def makeMovie(numClusts, frameRate):
real = int(numClusts)+1;
fr = int(frameRate)
movieSetup = "1 x" + str(real*fr)
cmd.mset(movieSetup)
#Load in all the system data.
for x in range(0, real):
# load the next system.
clustName = "system-" + str(x)
system = clustName + ".xyz"
cmd.load(system)
# Set the sphere scale and view
cmd.set("sphere_scale","0.5","all")
#Set the right view
cmd.set_view("0.910306633, -0.382467061, 0.158301696, 0.326706469, 0.898694992, 0.292592257, -0.254171938, -0.214630708, 0.943043232, 0.000000000, 0.000000000, -99.425979614, 10.461934090, 13.087766647, 11.786855698, 80.009132385, 118.842796326, -20.000000000")
#Set all the frame data
for x in range(0, real):
# set the current frame.
frameNum = (x*fr)+1
cmd.frame(frameNum)
clustName = "system-" + str(x)
movieState = "hide; show spheres, " + clustName
cmd.mdo(frameNum,movieState)
cmd.mview("store")
cmd.mview("reinterpolate")
cmd.mplay()
def testGetMovieLocked(self):
self.assertEqual(cmd.get_movie_locked(), 0)
cmd.mset('1x1')
cmd.mdo(1, 'cmd.color("blue")')
s = cmd.get_session()
cmd.set_session(s)
self.assertEqual(cmd.get_movie_locked(), 1)
cmd.set('security', 0)
cmd.set_session(s)
self.assertEqual(cmd.get_movie_locked(), 0)
def peak_tour(selection="mol", zbuff="6", framespermove=45, stallframes=5):
# zbuff is how far to stand back from the selection
# framespermove is how many frames to spend at each peak of the selection
# stallframes is how many frames to linger, unmoving before proceeding to next peak
framespermove = int(framespermove)
stallframes = int(stallframes)
# clear various movie memories, frames, caches
cmd.do("mclear")
cmd.do("mvClear")
cmd.do("mset")
cmd.do("frame 1")
# fetch model to find how many waypoints we will be visiting
model = cmd.get_model(selection).atom
stopovers = len(model)
# set up some landmarks within our visit to each peak so can divvy up the rotation
# or other movements easily
for waypoints in range(stopovers):
startframe = (waypoints) * framespermove + 1 + (
waypoints) * stallframes
mark1 = int(startframe + framespermove / 8)
mark2 = int(startframe + framespermove * 3 / 8)
mark3 = int(startframe + framespermove / 2)
mark4 = int(startframe + framespermove * 5 / 8)
mark5 = int(startframe + framespermove * 7 / 8)
endframe = startframe + framespermove
# This section describes whatever "dance" you want to do at each waypoint
# you can use the mark1-5 defined above to divvy up the time at this waypoint
# in this case it's 90 degree turn on y and x at each frame
lit1 = "mvSinturn %s-%s,y,90" % (startframe, mark3)
cmd.do(lit1)
lit2 = "mvSinturn %s-%s,x,90" % (mark3, endframe)
cmd.do(lit2)
cmd.do("movie")
# once you've defined the movie with "movie" (above) can then do the mdo
# commands to set the views at various points to be sure we go from one atom
# to the next. These mdo commands would be wiped out if the "movie" or "mset"
# commands were run after they are
for waypoints in range(stopovers):
startframe = (waypoints) * framespermove + 1 + (
waypoints) * stallframes
endframe = startframe + framespermove
zoomview = "zoom /%s///%s/, %s" % (selection, model[waypoints].resi,
zbuff)
cmd.mdo(startframe + 1, zoomview)
def chain_pull():
cmd.mstop
cmd.mclear
coor = { 2:'[0,0,0]', 3:'[75,0,0]', 4:'[0,75,0]',
5:'[0,0,75]', 6:'[-75,0,0]', 7:'[0,-75,0]',
8:'[0,0,-75]', 9:'[75,75,0]', 10:'[-75,-75,0]',
11:'[0,75,75]', 12:'[0,-75,-75]', 13:'[75,0,75]',
14:'[-75,0,-75]', 15:'[75,75,75]', 16:'[-75,-75,-75]',
17:'[75,-75,0]', 18:'[-75,75,0]', 19:'[0,75,-75]',
20:'[0,-75,75]', 21:'[75,0,-75]', 22:'[-75,0,75]',
23:'[75,75,-75]', 24:'[75,-75,75]', 25:'[-75,75,75]',
26:'[-75,-75,75]',27:'[75,-75,-75]',28:'[-75,-75,-75]'}
chainPullList = chain_contact()
if chainPullList == False:
return False
chainPullLen = len(chainPullList)
frames = 1+chainPullLen+172+chainPullLen+172
cmd.mset('1','%s'%frames)
i = chainPullLen+2
for h in range(2,i):
print 'translate %s,%s'%(coor[h],chainPullList[h-2])
cmd.mdo(h,'translate %s,%s'%(coor[h],chainPullList[h-2]))
cmd.mdo(i,'zoom all')
util.mroll(i+1,i+171,1)
i += 172
for g in range(i,chainPullLen+i):
c = coor[(g-i)+2].replace('7','-7').replace('--','-')
cmd.mdo(g,'translate %s,%s'%(c,chainPullList[g-i]))
g = chainPullLen+i
cmd.mdo(g,'zoom all')
util.mroll(g+1,g+171,1)
def highlight_chains():
cmd.mstop()
cmd.mclear()
cmd.mset()
glb.update()
colors = ['blue', 'orange', 'silver', 'green', 'yellow',
'purple', 'brightorange', 'lightblue', 'lightorange',
'pink', 'forest', 'firebrick', 'paleyellow', 'salmon',
'ruby', 'wheat', 'lightmagenta', 'nitblue']
chains = []
numChains = 0
objects = cmd.get_names('all')
for obj in objects:
split = obj.split('Chain-')
if len(split) == 2:
chains.append(split[1])
numChains += 1
numFrames = (numChains*200)+70
cmd.mset('1', numFrames)
cmd.mdo(1,'color red, all; hide cartoon, all')
cmd.orient()
cmd.mview('store', '1')
colorCount = 0
frameCount = 1
for i in chains:
cmd.orient('chain ' + i)
cmd.mview('store', frameCount+59)
cmd.mview('store', frameCount+115)
flash_chain(i, frameCount+59, 'red', colors[colorCount])
cmd.orient()
cmd.turn('x', '270')
