def showmol(mol, style="ball-and-stick", width=300, height=300):
v = QtViewer()
w = v.widget
if style == "ball-and-stick":
bs = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, mol.bonds)
elif style == "vdw":
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, backend="impostors")
w.camera.autozoom(mol.r_array)
# Make sure to finish everything
glBindTexture(w.textures["color"])
glActiveTexture(GL_TEXTURE0)
data = glGetTexImage(GL_TEXTURE_2D, 0, RGB, GL_UNSIGNED_BYTE)
# data = glReadPixels(0, 0, width, height, GL_RGB, GL_UNSIGNED_BYTE) # Make pil image to save as png
image = pil_Image.fromstring("RGB", (width, height), data)
b = BytesIO()
image.save(b, format="png")
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showmol(mol, style='ball-and-stick',
width=300, height=300):
v = QtViewer()
w = v.widget
if style == 'ball-and-stick':
bs = v.add_renderer(BallAndStickRenderer,
mol.r_array,
mol.type_array,
mol.bonds)
elif style == 'vdw':
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
backend='impostors')
w.camera.autozoom(mol.r_array)
# Make sure to finish everything
image = w.toimage(width, height)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showsys(sys, width=400, height=400):
v = QtViewer()
w = v.widget
sr = v.add_renderer(AtomRenderer, sys.r_array, sys.type_array,
backend='impostors')
if sys.box_vectors is not None:
v.add_renderer(BoxRenderer, sys.box_vectors)
w.camera.autozoom(sys.r_array)
w.camera.orbit_y(3.14/4)
w.camera.orbit_x(3.14/4)
image = w.toimage(width, height)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showsys(sys, width=400, height=400):
v = QtViewer()
w = v.widget
w.initializeGL()
w.resize(width, height)
w.resizeGL(width, height)
sr = v.add_renderer(AtomRenderer, sys.r_array, sys.type_array,
backend='impostors')
if sys.box_vectors is not None:
v.add_renderer(BoxRenderer, sys.box_vectors)
w.camera.autozoom(sys.r_array)
w.camera.orbit_y(3.14/4)
w.camera.orbit_x(3.14/4)
w.paintGL()
# Make sure to finish everything
data = glReadPixels(0, 0, width, height, GL_RGB, GL_UNSIGNED_BYTE)
# Make pil image to save as png
image = pil_Image.fromstring('RGB', (width, height), data)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showsys(sys, width=400, height=400):
v = QtViewer()
w = v.widget
sr = v.add_renderer(AtomRenderer,
sys.r_array,
sys.type_array,
backend='impostors')
if sys.box_vectors is not None:
v.add_renderer(BoxRenderer, sys.box_vectors)
w.camera.autozoom(sys.r_array)
w.camera.orbit_y(3.14 / 4)
w.camera.orbit_x(3.14 / 4)
image = w.toimage(width, height)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showmol(mol, style='ball-and-stick', width=300, height=300):
v = QtViewer()
w = v.widget
if style == 'ball-and-stick':
bs = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array,
mol.bonds)
elif style == 'vdw':
sr = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
backend='impostors')
w.camera.autozoom(mol.r_array)
# Make sure to finish everything
image = w.toimage(width, height)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def visualise(self, images, columns=1, width=None, height=None):
""" visualise image(s) in IPython
When this object is returned by an input cell or passed to the
display function, it will result in the image being displayed
in the frontend.
Parameters
----------
images : list/single PIL.Image or (x,y)
(x,y) denotes a blank space of size x,y e.g. [img1,(100,0),img2]
columns : int
number of image columns
width : int
Width to which to constrain the image in html
height : int
Height to which to constrain the image in html
Returns
-------
image : IPython.display.Image
"""
try:
img_iter = iter(images)
except TypeError:
img_iter = iter([images])
img_columns = []
img_rows = []
for image in img_iter:
# add blank
try:
x,y = image
image = Image.new("RGB", (x,y), "white")
except TypeError:
pass
if len(img_columns) < columns:
img_columns.append(image)
else:
img_rows.append(self._concat_images_horizontal(img_columns))
img_columns = [image]
if img_columns:
img_rows.append(self._concat_images_horizontal(img_columns))
image = self._concat_images_vertical(img_rows)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
b.close() #del b
return ipy_Image(data=data, width=width, height=height)
def visualise(self, images, columns=1, width=None, height=None):
""" visualise image(s) in IPython
When this object is returned by an input cell or passed to the
display function, it will result in the image being displayed
in the frontend.
Parameters
----------
images : list/single PIL.Image or (x,y)
(x,y) denotes a blank space of size x,y e.g. [img1,(100,0),img2]
columns : int
number of image columns
width : int
Width to which to constrain the image in html
height : int
Height to which to constrain the image in html
Returns
-------
image : IPython.display.Image
"""
try:
img_iter = iter(images)
except TypeError:
img_iter = iter([images])
img_columns = []
img_rows = []
for image in img_iter:
# add blank
try:
x, y = image
image = Image.new("RGB", (x, y), "white")
except TypeError:
pass
if len(img_columns) < columns:
img_columns.append(image)
else:
img_rows.append(self._concat_images_horizontal(img_columns))
img_columns = [image]
if img_columns:
img_rows.append(self._concat_images_horizontal(img_columns))
image = self._concat_images_vertical(img_rows)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
b.close() #del b
return ipy_Image(data=data, width=width, height=height)
def _show_molecule(self,
molecule,
active=False,
ball_stick=False,
zoom=1.,
width=300,
height=300,
rotations=[[0., 0., 0.]],
colorlist=[],
lines=[],
axis_length=0,
linestyle='impostors'):
if active:
return self._view_molecule(molecule,
ball_stick=ball_stick,
colorlist=colorlist)
else:
drawlines = lines[:]
if axis_length:
drawlines.append([(-1 * axis_length, 0, 0),
(axis_length, 0, 0), 'red', 'dark_red', 3,
True])
drawlines.append([(0, -1 * axis_length, 0),
(0, axis_length, 0), 'light_green',
'dark_green', 3, True])
drawlines.append([(0, 0, -1 * axis_length),
(0, 0, axis_length), 'light_blue',
'dark_blue', 3, True])
images = []
for rotation in rotations:
images.append(
self._image_molecule(molecule,
ball_stick=ball_stick,
colorlist=colorlist,
rotation=rotation,
zoom=zoom,
width=width,
height=width,
lines=drawlines,
linestyle=linestyle))
image = self._concat_images_horizontal(images)
del images
b = BytesIO()
image.save(b, format='png')
return ipy_Image(data=b.getvalue())
def showmol(mol, style='ball-and-stick',
width=300, height=300):
v = QtViewer()
w = v.widget
w.initializeGL()
w.resize(width, height)
w.resizeGL(width, height)
if style == 'ball-and-stick':
bs = v.add_renderer(BallAndStickRenderer,
mol.r_array,
mol.type_array,
mol.bonds)
elif style == 'vdw':
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
backend='impostors')
w.camera.autozoom(mol.r_array)
w.paintGL()
# Make sure to finish everything
data = glReadPixels(0, 0, width, height, GL_RGB, GL_UNSIGNED_BYTE)
# Make pil image to save as png
image = pil_Image.fromstring('RGB', (width, height), data)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
