def to_mdtraj(system, traj):
traj = [
Atoms(positions=xyz, numbers=system.get_atomic_numbers())
for xyz in traj['positions']
]
# create tmp file
ase.io.write("junk.pdb", traj)
traj = mdtraj.load_pdb("junk.pdb")
import os
os.remove('junk.pdb')
show_mdtraj(traj)
return traj
def _make_nglview(topology=None,positions=None):
mdtraj_aux_topology = mdtraj.Topology.from_openmm(topology)
traj_aux = mdtraj.Trajectory(positions._value, mdtraj_aux_topology)
view = nglview.show_mdtraj(traj_aux)
view.center()
return view
def test_just_runs_recomputes_kdtree(self):
plt.plot(self.pos[:, 0], self.pos[:, 1])
iax = plt.gca()
# Prepare a mouse event in the middle of the plot
x, y = np.array(iax.get_window_extent()).mean(0)
# Prepare event
lineh = iax.axhline(iax.get_ybound()[0])
setattr(lineh, 'whatisthis', 'lineh')
dot = iax.plot(self.pos[0, 0], self.pos[0, 1])[0]
setattr(dot, 'whatisthis', 'dot')
CLAL = molpx._linkutils.ClickOnAxisListener(
nglview.show_mdtraj(self.MD_trajectory), True, [lineh], iax,
self.pos, [dot])
# Resize the figure
CLAL.ax.figure.set_size_inches(1, 1)
# Send an event
CLAL(
MouseEvent(" ",
CLAL.ax.figure.canvas,
x,
y,
button=1,
key=None,
step=0,
dblclick=False,
guiEvent=None))
def visualize_trajectory(wd="./simulation/"):
xtcfile = path.join(wd, "traj_comp.xtc")
wrappedxtcfile = path.join(wd, "wrapped.xtc")
grofile = path.join(wd, "confout.gro")
try:
assert all([path.exists(f) for f in [xtcfile, grofile]])
except:
raise FileNotFoundError(f"traj_comp.xtc, and confout.gro were "
f"not found in {wd}")
grompp_command = (
f"echo 0 | gmx trjconv -f traj_comp.xtc -o wrapped.xtc -pbc whole")
proc = Popen(grompp_command,
stdout=PIPE,
stderr=PIPE,
universal_newlines=True,
shell=True,
cwd=wd)
out, err = proc.communicate()
if "Fatal error" in err:
print(err)
raise RuntimeError("Gromacs TRJCONV command failed")
import nglview as nv
import mdtraj as md
traj = md.load(wrappedxtcfile, top=grofile)
ngl_widget = nv.show_mdtraj(traj)
return ngl_widget
def view(self):
"""Return a nglview view for the actual positions."""
view = nglview.show_mdtraj(self.mdtraj)
if len(self.positions) < 10000:
view.add_ball_and_stick('all')
view.center(zoom=True)
return view
def generate_nglview_object(
traj: md.Trajectory,
tautomer_transformation: dict) -> nglview.NGLWidget:
"""
Generates nglview object from topology and trajectory files.
Parameters
----------
top_file : file path to mdtraj readable topology file
traj_file : file path to mdtraj readable trajectory file
Returns
-------
view: nglview object
"""
view = nglview.show_mdtraj(traj)
if 'donor_hydrogen_idx' in tautomer_transformation:
# Clear all representations to try new ones
print('Hydrogen in GREEN is real at lambda: 0.')
print('Hydrogen in YELLOW is real at lambda: 1.')