cmd.turn('y', '180')
cmd.mview('store', frameCount+150)
cmd.mview('store', frameCount+170)
colorCount += 1
frameCount += 200
if(frameCount > numFrames-100):
cmd.orient()
cmd.mdo(numFrames,'mstop')
cmd.mview('store', (numChains*200)+70)
cmd.mview('interpolate')
cmd.show('ribbon')
cmd.color('red', 'all')
def make_all():
#make the whole movie
global views
global frames
global models
#first get total number of frames
ftot = 0
i = 0
setcommand = ""
for nframes in frames[:-1]:
ftot += nframes
if models.has_key(i):
setcommand += " " + models[i] + " "
else:
setcommand += " 1 x%i" % nframes
i += 1
#initialize movie
#cmd.mset("1 x%i" % ftot)
#cmd.mset("1 x50 1 -30 30 x20")
cmd.mset( setcommand )
#loop through views
start_view = views[0][:]
i = 0
first_frame = 1
for view in views[1:]:
end_view = view[:]
if settings.has_key(i):
movs.animate_transition( start_view, end_view, frames[i], first_frame, settings[i] )
elif fades.has_key(i):
movs.animate_transition( start_view, end_view, frames[i], first_frame, fades[i] )
else:
movs.animate_transition( start_view, end_view, frames[i], first_frame )
#add an action
if actions.has_key(i):
mdo_cmd = actions[i]#+";set_view ("+str( views[i] )+")"
print mdo_cmd
cmd.mdo(first_frame, mdo_cmd)
first_frame += frames[i]
i += 1
start_view = end_view[:]
cmd.frame(1)
def make_all():
#make the whole movie
global views
global frames
global models
#first get total number of frames
ftot = 0
setcommand = ""
for i, nframes in enumerate(frames[:-1]):
ftot += nframes
if i in models:
setcommand += " " + models[i] + " "
else:
setcommand += " 1 x%i" % nframes
#initialize movie
#cmd.mset("1 x%i" % ftot)
#cmd.mset("1 x50 1 -30 30 x20")
cmd.mset(setcommand)
#loop through views
start_view = views[0][:]
first_frame = 1
for i, view in enumerate(views[1:]):
end_view = view[:]
if i in settings:
movs.animate_transition(start_view, end_view, frames[i],
first_frame, settings[i])
elif i in fades:
movs.animate_transition(start_view, end_view, frames[i],
first_frame, fades[i])
else:
movs.animate_transition(start_view, end_view, frames[i],
first_frame)
#add an action
if i in actions:
mdo_cmd = actions[i] #+";set_view ("+str( views[i] )+")"
print mdo_cmd
cmd.mdo(first_frame, mdo_cmd)
first_frame += frames[i]
start_view = end_view[:]
cmd.frame(1)
def make_all():
# make the whole movie
global views
global frames
global models
# first get total number of frames
ftot = 0
setcommand = ""
for i, nframes in enumerate(frames[:-1]):
ftot += nframes
if i in models:
setcommand += " " + models[i] + " "
else:
setcommand += " 1 x%i" % nframes
# initialize movie
# cmd.mset("1 x%i" % ftot)
# cmd.mset("1 x50 1 -30 30 x20")
cmd.mset(setcommand)
# loop through views
start_view = views[0][:]
first_frame = 1
for i, view in enumerate(views[1:]):
end_view = view[:]
if i in settings:
movs.animate_transition(start_view, end_view, frames[i], first_frame, settings[i])
elif i in fades:
movs.animate_transition(start_view, end_view, frames[i], first_frame, fades[i])
else:
movs.animate_transition(start_view, end_view, frames[i], first_frame)
# add an action
if i in actions:
mdo_cmd = actions[i] # +";set_view ("+str( views[i] )+")"
print mdo_cmd
cmd.mdo(first_frame, mdo_cmd)
first_frame += frames[i]
start_view = end_view[:]
cmd.frame(1)
def testMpng(self, modal):
import glob, os
shape2 = (100, 100)
cmd.mset("1x4")
cmd.mdo(1, 'bg_color red')
cmd.mdo(3, 'bg_color blue')
with testing.mkdtemp() as dirname:
cmd.mpng(os.path.join(dirname, 'image'), width=shape2[0], height=shape2[1])
filenames = glob.glob(os.path.join(dirname, 'image*.png'))
filenames.sort()
self.assertEqual(4, len(filenames))
img = self.get_imagearray(filenames[0])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('red', img)
img = self.get_imagearray(filenames[-1])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('blue', img)
def testMpng(self, modal):
import glob, os
shape2 = (100, 100)
cmd.mset("1x4")
cmd.mdo(1, 'bg_color red')
cmd.mdo(3, 'bg_color blue')
with testing.mkdtemp() as dirname:
cmd.mpng(os.path.join(dirname, 'image'),
width=shape2[0],
height=shape2[1])
filenames = glob.glob(os.path.join(dirname, 'image*.png'))
filenames.sort()
self.assertEqual(4, len(filenames))
img = self.get_imagearray(filenames[0])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('red', img)
img = self.get_imagearray(filenames[-1])
self.assertEqual(img.shape[:2], shape2)
self.assertImageHasColor('blue', img)
def test_mdo(self):
self._load_example()
cmd.mset('1x3')
cmd.mdo(1, 'disable m1')
cmd.mdo(2, 'enable m1')
cmd.mdo(3, 'enable g1')
with testing.mkdtemp() as tempdir:
# export
prefix = os.path.join(tempdir, 'frame')
cmd.mpng(prefix, width=100, height=100)
img = self.get_imagearray(prefix + '0001.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0002.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0003.png')
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
def test_mdo(self):
self._load_example()
cmd.mset('1x3')
cmd.mdo(1, 'disable m1')
cmd.mdo(2, 'enable m1')
cmd.mdo(3, 'enable g1')
with testing.mkdtemp() as tempdir:
# export
prefix = os.path.join(tempdir, 'frame')
