trajectory_0, 'get_structure_string')
c0.show()
c0.hide()
view.remove_component(c0.id)
assert not hasattr(view, 'component_2')
# negative indexing
assert view[-1]._index == c1._index
def test_component_for_duck_typing():
# FIXME: deprecate duck typing?
# syntax looks ugly.
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
# add 3 components (trajectory is a component)
view.add_component(get_fn('tz2.pdb'))
view.add_component(get_fn('tz2_2.pdb.gz'))
view.add_trajectory(nv.PyTrajTrajectory(traj))
view.component_0.add_representation('cartoon')
c0 = view[0]
c1 = view[1]
assert hasattr(view, 'component_0')
assert hasattr(view, 'component_1')
assert hasattr(view, 'trajectory_0')
assert hasattr(view.trajectory_0, 'n_frames')
assert hasattr(view.trajectory_0, 'get_coordinates')
assert hasattr(view.trajectory_0, 'get_structure_string')
c0.show()
c0.hide()
# 2 components left
view.remove_component(c0.id)
# c1 become 1st component
assert not hasattr(view, 'component_2')
assert len(view._ngl_component_ids) == 2
# negative indexing
assert view[0]._index == c1._index
def test_component_for_duck_typing():
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
view.add_component(get_fn('tz2.pdb'))
view.add_component(get_fn('tz2_2.pdb.gz'))
view.add_trajectory(nv.PyTrajTrajectory(traj))
view.component_0.add_representation('cartoon')
c0 = view[0]
c1 = view[1]
assert hasattr(view, 'component_0')
assert hasattr(view, 'component_1')
assert hasattr(view, 'trajectory_0')
assert hasattr(view.trajectory_0, 'n_frames')
assert hasattr(view.trajectory_0, 'get_coordinates')
assert hasattr(view.trajectory_0, 'get_structure_string')
c0.show()
c0.hide()
view.remove_component(c0.id)
assert not hasattr(view, 'component_2')
# negative indexing
assert view[-1]._index == c1._index
def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples, gui=False):
from htmd.builder.builder import sequenceID
if states is None:
states = range(self.macronum)
if isinstance(states, int):
states = [states]
if mols is None:
mols = self.getStates(states, statetype, numsamples=min(numsamples, 15))
colors = [0, 1, 3, 4, 5, 6, 7, 9]
hexcolors = {0: '#0000ff', 1: '#ff0000', 2: '#333333', 3: '#ff6600', 4: '#ffff00', 5: '#4c4d00', 6: '#b2b2cc',
7: '#33cc33', 8: '#ffffff', 9: '#ff3399', 10: '#33ccff'}
if protein is None and ligand is None:
raise NameError('Please provide either the "protein" or "ligand" parameter for viewStates.')
k = 0
from nglview import NGLWidget, HTMDTrajectory
view = NGLWidget(gui=gui)
ref = mols[0].copy()
for i, s in enumerate(states):
if protein:
mol = Molecule()
if ligand:
mol = ref.copy()
mol.remove(ligand, _logger=False)
mol.coords = np.atleast_3d(mol.coords[:, :, 0])
mols[i].filter(ligand, _logger=False)
mols[i].set('chain', '{}'.format(s))
tmpcoo = mols[i].coords
for j in range(mols[i].numFrames):
mols[i].coords = np.atleast_3d(tmpcoo[:, :, j])
if ligand:
mols[i].set('segid', sequenceID(mols[i].resid)+k)
k = int(mols[i].segid[-1])
mol.append(mols[i])
view.add_trajectory(HTMDTrajectory(mol))
# Setting up representations
if ligand:
view[i].add_cartoon('protein', color='sstruc')
view[i].add_hyperball(':{}'.format(s), color=hexcolors[np.mod(i, len(hexcolors))])
if protein:
view[i].add_cartoon('protein', color='residueindex')
self._nglButtons(view, statetype, states)
return view
def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples, gui=False):
from htmd.molecule.util import sequenceID
if states is None:
states = range(self.macronum)
if isinstance(states, int):
states = [states]
if mols is None:
mols = self.getStates(states, statetype, numsamples=min(numsamples, 15))
colors = [0, 1, 3, 4, 5, 6, 7, 9]
hexcolors = {0: '#0000ff', 1: '#ff0000', 2: '#333333', 3: '#ff6600', 4: '#ffff00', 5: '#4c4d00', 6: '#b2b2cc',
7: '#33cc33', 8: '#ffffff', 9: '#ff3399', 10: '#33ccff'}
if protein is None and ligand is None:
raise NameError('Please provide either the "protein" or "ligand" parameter for viewStates.')