view.add_representation(
'point',
selection=[tautomer_transformation['donor_hydrogen_idx']],
color='green',
pointSize=3.5)
view.add_representation(
'point',
selection=[tautomer_transformation['acceptor_hydrogen_idx']],
color='yellow',
pointSize=3.5)
return view
def view(self, re_create: bool = False) -> nj.NGLWidget:
if not hasattr(self, "_view") or not isinstance(
self._view, nj.NGLWidget) or re_create:
self._view = nj.show_mdtraj(self)
self.view.clear_representations()
self.view.add_representation("licorice", selection="all")
return self._view
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_system(traj: mdtraj.Trajectory) -> nj.NGLWidget:
protein_resi = set([
x.index + 1 for x in traj.top.residues
if (x.name in three_letter_aa_lib)
])
protein_resn = set([
x.name[:3] for x in traj.top.residues
if (x.name in three_letter_aa_lib)
])
water_resi = set(
[x.index + 1 for x in traj.top.residues if (x.name in solvents)])
ions_resn = set([x.name for x in traj.top.residues if (x.name in ions)])
if len(protein_resi) > 0 or len(water_resi) > 0 or len(ions_resn) > 0:
representation = [
{
"type": "cartoon",
"params": {
"sele": " ".join(map(str, protein_resi)),
"color": "residueindex"
}
},
]
view = nj.show_mdtraj(traj, representations=representation)
else:
view = nj.show_mdtraj(traj)
if len(protein_resn) > 0:
view.add_representation("cartoon",
selection=" ".join(map(str, protein_resn)),
color="residueindex")
if len(protein_resn) < 16:
view.add_representation("hyperball",
selection=" ".join(map(str, protein_resn)))
if len(water_resi) > 0 and traj.n_frames < 300:
view.add_representation("line",
selection=" ".join(map(str, water_resi)))
if len(ions_resn) > 0:
view.add_representation("hyperball",
selection=" ".join(map(str, ions_resn)),
radius=3,
color="green")
return view
def make_view(topology, positions):
if type(positions) == list:
positions = np.array([tmp_pos._value
for tmp_pos in positions]) * positions[0].unit
topology_mdtraj = md.Topology.from_openmm(topology)
positions_mdtraj = positions._value
aux_traj = md.Trajectory(positions_mdtraj, topology_mdtraj)
return nglview.show_mdtraj(aux_traj)
def _initialize_nglwidget_if_safe(geom, mock=True):
try:
return _nglview.show_mdtraj(geom)
except:
if mock:
print(
"molPX has to be used inside a notebook, not from terminal. A mock nglwidget is being returned."
"Ignore this message if testing, "
"otherwise refer to molPX documentation")
return _mock_nglwidget(geom)
else:
raise Exception(
"molPX has to be used inside a notebook, not from terminal")
def test_feature_color_list(self):
plt.figure()
iwd = nglview.show_mdtraj(self.MD_trajectories[0])
visualize.feature(self.feat.active_features[0],
iwd,
idxs=[0, 1],
color_list=['blue'])
try:
visualize.feature(self.feat.active_features[0],
iwd,
idxs=[0, 1],
color_list='blue')
except TypeError:
pass
def animate(
frames,
gui=False,
delete=True,
):
"""
Creates nglview widget for given list of molecule files (frames).
"""
T = mdtraj.load(frames, top=frames[0])
view = nglview.show_mdtraj(T, gui=gui)
view.add_ball_and_stick()
if delete:
for frame in frames:
os.remove(frame)
return view
def model_viewer(self, model_number = 0):
"""
Quick viewer for visually inspecting docking contacts output.
Takes aggregate_contacts output from contacts_iterator and plots contacts (in red)
onto receptor-ligand docking solution (blue).
"""
pdb = md.load(self.path + self.new_path + "model%s.pdb" % (model_number))
view_single_solution = nv.show_mdtraj(pdb)
view_single_solution.add_cartoon(selection ="protein", color = "blue")
view_single_solution.add_ball_and_stick(selection = self.aggregate_contacts[model_number], color = "red")
print("Single models ready for viewing...")