cmd.mpng(prefix, width=100, height=100)
img = self.get_imagearray(prefix + '0001.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0002.png')
self.assertImageHasNotColor('red', img)
self.assertImageHasColor('blue', img)
img = self.get_imagearray(prefix + '0003.png')
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
def reps(self,cleanup=0):
rep_list = [ "lines","sticks","spheres","surface","mesh","dots","ribbon","cartoon" ]
try:
if not cleanup:
cmd.disable()
cmd.set("suspend_updates",1,quiet=1)
cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
cmd.alter("rep1///1-5+8-13/","ss='S'")
cmd.cartoon("auto")
cmd.hide("everything","rep1")
for a in range(2,9):
cmd.create("rep%d"%a,"rep1")
for x, y in enumerate(rep_list, 1):
cmd.show(x, "rep%d" % y)
cmd.reset()
cmd.zoom("rep1",24)
util.cbay("rep2")
util.cbac("rep3")
util.cbas("rep4")
util.cbab("rep5")
util.cbaw("rep6")
util.cbay("rep8")
cmd.set("suspend_updates",0,quiet=1)
scale=0.5
for b in range(1,20):
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.set("suspend_updates",1,quiet=1)
xt=-3.2
yt=1.6
for a in range(1,5):
cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
yt=-yt
xt=-3.2
for a in range(5,9):
cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
for a in range(1,9):
cmd.origin("rep%d"%a,object="rep%d"%a)
cmd.mset("1")
st = ' '.join(map(lambda x,y:"rotate angle=-3,object=rep%d,axis=%s;"%(x,y),list(range(1,9)),
['x','y','x','y','x','y','x','y']))
cmd.mdo(1,st)
cmd.set("suspend_updates",0,quiet=1)
cmd.mplay()
cgo = []
axes = [[4.5,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]]
c = 1
for a in rep_list:
ext = cmd.get_extent("rep%d"%c)
pos = [(ext[0][0]+ext[1][0])/2,
(ext[0][1]+ext[1][1])/2+14,
(ext[0][2]+ext[1][2])/2]
c = c + 1
pos[0]=pos[0]-(measure_text(plain,a,axes)/2)
wire_text(cgo,plain,pos,a,axes)
cmd.set("cgo_line_width",1.5)
cmd.set("auto_zoom",0)
cmd.load_cgo(cgo,'reps')
cmd.set("auto_zoom",1)
else:
cmd.delete("rep*")
cmd.mset()
cmd.mstop()
except:
traceback.print_exc()
def surface_cartoon():
glb.update()
cmd.mstop()
cmd.mclear()
cmd.mset('1', '60')
cmd.hide('everything')
objects = cmd.get_names('all')
glb.procolor(None,show_all=('cartoon','surface'))
cmd.set("cartoon_fancy_helices", "1")
cmd.set("cartoon_fancy_sheets", "1")
cmd.mdo(1,'set transparency = 0.75, all;')
cmd.mdo(2,'set transparency = 0.7, all;')
cmd.mdo(3,'set transparency = 0.65, all;')
cmd.mdo(4,'set transparency = 0.6, all;')
cmd.mdo(5,'set transparency = 0.55, all;')
cmd.mdo(6,'set transparency = 0.5, all;')
cmd.mdo(7,'set transparency = 0.45, all;')
cmd.mdo(8,'set transparency = 0.4, all;')
cmd.mdo(9,'set transparency = 0.35, all;')
cmd.mdo(10,'set transparency = 0.3, all;')
cmd.mdo(11,'set transparency = 0.25, all;')
cmd.mdo(12,'set transparency = 0.2, all;')
cmd.mdo(13,'set transparency = 0.15, all;')
cmd.mdo(14,'set transparency = 0.1, all;')
cmd.mdo(15,'set transparency = 0.05, all;')
cmd.mdo(16,'set transparency = 0, all;')
cmd.mdo(17,'set transparency = 0, all;')
cmd.mdo(19,'set transparency = 0, all;')
cmd.mdo(20,'set transparency = 0, all;')
cmd.mdo(21,'set transparency = 0, all;')
cmd.mdo(22,'set transparency = 0, all;')
cmd.mdo(23,'set transparency = 0, all;')
cmd.mdo(24,'set transparency = 0, all;')
cmd.mdo(25,'set transparency = 0, all;')
cmd.mdo(26,'set transparency = 0, all;')
cmd.mdo(27,'set transparency = 0, all;')
cmd.mdo(28,'set transparency = 0, all;')
cmd.mdo(29,'set transparency = 0.05, all;')
cmd.mdo(30,'set transparency = 0.1, all;')
cmd.mdo(31,'set transparency = 0.15, all;')
cmd.mdo(32,'set transparency = 0.2, all;')
cmd.mdo(33,'set transparency = 0.25, all;')
cmd.mdo(34,'set transparency = 0.3, all;')
cmd.mdo(35,'set transparency = 0.35, all;')
cmd.mdo(36,'set transparency = 0.4, all;')
cmd.mdo(37,'set transparency = 0.45, all;')
cmd.mdo(38,'set transparency = 0.5, all;')
cmd.mdo(39,'set transparency = 0.55, all;')
cmd.mdo(40,'set transparency = 0.6, all;')
cmd.mdo(41,'set transparency = 0.65, all;')
cmd.mdo(42,'set transparency = 0.7, all;')
cmd.mdo(43,'set transparency = 0.75, all;')
cmd.mdo(44,'set transparency = 0.8, all;')
cmd.mdo(45,'set transparency = 0.85, all;')
cmd.mdo(46,'set transparency = 0.9, all;')
cmd.mdo(47,'set transparency = 0.9, all;')
cmd.mdo(48,'set transparency = 0.9, all;')
cmd.mdo(49,'set transparency = 0.85, all;')
cmd.mdo(50,'set transparency = 0.85, all;')
cmd.mdo(51,'set transparency = 0.85, all;')
cmd.mdo(52,'set transparency = 0.85, all;')
cmd.mdo(53,'set transparency = 0.85, all;')
cmd.mdo(54,'set transparency = 0.85, all;')
cmd.mdo(55,'set transparency = 0.85, all;')
cmd.mdo(56,'set transparency = 0.85, all;')
cmd.mdo(57,'set transparency = 0.85, all;')
cmd.mdo(58,'set transparency = 0.85, all;')
cmd.mdo(59,'set transparency = 0.85, all;')
cmd.mdo(60,'set transparency = 0.8, all;')
def show_transition(start_index=0, end_index=0):
#show the transition from the current view to the next view
global frames
global views
global cur_index
global actions
global models
if( start_index == 0 and end_index == 0 ):
if cur_index >= len(views)-1:
print "Current view is last in sequence."
