def set_atom_style(self, atoms=None, fill_color=None, outline_color=None):
if atoms is None:
indices = range(len(self.atoms))
else:
indices = map(self.get_atom_index, atoms)
spec = {}
if fill_color is not None: spec['fill'] = translate_color(fill_color, prefix='#')
if outline_color is not None: spec['stroke'] = translate_color(outline_color, prefix='#')
self.viewer('setAtomStyle', [indices, spec])
def draw_orbital(self,
orbname,
npts=50,
isoval=0.01,
opacity=0.8,
negative_color='red',
positive_color='blue',
remove_old_orbitals=True,
render=True):
"""Display a molecular orbital
Args:
orbname: name of the orbital (interface dependent)
npts (int): resolution in each dimension
isoval (float): isosurface value to draw
opacity (float): opacity of the orbital (between 0 and 1)
positive_color (str or int): color of the positive isosurfaces
negative_color (str or int): color of the negative isosurfaces
remove_old_orbitals (bool): remove any previously drawn orbitals
render (bool): update the 3D scene before returning
"""
self.orbital_spec = dict(npts=npts,
isoval=isoval,
opacity=opacity,
negative_color=negative_color,
positive_color=positive_color)
self.current_orbital = orbname
if remove_old_orbitals:
self.remove_orbitals(render=False)
positive_color = translate_color(positive_color)
negative_color = translate_color(negative_color)
orbidx = self.get_orbidx(orbname)
voldata = self.get_voldata(orbidx, npts, self.current_frame)
positive_orbital = JSObject('shape')
self.viewer('drawIsosurface', [
voldata.id, positive_orbital.id, {
'isoval': isoval,
'color': positive_color,
'opacity': opacity
}
])
negative_orbital = JSObject('shape')
self.viewer('drawIsosurface', [
voldata.id, negative_orbital.id, {
'isoval': -isoval,
'color': negative_color,
'opacity': opacity
}
])
self.current_js_orbitals.extend([positive_orbital, negative_orbital])
if render: self.render()
def draw_orbital(self, orbname, npts=50, isoval=0.01,
opacity=0.8,
negative_color='red',
positive_color='blue',
remove_old_orbitals=True,
render=True):
"""Display a molecular orbital
Args:
orbname: name of the orbital (interface dependent)
npts (int): resolution in each dimension
isoval (float): isosurface value to draw
opacity (float): opacity of the orbital (between 0 and 1)
positive_color (str or int): color of the positive isosurfaces
negative_color (str or int): color of the negative isosurfaces
remove_old_orbitals (bool): remove any previously drawn orbitals
render (bool): update the 3D scene before returning
"""
self.orbital_spec = dict(npts=npts, isoval=isoval,
opacity=opacity,
negative_color=negative_color,
positive_color=positive_color)
self.current_orbital = orbname
if remove_old_orbitals:
self.remove_orbitals(render=False)
positive_color = translate_color(positive_color)
negative_color = translate_color(negative_color)
orbidx = self.get_orbidx(orbname)
voldata = self.get_voldata(orbidx, npts, self.current_frame)
positive_orbital = JSObject('shape')
self.viewer('drawIsosurface',
[voldata.id,
positive_orbital.id,
{'isoval': isoval,
'color': positive_color,
'opacity': opacity}])
negative_orbital = JSObject('shape')
self.viewer('drawIsosurface',
[voldata.id,
negative_orbital.id,
{'isoval': -isoval,
'color': negative_color,
'opacity': opacity}])
self.current_js_orbitals.extend([positive_orbital, negative_orbital])
if render: self.render()
def draw_arrow(self,
start,
end=None,
vector=None,
radius=0.15,
color='red',
opacity=1.0,
clickable=False,
render=True):
if (end is None) == (vector is None):
raise ValueError(
"Either 'end' or 'vector' should be passed, but not both.")
if end is None: end = np.array(start) + np.array(vector)
facestart = self._convert_units(start)
faceend = self._convert_units(end)
color = translate_color(color)
spec = dict(start=self._list_to_jsvec(facestart),
end=self._list_to_jsvec(faceend),
radius=radius,
color=color,
alpha=opacity)
js_shape = JSObject('shape')
self.viewer('renderPyShape', ['Arrow', spec, js_shape.id, clickable])
if render: self.render()
return js_shape
def draw_label(self, position, text,
background='black',
border='black',
color='white',
fontsize=14, opacity=1.0,
render=True):
js_label = JSObject('label')
position = self._convert_units(position)
color = translate_color(color)
background = translate_color(background)
spec = dict(position=self._list_to_jsvec(position),
fontColor=color,
backgroundColor=background,
borderColor=border,
fontSize=fontsize,
backgroundOpacity=opacity)
self.viewer('renderPyLabel', [text, spec, js_label.id])
if render: self.render()
return js_label
def set_colors(self, colormap, render=True):
"""
Args:
colormap(Mapping[str,List[Atoms]]): mapping of colors to atoms
"""
json = {}
for color, atoms in colormap.iteritems():
json[translate_color(color)] = self._atoms_to_json(atoms)
self.viewer('setColorArray', [json,])
if render: self.render()
def set_colors(self, colormap, render=True):
"""
Args:
colormap(Mapping[str,List[Atoms]]): mapping of colors to atoms
"""
json = {}
for color, atoms in colormap.iteritems():
json[translate_color(color)] = self._atoms_to_json(atoms)
self.viewer('setColorArray', [
json,
])
if render: self.render()
def draw_label(self,
position,
text,
background='black',
border='black',
color='white',
fontsize=14,
opacity=1.0,
render=True):
js_label = JSObject('label')
position = self._convert_units(position)