return view_single_solution
def to_nglview_NGLWidget(item, atom_indices='all', structure_indices='all', check=True):
if check:
digest_item(item, 'mdtraj.Trajectory')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import extract
from nglview import show_mdtraj as show_mdtraj
tmp_item = extract(item, atom_indices=atom_indices, structure_indices=structure_indices,
copy_if_all=False, check=False)
tmp_item = show_mdtraj(tmp_item)
return tmp_item
def visualize(self, show_ports=False):
"""Visualize the Compound using nglview. """
if run_from_ipython():
structure = self.to_trajectory(show_ports)
return nglview.show_mdtraj(structure)
else:
try:
"""Visualize the Compound using imolecule. """
import imolecule
json_mol = self._to_json(show_ports)
return imolecule.draw(json_mol, format='json', shader='lambert',
drawing_type='ball and stick', camera_type='perspective',
element_properties=None)
except ImportError:
raise RuntimeError('Visualization is only supported in Jupyter '
'Notebooks.')
def setUpClass(self):
self.MD_trajectory_files = glob(
molpx._molpxdir(
join='notebooks/data/c-alpha_centered.stride.1000*xtc'))
self.MD_topology_file = molpx._molpxdir(
join='notebooks/data/bpti-c-alpha_centered.pdb')
self.MD_topology = md.load(self.MD_topology_file).top
self.MD_trajectories = [
md.load(ff, top=self.MD_topology_file)
for ff in self.MD_trajectory_files
]
self.n_sample = 20
self.pos = np.zeros((self.n_sample, 2))
self.pos[:, 0] = np.linspace(0, 1, self.n_sample)
self.pos[:, 1] = np.random.randn(self.n_sample)
self.geom = self.MD_trajectories[0][:20]
self.ngl_wdg = nglview.show_mdtraj(self.geom)
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 generate_nglview_object(
traj: md.Trajectory,
radius: int = 0.0,
donor_hydrogen_idx: int = -1,
acceptor_hydrogen_idx: int = -1,
mark_residues=[],
) -> nglview.NGLWidget:
"""
Generates nglview object from a trajectory object. Generated with md.Trajectory(traj, top).
Parameters
----------
traj : md.Trajectory
donor_hydrogen_idx : int
acceptor_hydrogen_idx : int
Returns
-------
view: nglview object
"""
view = nglview.show_mdtraj(traj)
view.add_representation(
repr_type="ball+stick", selection="water", opacity=0.4, color="blue"
)
if radius > 0.0:
view.shape.add_sphere(
[radius / 2, radius / 2, radius / 2], [0, 0, 1], (radius) / 2
)
view.update_representation(component=1, repr_index=0, opacity=0.2)
if donor_hydrogen_idx != -1 and acceptor_hydrogen_idx != -1:
# Clear all representations to try new ones
print("Hydrogen in GREEN is real at lambda: 0.")
print("Hydrogen in YELLOW is real at lambda: 1.")
view.add_representation(
"point", selection=[donor_hydrogen_idx], color="green", pointSize=3.5
)
view.add_representation(
"point", selection=[acceptor_hydrogen_idx], color="yellow", pointSize=3.5
)
return view
def show_mdtraj(fp, stride=None, atom_indices=None, top=None, **kwargs):
"""
Return a trajectory view.
Parameters
----------
fp : filename or list of filenames
stride : int, optional
Read every stride-th frame
atom_indices : array, optional
Read only a subset of the atoms coordinates from the file
top : {str, Trajectory, Topology}
kwargs : dict
Molecular representation of selections, e.g. protein='cartoon'
Returns
-------
View object
"""
load_args = dict(stride=stride, atom_indices=atom_indices)
topography = None
topology = None
if isinstance(top, yank.Topography):
topography = top
topology = top.topology
if isinstance(top, mm.app.Topology):
topology = mdtraj.Topology.from_openmm(top)
if isinstance(top, mdtraj.Topology):
topology = top
if topology:
load_args['top'] = topology
if isinstance(fp, mdtraj.Trajectory):
traj = fp
else:
traj = mdtraj.load(fp, **load_args)
view = nglview.show_mdtraj(traj)
top = topography or topology
setup_view(view, top=top, **kwargs) # TODO: fix
return view
def plot_frame(xp, top):
"""Create an MDTraj Trajectory object and return a nglview view.