return
start_index=cur_index
end_index=cur_index+1
else:
start_index = int(start_index)
end_index = int(end_index)
ftot = 0
setcommand = ""
i = start_index
for nframes in frames[start_index:end_index]:
#ftot += nframes
if models.has_key(i):
setcommand += " " + models[i] + " "
else:
setcommand += " 1 x%i" % nframes
i += 1
# cmd.mset("1 x%i" % ftot)
cmd.mset( setcommand )
start_frame = 1
#first do all actions that happen up to this point to make sure
#things look the way they should
first_action = ""
for i in range( 0, start_index ):
if actions.has_key(i):
first_action += actions[i] + ';'
#print "Executing %s from actions %d" % (actions[i],i)
#cmd.do( actions[i] )
if settings.has_key(i):
settingName, selection, startVal, endVal = settings[i]
action = "set %s, %f, %s;" % (settingName, endVal, selection)
first_action += action
#print "Executing %s from settings %d" % (action,i)
#cmd.do( action )
if fades.has_key(i):
startVisSelection, endVisSelection, sticksOnly = fades[i]
action = "set stick_transparency, 0, %s; set stick_transparency, 1, %s;" % (endVisSelection, startVisSelection)
first_action += action
#print "Executing %s from fades %d" % (action, i)
#cmd.do( action )
for i in range( start_index, end_index ):
if settings.has_key(i):
movs.animate_transition( views[i], views[i+1], frames[i], start_frame, settings[i] )
elif fades.has_key(i):
movs.animate_transition( views[i], views[i+1], frames[i], start_frame, fades[i] )
else:
movs.animate_transition( views[i], views[i+1], frames[i], start_frame )
#add an action
if start_frame == 1:
mdo_cmd = first_action
if actions.has_key(i):
mdo_cmd += actions[i]+";"
#mdo_cmd += "set_view("+str(views[i])+")"
print mdo_cmd
cmd.mdo(start_frame, mdo_cmd)
elif actions.has_key(i):
mdo_cmd = actions[i]+";set_view("+str(views[i])+")"
cmd.mdo(start_frame, mdo_cmd)
#print mdo_cmd
start_frame += frames[i]
cmd.frame(1)
cmd.mplay()
def surface_stick():
'''surface over stick movie'''
glb.update()
cmd.mstop()
cmd.mclear()
cmd.mset()
cmd.mset('1', '60')
glb.procolor(None,show_all=('sticks','surface'))
cmd.mdo(1,'set transparency = 0.75, all;')
cmd.mdo(2,'set transparency = 0.7, all;')
cmd.mdo(3,'set transparency = 0.65, all;')
cmd.mdo(4,'set transparency = 0.6, all;')
cmd.mdo(5,'set transparency = 0.55, all;')
cmd.mdo(6,'set transparency = 0.5, all;')
cmd.mdo(7,'set transparency = 0.45, all;')
cmd.mdo(8,'set transparency = 0.4, all;')
cmd.mdo(9,'set transparency = 0.35, all;')
cmd.mdo(10,'set transparency = 0.3, all;')
cmd.mdo(11,'set transparency = 0.25, all;')
cmd.mdo(12,'set transparency = 0.2, all;')
cmd.mdo(13,'set transparency = 0.15, all;')
cmd.mdo(14,'set transparency = 0.1, all;')
cmd.mdo(15,'set transparency = 0.05, all;')
cmd.mdo(16,'set transparency = 0, all;')
cmd.mdo(17,'set transparency = 0, all;')
cmd.mdo(19,'set transparency = 0, all;')
cmd.mdo(20,'set transparency = 0, all;')
cmd.mdo(21,'set transparency = 0, all;')
cmd.mdo(22,'set transparency = 0, all;')
cmd.mdo(23,'set transparency = 0, all;')
cmd.mdo(24,'set transparency = 0, all;')
cmd.mdo(25,'set transparency = 0, all;')
cmd.mdo(26,'set transparency = 0, all;')
cmd.mdo(27,'set transparency = 0, all;')
cmd.mdo(28,'set transparency = 0, all;')
cmd.mdo(29,'set transparency = 0.05, all;')
cmd.mdo(30,'set transparency = 0.1, all;')
cmd.mdo(31,'set transparency = 0.15, all;')
cmd.mdo(32,'set transparency = 0.2, all;')
cmd.mdo(33,'set transparency = 0.25, all;')
cmd.mdo(34,'set transparency = 0.3, all;')
cmd.mdo(35,'set transparency = 0.35, all;')
cmd.mdo(36,'set transparency = 0.4, all;')
cmd.mdo(37,'set transparency = 0.45, all;')
cmd.mdo(38,'set transparency = 0.5, all;')
cmd.mdo(39,'set transparency = 0.55, all;')
cmd.mdo(40,'set transparency = 0.6, all;')
cmd.mdo(41,'set transparency = 0.65, all;')
cmd.mdo(42,'set transparency = 0.7, all;')
cmd.mdo(43,'set transparency = 0.75, all;')
cmd.mdo(44,'set transparency = 0.8, all;')
cmd.mdo(45,'set transparency = 0.85, all;')
cmd.mdo(46,'set transparency = 0.9, all;')
cmd.mdo(47,'set transparency = 0.9, all;')
cmd.mdo(48,'set transparency = 0.9, all;')
cmd.mdo(49,'set transparency = 0.85, all;')
cmd.mdo(50,'set transparency = 0.85, all;')
cmd.mdo(51,'set transparency = 0.85, all;')
cmd.mdo(52,'set transparency = 0.85, all;')
cmd.mdo(53,'set transparency = 0.85, all;')
cmd.mdo(54,'set transparency = 0.85, all;')
cmd.mdo(55,'set transparency = 0.85, all;')
cmd.mdo(56,'set transparency = 0.85, all;')
cmd.mdo(57,'set transparency = 0.85, all;')
cmd.mdo(58,'set transparency = 0.85, all;')
cmd.mdo(59,'set transparency = 0.85, all;')
cmd.mdo(60,'set transparency = 0.8, all;')
def movsetz(event):
a = int(scriptent.get()) +1
scriptent.delete(0,100000)
scriptent.insert(0,a)
cmd.mdo( scriptent.get(), "move z," + entmz.get())
def show_transition(start_index=0, end_index=0):
#show the transition from the current view to the next view
global frames
global views
global cur_index
global actions
global models
if start_index == 0 and end_index == 0:
if cur_index >= len(views) - 1:
print "Current view is last in sequence."