k = 0
from nglview import NGLWidget, HTMDTrajectory
view = NGLWidget(gui=gui)
ref = mols[0].copy()
for i, s in enumerate(states):
if protein:
mol = Molecule()
if ligand:
mol = ref.copy()
mol.remove(ligand, _logger=False)
mol.dropFrames(keep=0)
mols[i].filter(ligand, _logger=False)
mols[i].set('chain', '{}'.format(s))
tmpcoo = mols[i].coords
for j in range(mols[i].numFrames):
mols[i].coords = np.atleast_3d(tmpcoo[:, :, j])
if ligand:
mols[i].set('segid', sequenceID(mols[i].resid)+k)
k = int(mols[i].segid[-1])
mol.append(mols[i])
view.add_trajectory(HTMDTrajectory(mol))
# Setting up representations
if ligand:
view[i].add_cartoon('protein', color='sstruc')
view[i].add_hyperball(':{}'.format(s), color=hexcolors[np.mod(i, len(hexcolors))])
if protein:
view[i].add_cartoon('protein', color='residueindex')
self._nglButtons(view, statetype, states)
return view
def test_component_for_duck_typing():
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
view.add_component('data/tz2.pdb')
view.add_component('data/tz2_2.pdb.gz')
view.add_trajectory(nv.PyTrajTrajectory(traj))
c0 = view[0]
c1 = view[1]
nt.assert_true(hasattr(view, 'component_0'))
nt.assert_true(hasattr(view, 'component_1'))
nt.assert_true(hasattr(view, 'trajectory_0'))
nt.assert_true(hasattr(view.trajectory_0, 'n_frames'))
nt.assert_true(hasattr(view.trajectory_0, 'get_coordinates'))
nt.assert_true(hasattr(view.trajectory_0, 'get_structure_string'))
c0.show()
c0.hide()
view.remove_component(c0.id)
nt.assert_false(hasattr(view, 'component_2'))
def test_component_for_duck_typing():
view = NGLWidget()
view.add_component('data/tz2.pdb')
view.add_component('data/tz2_2.pdb.gz')
c0 = view[0]
c1 = view[1]
nt.assert_true(hasattr(view, 'component_0'))
nt.assert_true(hasattr(view, 'component_1'))
c0.show()
c0.hide()
view.remove_component(c0.id)
nt.assert_false(hasattr(view, 'component_1'))
def add_to_NGLView(self, view: nv.NGLWidget, palette: str = 'openpharmacophore') -> None:
"""Add the pharmacophore representation to a view (NGLWidget) from NGLView.
Each pharmacophoric element is added to the NGLWidget as a new component.
Parameters
----------
view : nglview.NGLWidget
View as NGLView widget where the pharmacophore will be added.
palette : str or dict
Color palette name or dictionary. (Default: 'openpharmacophore')
"""
first_element_index = len(view._ngl_component_ids)
for ii, element in enumerate(self._pharmacophoric_points):
# Add Spheres
center = puw.get_value(element.center, to_unit="angstroms").tolist()
radius = puw.get_value(element.radius, to_unit="angstroms")
feature_color = get_color_from_palette_for_feature(element.feature_name, color_palette=palette)
label = f"{element.feature_name}_{ii}"
view.shape.add_sphere(center, feature_color, radius, label)
# Add vectors
if element.has_direction:
label = f"{element.feature_name}_vector"
if element.feature_name == "hb acceptor":
end_arrow = puw.get_value(element.center - 2 * radius * puw.quantity(element.direction, "angstroms"), to_unit='angstroms').tolist()
view.shape.add_arrow(end_arrow, center, feature_color, 0.2, label)
else:
end_arrow = puw.get_value(element.center + 2 * radius * puw.quantity(element.direction, "angstroms"), to_unit='angstroms').tolist()
view.shape.add_arrow(center, end_arrow, feature_color, 0.2, label)
# Add opacity to spheres
last_element_index = len(view._ngl_component_ids)
for jj in range(first_element_index, last_element_index):
view.update_representation(component=jj, opacity=0.8)
def test_component_for_duck_typing():
view = NGLWidget()
view.add_component('data/tz2.pdb')
view.add_component('data/tz2_2.pdb.gz')
c0 = view[0]
c1 = view[1]
nt.assert_true(hasattr(view, 'component_0'))
nt.assert_true(hasattr(view, 'component_1'))
c0.show()
c0.hide()
view.remove_component(c0.id)
nt.assert_false(hasattr(view, 'component_1'))
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_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
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_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