Parameters
----------
xp : array-like
top : topology
Return
------
nglview view object
"""
mdtop = mdtraj.Topology.from_openmm(top)
traj = mdtraj.Trajectory(xp / unit.nanometers, mdtop)
view = nglview.show_mdtraj(traj)
if len(xp) < 10000:
view.add_ball_and_stick('all')
view.center(zoom=True)
return view
def __init__(self, traj, figure, *args, **kwargs):
super().__init__(*args, **kwargs)
view = nv.show_mdtraj(traj, **kwargs)
self.traj = traj
self.view = view
self.figure = figure
self.children = [figure, view]
link((self, 'frame'), (self.view, 'frame'))
self.view._remote_call("setSize",
target='Widget',
args=['100%', '100%'])
self.view.layout = w.Layout(max_width="1000px")
self.figure.layout = w.Layout()
self.layout = w.Layout(display='flex',
flex_flow='row wrap',
align_items='flex-start')
def _nglwidget_wrapper(geom, ngl_wdg=None, n_small=10):
r""" Wrapper to nlgivew.show_geom's method that allows for some other automatic choice of
representation
Parameters
----------
geom : :obj:`mdtraj.Trajectory` object or str with a filename to anything that :obj:`mdtraj` can read
ngl_wdg : an already instantiated widget to add the geom, default is None
n_small : if the geometry has less than n_small residues, force a "ball and stick" represenation
:return: :nglview.widget object
"""
if isinstance(geom, str):
geom = _md.load(geom)
if ngl_wdg is None:
if geom is None:
ngl_wdg = _nglview.NGLWidget()
else:
ngl_wdg = _nglview.show_mdtraj(geom)
else:
ngl_wdg.add_trajectory(geom)
# Let' some customization take place
## Do we need a ball+stick representation?
if geom is not None:
if geom.top.n_residues < n_small:
for ic in range(len(ngl_wdg._ngl_component_ids)):
# TODO FIND OUT WHY THIS FAILS FOR THE LAST REPRESENTATION
#print("removing reps for component",ic)
ngl_wdg.remove_cartoon(component=ic)
ngl_wdg.clear_representations(component=ic)
ngl_wdg.add_ball_and_stick(component=ic)
return ngl_wdg
def setUpClass(self):
self.MD_trajectory_files = glob(
molpx._molpxdir(
join='notebooks/data/c-alpha_centered.stride.1000*xtc'))
self.MD_topology_file = molpx._molpxdir(
join='notebooks/data/bpti-c-alpha_centered.pdb')
self.MD_topology = md.load(self.MD_topology_file).top
self.MD_trajectories = [
md.load(ff, top=self.MD_topology_file)
for ff in self.MD_trajectory_files
]
self.MD_trajectory = self.MD_trajectories[0]
self.pos = np.random.rand(self.MD_trajectory.n_frames, 2)
plt.plot(self.pos[:, 0], self.pos[:, 1])
iax = plt.gca()
# Prepare event
self.lineh = iax.axhline(iax.get_ybound()[0])
setattr(self.lineh, 'whatisthis', 'lineh')
self.dot = iax.plot(self.pos[0, 0], self.pos[0, 1])[0]
setattr(self.dot, 'whatisthis', 'dot')
self.ngl_wdg = nglview.show_mdtraj(self.MD_trajectory)
def display(systems, topology=None):
"""
Produce an ngl wiget for a molecular system.
Args:
system (object): An mdtraj.Trajectory or something that can be made into one
Returns:
ngl wiget for the system.
