def test_animate(file_3frames):
m = molecule.load("pdb", file_3frames)
assert molecule.numframes(m) == 3
molecule.set_frame(m, 0)
with pytest.raises(ValueError):
animate.activate(-3000, True)
animate.activate(molid=m, active=False)
assert not animate.is_active(m)
animate.activate(m, True)
assert animate.is_active(m)
animate.goto(0)
display.update()
assert molecule.get_frame(m) == 0
animate.goto(1)
display.update()
assert molecule.get_frame(m) == 1
animate.forward()
animate.reverse()
animate.next()
animate.prev()
animate.pause()
molecule.delete(m)
def test_animate(file_3frames):
m = molecule.load("pdb", file_3frames)
assert molecule.numframes(m) == 3
molecule.set_frame(m, 0)
with pytest.raises(ValueError):
animate.activate(-3000, True)
animate.activate(molid=m, active=False)
assert not animate.is_active(m)
animate.activate(m, True)
assert animate.is_active(m)
animate.goto(0)
display.update()
assert molecule.get_frame(m) == 0
animate.goto(1)
display.update()
assert molecule.get_frame(m) == 1
animate.forward()
animate.reverse()
animate.next()
animate.prev()
animate.pause()
molecule.delete(m)
def generate_rotation_movie(molecule,
filename,
save_dir='.',
frame=0,
angle=360,
division=1.0,
renderer='Tachyon',
render_ext='dat'):
"""Function for generating movies where a static molecule frame is
rotated through an angle. Individual files for each subrotation
are generated, which can then be processed and combined into a
movie file.
Parameters
----------
molecule : VMDMolecule
Molecule for which the movie is made.
filename : str
The basename of the individual files for each subrotation
save_dir : str (default='.')
The directory in which generated files will be saved.
frame : int (default=0)
The trajectory frame that is rotated about.
angle : float (default=360.0)
The angle through which the molecule is rotated through.
division : float (default=1.0)
The angular (degree) for each subrotation.
renderer : str (default='Tachyon')
Program for rendering individual images. Must be a valid
rendering program bundled with VMD. For available rendering
programs, see:
https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node89.html
render_ext : str (default='dat')
filename extension for indivudally rendered files.
"""
check = dir_check(save_dir)
if not check:
return None
print("generating rotation movie...")
if angle % division != 0:
raise RuntimeError("Angle must be evenly divisble by dvision")
else:
if frame == -1:
frame = mol.numframes(molecule.molid) - 1
mol.set_frame(molecule.molid, frame)
display.update()
sub_rotations = int(angle / division)
current_angle = 0.0
for i in range(0, sub_rotations):
render.render(
renderer, save_dir + '/' + filename +
'{:0>9}.{}'.format(int(i), render_ext))
trans.rotate_scene('y', division)
display.update()
current_angle += division
def self_align(self):
"""Method for align trajectory frames to the initial frame
to prevent the molecule from drifting out of focus during the
simulation visualiation. This method can only be called after
trajectory frames have been loaded into the VMDMolecule.
"""
print("Self aligning molecule...")
mol.set_frame(self.molid, 0)
base_selection = atomsel('all', frame=0)
current_selection = atomsel('all')
for i in range(mol.numframes(self.molid)):
mol.set_frame(self.molid, i)
current_selection.update()
trans_matrix = current_selection.fit(base_selection)
current_selection.move(trans_matrix)
display.update()
def init_display(display_options, axes_options):
"""Function for initializing VMD scene options
Parameters
----------
display_options : dict
scene/display options for VMD. These are specified as key-value
pairs for each attribute in the VMD display options list. For
this complete list, see the following:
https://www.ks.uiuc.edu/Research/vmd/current/ug/node126.html
"""
display.set(**display_options)
if 'set_location' in axes_options.keys():
axes.set_location(axes_options['set_location'])
display.update()
def test_update():
display.update_off()
display.update()
display.update_on()
def test_update():
display.update_off()
display.update()
display.update_on()
def generate_trajectory_movie(molecule,
filename,
save_dir='.',
start=0,
stop=-1,
step=1,
smoothing=0,
renderer='Tachyon',
render_ext='dat'):
"""Function for generating movies of molecular trajectories
Parameters
----------
molecule : VMDMolecule
Molecule for which the movie is made.
filename : str
The basename of the individual files for each subrotation
save_dir : str (default='.')
The directory in which generated files will be saved.
start : int (default=0)
The starting frame
stop : float (default=360.0)
The ending frame
step : float (default=1.0)
The the step stride of the loaded frames
smoothing : int (default=0)
Size of smoothing window in frames to be applied to all
representations of the VMDMolecule
renderer : str (default='Tachyon')
Program for rendering individual images. Must be a valid
rendering program bundled with VMD. For available rendering
programs, see:
https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node89.html
render_ext : str (default='dat')
filename extension for indivudally rendered files.
"""
# Perform checks
check = dir_check(save_dir)
if not check:
return None
if stop < 0:
if stop != -1:
raise ValueError("negative values for 'stop' can only be -1, "
"in which case the stop frame is the final "
"loaded frame.")
num_loaded_frames = mol.numframes(molecule.molid)
# explicitly switch 'stop' to the last frame index
if stop == -1:
stop = num_loaded_frames - 1
if smoothing > 0:
reps = molrep.num(molecule.molid)
for i in range(reps):
molrep.set_smoothing(molecule.molid, i, smoothing)
print("generating '{}' trajectory movie...".format(filename))
frames = np.arange(start, stop, step)
mol.set_frame(molecule.molid, start)
current_frame = start
display.update()
for i in frames:
mol.set_frame(molecule.molid, i)
display.update()
render.render(
renderer, save_dir + '/' + filename +
'_{:0>9}.{}'.format(int(i), render_ext))