def visualize(self, show_ports=False, backend='py3dmol',
color_scheme={}, show_atomistic=False, scale=1.0): # pragma: no cover
"""
Visualize the Compound using py3dmol (default) or nglview.
Allows for visualization of a Compound within a Jupyter Notebook.
Parameters
----------
show_ports : bool, optional, default=False
Visualize Ports in addition to Particles
backend : str, optional, default='py3dmol'
Specify the backend package to visualize compounds
Currently supported: py3dmol, nglview
color_scheme : dict, optional
Specify coloring for non-elemental particles
keys are strings of the particle names
values are strings of the colors
i.e. {'_CGBEAD': 'blue'}
NOTE!: Only py3dmol will work with CG_Compounds
"""
viz_pkg = {'nglview': self._visualize_nglview,
'py3dmol': self._visualize_py3dmol}
if run_from_ipython():
if backend.lower() in viz_pkg:
return viz_pkg[backend.lower()](show_ports=show_ports,
color_scheme=color_scheme, show_atomistic=show_atomistic, scale=scale)
else:
raise RuntimeError("Unsupported visualization " +
"backend ({}). ".format(backend) +
"Currently supported backends include nglview and py3dmol")
else:
raise RuntimeError('Visualization is only supported in Jupyter '
'Notebooks.')
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 visualize(self, show_ports=False):
"""Visualize the Compound using nglview. """
nglview = import_('nglview')
if run_from_ipython():
structure = self.to_trajectory(show_ports)
return nglview.show_mdtraj(structure)
else:
raise RuntimeError('Visualization is only supported in Jupyter '
'Notebooks.')
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 visualize(self, show_ports=False):
"""Visualize the Compound using nglview. """
nglview = import_('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)
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 test_has_ipython(self):
__IPYTHON__ = None
assert run_from_ipython() is False
def visualize(self,
show_ports=False,
color_scheme={},
show_atomistic=False,
scale=1.0): # pragma: no cover
"""Visualize the Compound using py3dmol.
Allows for visualization of a Compound within a Jupyter Notebook.
Modified to from :py:meth:`mbuild.Compound.visualize` to show atomistic
elements (translucent) with larger CG beads.
Parameters
----------
show_ports : bool, default False
Visualize Ports in addition to Particles
color_scheme : dict, default {}
Specify coloring for non-elemental particles keys are strings of
the particle names values are strings of the colors::
{'_CGBEAD': 'blue'}
show_atomistic : bool, default False
Show the atomistic structure stored in
:py:attr:`CG_Compound.atomistic`
scale : float, default 1.0
Scaling factor to modify the size of objects in the view.
Returns
-------
view : py3Dmol.view
"""
if not run_from_ipython():
raise RuntimeError(
"Visualization is only supported in Jupyter Notebooks.")
import py3Dmol
atom_names = []
if self.atomistic is not None and show_atomistic:
atomistic = clone(self.atomistic)
for particle in atomistic:
if not particle.name:
particle.name = "UNK"
else:
if particle.name not in ("Compound", "CG_Compound"):
atom_names.append(particle.name)
coarse = clone(self)
modified_color_scheme = {}
for name, color in color_scheme.items():
# Py3dmol does some element string conversions,
# first character is as-is, rest of the characters are lowercase
new_name = name[0] + name[1:].lower()
modified_color_scheme[new_name] = color
modified_color_scheme[name] = color
cg_names = []
for particle in coarse:
if not particle.name:
particle.name = "UNK"
else:
if particle.name not in ("Compound", "CG_Compound"):
cg_names.append(particle.name)
tmp_dir = tempfile.mkdtemp()
view = py3Dmol.view()
if atom_names:
atomistic.save(
os.path.join(tmp_dir, "atomistic_tmp.mol2"),
show_ports=show_ports,
overwrite=True,
)
# atomistic
with open(os.path.join(tmp_dir, "atomistic_tmp.mol2"), "r") as f:
view.addModel(f.read(), "mol2", keepH=True)
if cg_names:
opacity = 0.6
else:
opacity = 1.0
view.setStyle({
"stick": {
"radius": 0.2 * scale,
"opacity": opacity,
"color": "grey",
},
"sphere": {
"scale": 0.3 * scale,
"opacity": opacity,
"colorscheme": modified_color_scheme,
},
})
# coarse
if cg_names:
# silence warning about No element found for CG bead
with catch_warnings():
simplefilter("ignore")
coarse.save(
os.path.join(tmp_dir, "coarse_tmp.mol2"),
show_ports=show_ports,
overwrite=True,
)
with open(os.path.join(tmp_dir, "coarse_tmp.mol2"), "r") as f:
view.addModel(f.read(), "mol2", keepH=True)
if self.atomistic is None:
scale = 0.3 * scale
else:
scale = 0.7 * scale
view.setStyle(
{"atom": cg_names},
{
"stick": {
"radius": 0.2 * scale,
"opacity": 1,
"color": "grey",
},
"sphere": {
"scale": scale,
"opacity": 1,
"colorscheme": modified_color_scheme,
},
},
)
view.zoomTo()
return view