"""
import nglview
import mdtraj as mdt
bigsys = None
if not isinstance(systems, list):
lsys = [systems]
else:
lsys = systems
for system in lsys:
if not isinstance(system, mdt.Trajectory):
if topology is None:
sys = mdt.load(system.as_file())
else:
sys = mdt.load(system.as_file(), top=topology.as_file())
else:
sys = system
if bigsys is None:
bigsys = sys
else:
bigsys = bigsys + sys
print(len(bigsys))
view = nglview.show_mdtraj(bigsys)
view.add_representation('line', selection='water')
view.add_representation('licorice', selection='protein')
return view
def test_show_mdtraj():
import mdtraj as md
from mdtraj.testing import get_fn
fn = nv.datafiles.PDB
traj = md.load(fn)
view = nv.show_mdtraj(traj)
def render_traj(topology, positions):
traj = Trajectory(positions / unit.nanometers,
Topology.from_openmm(topology))
return (show_mdtraj(traj).add_ball_and_stick('all').center_view(zoom=True))
def test_show_mdtraj():
import mdtraj as md
traj = md.load(nv.datafiles.PDB)
view = nv.show_mdtraj(traj)
def heatmap(self, plot_receptor = True, plot_ligand = False):
"""
Constructs a heatmap of contact points onto receptor and ligand structures.
Requires input from atom_contacts_parser. Color cutoffs are currently hard-coded
for this particular data set, but can be easily modified.
"""
pdb = md.load(self.path + self.new_path + "model0.pdb")
rec = []
for i in range(len(self.receptor_chains)):
c = [atom.index for atom in pdb.topology.chain(self.receptor_chains[i]).atoms]
rec.append(c)
rec = np.array(rec)
rec = np.hstack(rec).tolist()
rec_structure = md.load(self.path + self.new_path + "model0.pdb", atom_indices=rec)
lig = []
for i in range(len(self.ligand_chains)):
c = [atom.index for atom in pdb.topology.chain(self.ligand_chains[i]).atoms]
lig.append(c)
lig = np.array(lig)
lig = np.hstack(lig).tolist()
lig_structure = md.load(self.path + self.new_path + "model0.pdb", atom_indices=lig)
if plot_receptor == True:
heatmap_viewer = nv.show_mdtraj(rec_structure)
heatmap_viewer.clear()
heatmap_viewer.add_ball_and_stick(selection ="residue", color = "blue")
low = []
med = []
hi = []
for i in range(len(self.receptor_atoms)):
if self.receptor_atom_counts[i] > 1 and self.receptor_atom_counts[i] < 6:
low.append(self.receptor_atoms[i])
elif self.receptor_atom_counts[i] > 5 and self.receptor_atom_counts[i] < 11:
med.append(self.receptor_atoms[i])
else:
hi.append(self.receptor_atoms[i])
heatmap_viewer.add_ball_and_stick(selection = low, color = "yellow")
heatmap_viewer.add_ball_and_stick(selection = med, color = "orange")
heatmap_viewer.add_ball_and_stick(selection = hi, color = "red")
if plot_ligand == True:
heatmap_viewer = nv.show_mdtraj(lig_structure)
heatmap_viewer.clear()
heatmap_viewer.add_ball_and_stick(selection ="residue", color = "blue")
l = []
m = []
h = []
for i in range(len(self.actual_ligand_atoms)):
if self.ligand_atom_counts[i] > 6 and self.ligand_atom_counts[i] < 26:
l.append(self.actual_ligand_atoms[i])
elif self.ligand_atom_counts[i] > 25 and self.ligand_atom_counts[i] < 51:
m.append(self.actual_ligand_atoms[i])
else:
h.append(self.actual_ligand_atoms[i])
heatmap_viewer.add_ball_and_stick(selection = l, color = "yellow")
heatmap_viewer.add_ball_and_stick(selection = m, color = "orange")
heatmap_viewer.add_ball_and_stick(selection = h, color = "red")
print("Heatmaps constructed...done")
return heatmap_viewer
def display_traj(system, traj):
from nglview import show_mdtraj
return show_mdtraj(to_mdtraj(system, traj))
def test_show_mdtraj():
import mdtraj as md
from mdtraj.testing import get_fn
fn = nv.datafiles.PDB
traj = md.load(fn)
view = nv.show_mdtraj(traj)
def test_feature(self):
plt.figure()
iwd = nglview.show_mdtraj(self.MD_trajectories[0])
visualize.feature(self.feat.active_features[0], iwd)
def test_just_runs(self):
self.just_runs(nglview.show_mdtraj(self.MD_trajectory))