return
start_index = cur_index
end_index = cur_index + 1
else:
start_index = int(start_index)
end_index = int(end_index)
ftot = 0
setcommand = ""
i = start_index
for nframes in frames[start_index:end_index]:
#ftot += nframes
if i in models:
setcommand += " " + models[i] + " "
else:
setcommand += " 1 x%i" % nframes
i += 1
# cmd.mset("1 x%i" % ftot)
cmd.mset(setcommand)
start_frame = 1
#first do all actions that happen up to this point to make sure
#things look the way they should
first_action = ""
for i in range(start_index):
if i in actions:
first_action += actions[i] + ';'
#print "Executing %s from actions %d" % (actions[i],i)
#cmd.do( actions[i] )
if i in settings:
settingName, selection, startVal, endVal = settings[i]
action = "set %s, %f, %s;" % (settingName, endVal, selection)
first_action += action
#print "Executing %s from settings %d" % (action,i)
#cmd.do( action )
if i in fades:
startVisSelection, endVisSelection, sticksOnly = fades[i]
action = "set stick_transparency, 0, %s; set stick_transparency, 1, %s;" % (
endVisSelection, startVisSelection)
first_action += action
#print "Executing %s from fades %d" % (action, i)
#cmd.do( action )
for i in range(start_index, end_index):
if i in settings:
movs.animate_transition(views[i], views[i + 1], frames[i],
start_frame, settings[i])
elif i in fades:
movs.animate_transition(views[i], views[i + 1], frames[i],
start_frame, fades[i])
else:
movs.animate_transition(views[i], views[i + 1], frames[i],
start_frame)
#add an action
if start_frame == 1:
mdo_cmd = first_action
if i in actions:
mdo_cmd += actions[i] + ";"
#mdo_cmd += "set_view("+str(views[i])+")"
print mdo_cmd
cmd.mdo(start_frame, mdo_cmd)
elif i in actions:
mdo_cmd = actions[i] + ";set_view(" + str(views[i]) + ")"
cmd.mdo(start_frame, mdo_cmd)
#print mdo_cmd
start_frame += frames[i]
cmd.frame(1)
cmd.mplay()
def animate_transition( start_view, end_view, nframes, first_frame, settings = [] ):
#print "Views"
#print start_view,'\n',end_view
cview = start_view[:]
cmd.set_view( start_view )
#get initial and final quaternions for interpolation
#print start_view[0:9]
#get quaternions
qstart = rmat2quat( start_view[0:9] )
qend = rmat2quat( end_view[0:9] )
#test for long way vs. short way
if( quatdotprod( qstart,qend ) < 0 ):
qstart = [-q for q in qstart]
axan_start = quat2axisangle( qstart )
axan_end = quat2axisangle( qend )
axan_cur = axan_start[:]
frame_start = first_frame
frame_end = frame_start + nframes
doFade = 0
doSetting = 0
if len( settings ) == 4:
settingName, selection, startVal, endVal = settings
settingStep = (endVal-startVal)/float(nframes)
print "Setting step ", settingStep
doSetting = 1
elif len( settings ) == 3:
startVisSelection, endVisSelection, sticksOnly = settings
settingStep = 1.0/float(nframes)
doFade = 1
for f in range( frame_start , frame_end):
#get rotmat
#using angle axis
for i in range(0,4):
axan_cur[i] = axan_cur[i] + (axan_end[i]-axan_start[i])/nframes
newmat = axisangle2rmat( axan_cur )
#print cview
for i in range(0,9):
cview[i] = newmat[i]
mdo_cmd = "set_view (["
for i in range(0,18):
if( i>8 ):
cview[i] = cview[i]+(end_view[i]-start_view[i])/nframes
mdo_cmd += "%12.7f,"% cview[i]
mdo_cmd = mdo_cmd[:-1]+"])"
if doSetting:
val = float(f-frame_start)*settingStep + startVal
print val;
mdo_cmd += "; set %s, %f, %s" % (settingName, val, selection)
print mdo_cmd;
#print "mdo ", mdo_cmd
if doFade:
val = float(f-frame_start)*settingStep
otherVal = 1.0 - val
mdo_cmd += "; set stick_transparency, %f, %s; set stick_transparency, %f, %s" % ( val, startVisSelection, otherVal, endVisSelection )
if not sticksOnly:
#comment out surface transparency interpolation due to problem with transparent sticks in front of
#transparent surfaces (get black holes)
# mdo_cmd += "; set transparency, %f, %s; set transparency, %f, %s" % ( val, startVisSelection, otherVal, endVisSelection )
mdo_cmd += "; set cartoon_transparency, %f, %s; set cartoon_transparency, %f, %s" % ( val, startVisSelection, otherVal, endVisSelection )
cmd.mdo(f,mdo_cmd)
def flash_chain(chainID, frame, initialColor, afterColor):
cmd.mdo(frame, 'show cartoon, chain %s'%chainID)
cmd.mdo(frame+7, 'color %s, chain %s'%(afterColor,chainID))
cmd.mdo(frame+14, 'color %s, chain %s'%(initialColor,chainID))
cmd.mdo(frame+21, 'color %s, chain %s'%(afterColor,chainID))
cmd.mdo(frame+28, 'color %s, chain %s'%(initialColor,chainID))
cmd.mdo(frame+35, 'color %s, chain %s'%(afterColor,chainID))
cmd.mdo(frame+42, 'color %s, chain %s'%(initialColor,chainID))
cmd.mdo(frame+49, 'color %s, chain %s'%(afterColor,chainID))
def tursetxyzmovsetxyz(event):
a = int(scriptent.get()) +1
scriptent.delete(0,100000)
scriptent.insert(0,a)
cmd.mdo( scriptent.get(), "turn x, %s; turn y, %s; turn z, %s; move x, %s; move y, %s; move z, %s" % (enttx.get(),entty.get(),enttz.get(),entmx.get(),entmy.get(),entmz.get()))
def movsetxyz(event):
a = int(scriptent.get()) +1
scriptent.delete(0,100000)
scriptent.insert(0,a)
cmd.mdo( scriptent.get(), "move x, %s; move y, %s; move z, %s" % (entmx.get(),entmy.get(),entmz.get()))
def tursetz(event):
a = int(scriptent.get()) +1