color = translate_color(color)
background = translate_color(background)
spec = dict(position=self._list_to_jsvec(position),
fontColor=color,
backgroundColor=background,
borderColor=border,
fontSize=fontsize,
backgroundOpacity=opacity)
self.viewer('renderPyLabel', [text, spec, js_label.id])
if render: self.render()
return js_label
def draw_sphere(self, position,
radius=2.0, color='red',
opacity=1.0, clickable=False, render=True):
js_shape = JSObject('shape')
position = self._convert_units(position)
radius = self._convert_units(radius)
center = dict(x=position[0], y=position[1], z=position[2])
color = translate_color(color)
self.viewer('renderPyShape', ['Sphere',
dict(center=center, radius=radius,
color=color, alpha=opacity),
js_shape.id,
clickable])
if render: self.render()
return js_shape
def draw_sphere(self,
position,
radius=2.0,
color='red',
opacity=1.0,
clickable=False,
render=True):
js_shape = JSObject('shape')
position = self._convert_units(position)
radius = self._convert_units(radius)
center = dict(x=position[0], y=position[1], z=position[2])
color = translate_color(color)
self.viewer('renderPyShape', [
'Sphere',
dict(center=center, radius=radius, color=color, alpha=opacity),
js_shape.id, clickable
])
if render: self.render()
return js_shape
def _change_style(self, backend_call, style_string,
atoms, options, render):
if atoms is None:
atom_json = {}
else:
atom_json = self._atoms_to_json(atoms)
if 'color' in options:
try:
options['color'] = translate_color(options['color'])
except AttributeError:
pass
style = self.convert_style_name(style_string)
if style is None:
style_spec = {}
else:
style_spec = {style: options}
self.viewer(backend_call, [atom_json, style_spec])
if render: self.render()
def _change_style(self, backend_call, style_string, atoms, options,
render):
if atoms is None:
atom_json = {}
else:
atom_json = self._atoms_to_json(atoms)
if 'color' in options:
try:
options['color'] = translate_color(options['color'])
except AttributeError:
pass
style = self.convert_style_name(style_string)
if style is None:
style_spec = {}
else:
style_spec = {style: options}
self.viewer(backend_call, [atom_json, style_spec])
if render: self.render()
def _draw3dmol_cylinder(self, color, start, end,
draw_start_face, draw_end_face,
opacity, radius, clickable, render, batch):
color = translate_color(color)
js_shape = JSObject('shape')
facestart = self._convert_units(start)
faceend = self._convert_units(end)
radius = self._convert_units(radius)
spec = dict(
start=self._list_to_jsvec(facestart),
end=self._list_to_jsvec(faceend),
radius=radius,
color=color,
alpha=opacity,
fromCap=draw_start_face, toCap=draw_end_face)
args = ['Cylinder', spec, js_shape.id, clickable]
if batch:
self.batch_message('renderPyShape', args)
else:
self.viewer('renderPyShape', args)
if render: self.render()
return js_shape
def _draw3dmol_cylinder(self, color, start, end, draw_start_face,
draw_end_face, opacity, radius, clickable, render,
batch):
color = translate_color(color)
js_shape = JSObject('shape')
facestart = self._convert_units(start)
faceend = self._convert_units(end)
radius = self._convert_units(radius)
spec = dict(start=self._list_to_jsvec(facestart),
end=self._list_to_jsvec(faceend),
radius=radius,
color=color,
alpha=opacity,
fromCap=draw_start_face,
toCap=draw_end_face)
args = ['Cylinder', spec, js_shape.id, clickable]
if batch:
self.batch_message('renderPyShape', args)
else:
self.viewer('renderPyShape', args)
if render: self.render()
return js_shape
def draw_arrow(self, start, end=None, vector=None,
radius=0.15, color='red',
opacity=1.0, clickable=False,
render=True):
if (end is None) == (vector is None):
raise ValueError("Either 'end' or 'vector' should be passed, but not both.")
if end is None: end = np.array(start) + np.array(vector)
facestart = self._convert_units(start)
faceend = self._convert_units(end)
color = translate_color(color)
spec = dict(
start=self._list_to_jsvec(facestart),
end=self._list_to_jsvec(faceend),
radius=radius,
color=color,
alpha=opacity)
js_shape = JSObject('shape')
self.viewer('renderPyShape', ['Arrow',
spec,
js_shape.id,
clickable])
if render: self.render()
return js_shape
def test_example():
css_color = 'tomato'
translated_color = translate_color(css_color)
assert translated_color == '0xff6347'
def set_color(self, color, atoms=None, render=True):
atom_json = self._atoms_to_json(atoms)
color = translate_color(color)
self.viewer('setAtomColor', [atom_json, color])
if render: self.render()
def set_background_color(self, color, opacity=1.0, render=True):
color = translate_color(color)
self.viewer('setBackgroundColor', args=[color, opacity])
if render: self.render()
def test_color_translation():
css_color = 'tomato'
translated_color = translate_color(css_color)
assert translated_color == '0xff6347'
def test_color_translation():
css_color = 'tomato'
translated_color = translate_color(css_color)
assert translated_color == '0xff6347'
def set_color(self, color, atoms=None, render=True):
atom_json = self._atoms_to_json(atoms)
color = translate_color(color)
self.viewer('setAtomColor', [atom_json, color])
if render: self.render()
def set_background_color(self, color, opacity=1.0, render=True):
color = translate_color(color)
self.viewer('setBackgroundColor', args=[color, opacity])
if render: self.render()