scriptent.delete(0,100000)
scriptent.insert(0,a)
cmd.mdo( scriptent.get(), "turn z," + enttz.get())
def animate_transition(start_view,
end_view,
nframes,
first_frame,
settings=[]):
#print "Views"
#print start_view,'\n',end_view
cview = start_view[:]
cmd.set_view(start_view)
#get initial and final quaternions for interpolation
#print start_view[0:9]
#get quaternions
qstart = rmat2quat(start_view[0:9])
qend = rmat2quat(end_view[0:9])
#test for long way vs. short way
if quatdotprod(qstart, qend) < 0:
qstart = [-q for q in qstart]
axan_start = quat2axisangle(qstart)
axan_end = quat2axisangle(qend)
axan_cur = axan_start[:]
frame_start = first_frame
frame_end = frame_start + nframes
doFade = 0
doSetting = 0
if len(settings) == 4:
settingName, selection, startVal, endVal = settings
settingStep = (endVal - startVal) / float(nframes)
print "Setting step ", settingStep
doSetting = 1
elif len(settings) == 3:
startVisSelection, endVisSelection, sticksOnly = settings
settingStep = 1.0 / float(nframes)
doFade = 1
for f in range(frame_start, frame_end):
#get rotmat
#using angle axis
for i in range(4):
axan_cur[i] = axan_cur[i] + (axan_end[i] - axan_start[i]) / nframes
newmat = axisangle2rmat(axan_cur)
#print cview
for i in range(9):
cview[i] = newmat[i]
mdo_cmd = "set_view (["
for i in range(18):
if i > 8:
cview[i] = cview[i] + (end_view[i] - start_view[i]) / nframes
mdo_cmd += "%12.7f," % cview[i]
mdo_cmd = mdo_cmd[:-1] + "])"
if doSetting:
val = float(f - frame_start) * settingStep + startVal
print val
mdo_cmd += "; set %s, %f, %s" % (settingName, val, selection)
print mdo_cmd
#print "mdo ", mdo_cmd
if doFade:
val = float(f - frame_start) * settingStep
otherVal = 1.0 - val
mdo_cmd += "; set stick_transparency, %f, %s; set stick_transparency, %f, %s" % (
val, startVisSelection, otherVal, endVisSelection)
if not sticksOnly:
#comment out surface transparency interpolation due to problem with transparent sticks in front of
#transparent surfaces (get black holes)
# mdo_cmd += "; set transparency, %f, %s; set transparency, %f, %s" % ( val, startVisSelection, otherVal, endVisSelection )
mdo_cmd += "; set cartoon_transparency, %f, %s; set cartoon_transparency, %f, %s" % (
val, startVisSelection, otherVal, endVisSelection)
cmd.mdo(f, mdo_cmd)
def growProtein():
cmd.mstop()
cmd.mclear()
cmd.mset()
glb.update()
objects = cmd.get_names('all')
if 'protein' in objects:
cmd.bg_color('black')
# create the objects to be used in this movie
cmd.create('helix', 'ss h and protein')
cmd.create('sheets', 'ss s and protein')
cmd.create('surface', objects[0])
cmd.mset('1', '1400')
# dna and rna will be represented as sticks
# to make them stand out from the protein
if 'dna' in objects:
glb.procolor('dna','sticks','cpk',None)
if 'rna' in objects:
glb.procolor('rna','sticks','cpk',None)
# coloring the protein and secondary structures
cmd.color('white', 'protein')
cmd.color('purple', 'helix')
cmd.color('teal', 'sheets')
cmd.cartoon('loop', 'protein')
cmd.cartoon('automatic', 'helix')
cmd.cartoon('automatic', 'sheets')
cmd.hide('all')
cmd.show('cartoon', 'protein')
#cmd.mdo(1,'hide cartoon, helix; hide cartoon, sheets;')
cmd.util.mrock('2', '200', '90', '1', '1')
cmd.mdo(201,'show cartoon, helix;')
cmd.util.mrock('202', '400', '90', '1', '1')
cmd.mdo(401,'show cartoon, sheets;')
cmd.util.mrock('402', '600', '90', '1', '1')
if 'ligands' in objects:
cmd.color('hotpink', 'ligands')
cmd.mdo(600, 'show spheres, ligands; show sticks, ligands;'+
' set sphere_transparency = 0.5, ligands;')
cmd.util.mroll('601', '800', '1', axis = "x")
cmd.color('blue', 'surface')
cmd.mview('store', '800')
cmd.turn('z', 180)
cmd.mview('store' , '1000')
cmd.turn('z', 180)
cmd.mdo(800, 'show surface, surface; '+
'set transparency = 0.8, surface;')
cmd.mdo(850,'set transparency = 0.7, surface;')
cmd.mdo(900,'set transparency = 0.6, surface;')
cmd.mdo(950,'set transparency = 0.5, surface;')
cmd.mdo(1000,'set transparency = 0.4, surface;')
cmd.mdo(1050,'set transparency = 0.3, surface;')
cmd.mdo(1100,'set transparency = 0.2, surface;')
cmd.mdo(1150,'set transparency = 0.1, surface;')
cmd.mdo(1200,'set transparency = 0.0, surface;')
cmd.mview('store', '1200')
cmd.util.mrock('1201', '1399', '180', '1', '1')
cmd.hide('everything', 'surface')
cmd.hide('everything', 'helix')
cmd.hide('everything', 'sheets')
cmd.reset()
cmd.orient()
cmd.mdo(1400,'hide everything, all; show cartoon, protein;')
cmd.mdo(1400,'mstop')
cmd.mview('interpolate')
cmd.rewind()
for line in f.readlines():
# Read in radius
if line.startswith('REMARK RADIUS'):
radius = float(line.split()[3])
break
# Load the sphere
cmd.load(args.sphere, 'sphere')
# Format the size of the sphere - may need to adjust settings later
cmd.hide('everything', 'sphere')
cmd.show('spheres', 'sphere')
cmd.alter('sphere', 'vdw={}'.format(radius))
cmd.rebuild()
cmd.set('sphere_color', 'grey90', 'sphere')
cmd.set('sphere_transparency', '0.5', 'sphere')
# Format the trajectory to show the waters within the GCMC sphere as sticks
if args.trajectory is not None:
cmd.hide('everything', 'resn HOH') # Hide waters first...
n_frames = cmd.count_states()
cmd.mset('1 -{}'.format(n_frames))
for f in range(1, n_frames + 1):
# Need to write a command to update the movie to show GCMC waters as sticks
movie_command = (
"hide sticks, resn HOH;"
"sele gcmcwats, resn SPH around {} and (resn HOH and name O), state={};"
"sele gcmcwats, byres gcmcwats;"
"show sticks, gcmcwats;").format(radius, f)
cmd.mdo(f, movie_command)
def reps(self, cleanup=0):
rep_list = [
"lines", "sticks", "spheres", "surface", "mesh", "dots", "ribbon",
"cartoon"
]
try:
if not cleanup:
cmd.disable()
cmd.set("suspend_updates", 1, quiet=1)
cmd.load("$PYMOL_DATA/demo/pept.pdb", "rep1")
cmd.alter("rep1///1-5+8-13/", "ss='S'")
cmd.cartoon("auto")
cmd.hide("everything", "rep1")
for a in range(2, 9):
cmd.create("rep%d" % a, "rep1")
for x, y in enumerate(rep_list, 1):
cmd.show(x, "rep%d" % y)
cmd.reset()
cmd.zoom("rep1", 24)
util.cbay("rep2")
util.cbac("rep3")
util.cbas("rep4")
util.cbab("rep5")
util.cbaw("rep6")
util.cbay("rep8")
cmd.set("suspend_updates", 0, quiet=1)
scale = 0.5
for b in range(1, 20):
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
cmd.set("suspend_updates", 1, quiet=1)
xt = -3.2
yt = 1.6
for a in range(1, 5):
cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
yt = -yt
xt = -3.2
for a in range(5, 9):
cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
for a in range(1, 9):
cmd.origin("rep%d" % a, object="rep%d" % a)
cmd.mset("1")
st = ' '.join(
map(
lambda x, y: "rotate angle=-3,object=rep%d,axis=%s;" %
(x, y), list(range(1, 9)),
['x', 'y', 'x', 'y', 'x', 'y', 'x', 'y']))
cmd.mdo(1, st)
cmd.set("suspend_updates", 0, quiet=1)
cmd.mplay()
cgo = []
axes = [[4.5, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]
c = 1
for a in rep_list:
ext = cmd.get_extent("rep%d" % c)
pos = [(ext[0][0] + ext[1][0]) / 2,
(ext[0][1] + ext[1][1]) / 2 + 14,
(ext[0][2] + ext[1][2]) / 2]
c = c + 1
pos[0] = pos[0] - (measure_text(plain, a, axes) / 2)
wire_text(cgo, plain, pos, a, axes)
cmd.set("cgo_line_width", 1.5)
cmd.set("auto_zoom", 0)
cmd.load_cgo(cgo, 'reps')
cmd.set("auto_zoom", 1)
else:
cmd.delete("rep*")
cmd.mset()
cmd.mstop()
except:
traceback.print_exc()
cmd.do('set all_states,0')
cmd.set('two_sided_lighting', 'on')
cmd.set('transparency', '0.2')
cmd.load('../data/origins.pdb', 'origins')
cmd.load('../data/v_origins.pdb', 'v_origins')
cmd.show('nb_spheres', 'origins')
cmd.show('nb_spheres', 'v_origins')
load_trajectory = $load_trajectory
if load_trajectory:
cmd.load("../data/trajectory.pdb", "structure", discrete=1)
cmd.dss("structure")
else:
cmd.load('../data/$pdb_representant', 'structure')
cmd.hide('lines', 'structure')
cmd.show('cartoon', 'structure')
cmd.color('gray', 'structure')
cmd.mset("1 -%d" % cmd.count_states())
for frame in range(1,cmd.count_states()+1):
cmd.mdo(frame, "computeSpheres(" + str(frame) + ")")
cmd.frame(1)
def testMdo(self):
self.prep_movie()
cmd.fragment("ala")
cmd.mdo(5, "delete *")
cmd.frame(5)
self.assertEquals(len(cmd.get_names()), 0)
def Ligand_Pull():
glb.update()
cmd.mstop()
cmd.mclear()
cmd.mset('1', '442')
cmd.hide('everything')
cmd.remove('resn HOH')
cmd.color('green', 'all')
objects = cmd.get_names('all')
if 'ligands' in objects:
cmd.set('stick_radius', '0.3')
glb.procolor('ligands around 6','sticks','cpk','cartoon')
glb.procolor('ligands','spheres','orange',None)
cmd.set("cartoon_fancy_helices", "1")
cmd.set("cartoon_fancy_sheets", "1")
cmd.set('cartoon_transparency', '0.5')
cmd.zoom()
cmd.orient()
cmd.mdo(1,'orient')
cmd.mdo(2,'translate [2,0,0],ligands;')
cmd.mdo(3,'translate [2,0,0],ligands;')
cmd.mdo(4,'translate [2,0,0],ligands;')
cmd.mdo(5,'translate [2,0,0],ligands;')
cmd.mdo(6,'translate [2,0,0],ligands;')
cmd.mdo(7,'translate [2,0,0],ligands;')
cmd.mdo(8,'translate [2,0,0],ligands;')
cmd.mdo(9,'translate [2,0,0],ligands;')
cmd.mdo(10,'translate [2,0,0],ligands;')
cmd.mdo(11,'translate [2,0,0],ligands;')
cmd.mdo(12,'translate [2,0,0],ligands;')
cmd.mdo(13,'translate [2,0,0],ligands;')
cmd.mdo(14,'translate [2,0,0],ligands;')
cmd.mdo(15,'translate [2,0,0],ligands;')
cmd.mdo(16,'translate [2,0,0],ligands;')
cmd.mdo(17,'translate [2,0,0],ligands;')
cmd.mdo(18,'translate [2,0,0],ligands;')
cmd.mdo(19,'translate [2,0,0],ligands;')
cmd.mdo(20,'translate [2,0,0],ligands;')
cmd.mdo(21,'translate [2,0,0],ligands;')
cmd.mdo(22,'translate [2,0,0],ligands;')
cmd.mdo(23,'translate [2,0,0],ligands;')
cmd.mdo(24,'translate [2,0,0],ligands;')
cmd.mdo(25,'translate [2,0,0],ligands;')
cmd.mdo(26,'translate [2,0,0],ligands;')
cmd.mdo(27,'translate [2,0,0],ligands;')
cmd.mdo(28,'translate [2,0,0],ligands;')
cmd.mdo(29,'translate [2,0,0],ligands;')
cmd.mdo(30,'translate [2,0,0],ligands;')
cmd.mdo(31,'translate [2,0,0],ligands;')
cmd.mdo(32,'translate [2,0,0],ligands;')
cmd.mdo(33,'translate [2,0,0],ligands;')
cmd.mdo(34,'translate [2,0,0],ligands;')
cmd.mdo(35,'translate [2,0,0],ligands;')
cmd.mdo(36,'translate [2,0,0],ligands;')
cmd.mdo(37,'translate [2,0,0],ligands;')
cmd.mdo(38,'translate [2,0,0],ligands;')
cmd.mdo(39,'translate [2,0,0],ligands;')
cmd.mdo(40,'translate [2,0,0],ligands;')
cmd.mdo(41,'translate [2,0,0],ligands;')
cmd.mdo(42,'orient')
cmd.util.mroll('42','222','1')
cmd.mdo(223,'translate [-2,0,0],ligands;')
cmd.mdo(224,'translate [-2,0,0],ligands;')
cmd.mdo(225,'translate [-2,0,0],ligands;')
cmd.mdo(226,'translate [-2,0,0],ligands;')
cmd.mdo(227,'translate [-2,0,0],ligands;')
cmd.mdo(228,'translate [-2,0,0],ligands;')
cmd.mdo(229,'translate [-2,0,0],ligands;')
cmd.mdo(230,'translate [-2,0,0],ligands;')
cmd.mdo(231,'translate [-2,0,0],ligands;')
cmd.mdo(232,'translate [-2,0,0],ligands;')
cmd.mdo(233,'translate [-2,0,0],ligands;')
cmd.mdo(234,'translate [-2,0,0],ligands;')
cmd.mdo(235,'translate [-2,0,0],ligands;')
cmd.mdo(236,'translate [-2,0,0],ligands;')
cmd.mdo(237,'translate [-2,0,0],ligands;')
cmd.mdo(238,'translate [-2,0,0],ligands;')
cmd.mdo(239,'translate [-2,0,0],ligands;')
cmd.mdo(240,'translate [-2,0,0],ligands;')
cmd.mdo(241,'translate [-2,0,0],ligands;')
cmd.mdo(242,'translate [-2,0,0],ligands;')
cmd.mdo(243,'translate [-2,0,0],ligands;')
cmd.mdo(244,'translate [-2,0,0],ligands;')
cmd.mdo(245,'translate [-2,0,0],ligands;')
cmd.mdo(246,'translate [-2,0,0],ligands;')
cmd.mdo(247,'translate [-2,0,0],ligands;')
cmd.mdo(248,'translate [-2,0,0],ligands;')
cmd.mdo(249,'translate [-2,0,0],ligands;')
cmd.mdo(250,'translate [-2,0,0],ligands;')
cmd.mdo(251,'translate [-2,0,0],ligands;')
cmd.mdo(252,'translate [-2,0,0],ligands;')
cmd.mdo(253,'translate [-2,0,0],ligands;')
cmd.mdo(254,'translate [-2,0,0],ligands;')
cmd.mdo(255,'translate [-2,0,0],ligands;')
cmd.mdo(256,'translate [-2,0,0],ligands;')
cmd.mdo(257,'translate [-2,0,0],ligands;')
cmd.mdo(258,'translate [-2,0,0],ligands;')
cmd.mdo(259,'translate [-2,0,0],ligands;')
cmd.mdo(260,'translate [-2,0,0],ligands;')
cmd.mdo(261,'translate [-2,0,0],ligands;')
cmd.mdo(262,'translate [-2,0,0],ligands;')
cmd.mdo(263,'orient')
cmd.util.mroll('264','442','1')
else:
showinfo('No ligands','There are no ligands in this PDB.')
def testMdo(self):
self.prep_movie()
cmd.fragment("ala")
cmd.mdo(5,"delete *")
cmd.frame(5)
self.assertEquals(len(cmd.get_names()),0)
def movie():
"""Creates the movie and plays it."""
cmd.frame(1) # reset frame counter
nFrames = mv.maxframe
# compile list of molecule states
states = []
for n in range(nFrames):
states.append(mv.getState(n + 1))
# compile mset command string "1 2 3 4 x3 5" from state list [1,2,3,4,4,4,5]
statelist = ""
n = 0
count = 0
while n < nFrames:
actual = states[n]
next = 0
if n < nFrames - 1:
next = states[n + 1]
if next == actual:
count = count + 1
else:
if count > 0:
statelist = statelist + "%s x%i " % (actual, count + 1)
else:
statelist = statelist + "%s " % (actual)
count = 0
n = n + 1
# Specify movie length
print "creating movie with %i frames." % (nFrames)
# cmd.mset("1 x%i"%(nFrames)) # earlier, without state support
cmd.mset(statelist)
# create empty frame-2do-lists
do = ["zero frame is unused"]
for i in range(nFrames):
do.append("")
# push all movie commands to the 2do-list
for m in mv.movie:
do[m[0]] = do[m[0]] + m[2] + ";"
# check for png output and raytracing:
if mv.pngPath != "":
i = 1
while i <= nFrames:
num = str(i)
null = "0000"
num = null[0:4 - len(num)] + num # create numbered file names
if mv.ray:
do[i] = do[i] + "ray;"
do[i] = do[i] + "png %spymol%s.png;" % (mv.pngPath, num)
i = 1 + 1
nFrames = nFrames + 1
do.append("mstop")
# now let action happen in the frames
i = 1
while i <= nFrames:
cmd.mdo(i, do[i])
i = i + 1