def vis(res,
path_prefix,
c=["firebrick", "forest", 'purple', 'salmon', "gold", "red"]):
for ind, r in enumerate(res):
for a in r.atoms:
cmd.show("spheres", "id " + str(a.id))
cmd.set("sphere_color", c[ind], "id " + str(a.id))
cmd.distance("d" + str(ind), "id " + str(r.atoms[0].id),
"id " + str(r.atoms[1].id))
cmd.hide("labels")
cmd.set("grid_slot", -2, "d" + str(ind))
cmd.ray(1200)
time.sleep(2)
cmd.set("grid_mode", 0)
cmd.png(path_prefix + "_restraints.png")
#cmd.set("grid_mode", 1)
cmd.move("zoom", -10)
cmd.ray(1200, )
time.sleep(4)
cmd.png(path_prefix + "_grid_restraints.png")
cmd.set("grid_mode", 0)
cmd.hide("spheres")
cmd.delete("d*")
def save_image_closeup(filename, width=ray_width_closeups(), height=ray_height_closeups()):
cmd.bg_color("white")
# cmd.ray(ray_width_closeups(), ray_height_closeups())
cmd.ray(width, height)
cmd.png("./output/" + filename + ".png", dpi=dpi())
cmd.bg_color("black")
return
def stereo_ray(filename, width=0, height=0, quiet=1):
'''
DESCRIPTION
"stereo_ray" ray-traces the current scene twice (separated by
a six-degree rotation around the y axis)
and saves a pair of images that can be combined in any image
manipulation software to form a stereoimage.
The first argument, the output file name, is mandatory.
The second and third arguments, the size of the image, are not.
If the width is given, the height will be calculated.
USAGE
stereo_ray filename [, width [, height]]
EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
'''
if filename.lower().endswith('.png'):
filename = filename[:-4]
cmd.ray(width, height, angle=-3)
cmd.png(filename + "_r", quiet=quiet)
cmd.ray(width, height, angle=3)
cmd.png(filename + "_l", quiet=quiet)
def stereo_ray(filename, width=0, height=0, quiet=1):
"""
DESCRIPTION
"stereo_ray" ray-traces the current scene twice (separated by
a six-degree rotation around the y axis)
and saves a pair of images that can be combined in any image
manipulation software to form a stereoimage.
The first argument, the output file name, is mandatory.
The second and third arguments, the size of the image, are not.
If the width is given, the height will be calculated.
USAGE
stereo_ray filename [, width [, height]]
EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
"""
if filename.lower().endswith(".png"):
filename = filename[:-4]
cmd.ray(width, height, angle=-3)
cmd.png(filename + "_r", quiet=quiet)
cmd.ray(width, height, angle=3)
cmd.png(filename + "_l", quiet=quiet)
def render_to_file(fname, top=True, side=True, vesicle=False,
zoom_obj="pbcbox",
zoom_distance=10):
fname = os.path.splitext(fname)[0]
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
if top:
cmd.ray("2048")
cmd.png("%s_top.png" % fname)
if side:
cmd.turn("x", -90)
if vesicle:
cmd.move("y", 150)
cmd.ray("2048")
cmd.png("%s_side.png" % fname)
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
def test(self):
cmd.fragment('ala')
cmd.ray(100, 100)
img = self.get_imagearray() # cmd.png without optional arguments
# bug was: ray tracing twice, second time would not be 100x100
self.assertEqual(img.shape[:2], (100,100))
def abl(*files, **kwargs):
MdsPymol.reset(options)
if 'optionsFile' in kwargs:
execfile(kwargs['optionsFile'], globals(), locals())
for file in files:
print "Processing file '%s'." % file
fileOptions = perMapOptions.get(file, {})
# Add a CGO prefix if we have multiple files and a prefix was not given.
if len(files) > 1 and 'cgo prefix' not in fileOptions:
basename, _ = os.path.splitext(os.path.basename(file))
fileOptions['cgo prefix'] = basename + '_'
mapOptions = defaultMapOptions.copy()
restrictedUpdate(mapOptions, fileOptions)
ACmap(file, mapOptions)
# Process global options.
cmd.clip('far', -20.0)
#cmd.clip('near', 100.0)
if options['axes compute']:
Axes(options)
if options['base grid compute']:
BaseGrid(options)
if options['view']:
cmd.set_view(options['view'])
if options['ray']:
cmd.ray()
if options['png file']:
cmd.png(options['png file'])
if options['quit']:
cmd.quit()
def saveMultiplepng(pnamein, nbstates):
finish_launching()
for state in range(0,nbstates):
print(state, nbstates)
finish_launching()
pfilin = pnamein + "_state" + str(state) + ".pdb"
print (pfilin)
cmd.load(pfilin, "state" + str(state))
cmd.hide("everything", "all")
for state in range(0, nbstates):
cmd.show("surface", selection="state" + str(state))
cmd.set("transparency", value=0.4)
cmd.show("cartoon", selection="state" + str(state))
cmd.spectrum("b", "chocolate_firebrick_red_tv_red_deepsalmon_darksalmon_salmon_lightpink_white",
selection="all", minimum=0, maximum=100)
cmd.select("lig" + str(state), "resn UNK and state" + str(state))
cmd.show("stick", selection="lig" + str(state))
cmd.bg_color("white")
cmd.ray(2000, 2000)
cmd.save(pnamein + "_state" + str(state) + ".png", selection="state" + str(state))
cmd.hide("everything", "all")
cmd.quit()
def surfback(width,height,color="gray",showcartoon=True,dname=""):
#if (cmd.get("bg_image_filename")==None):
cmd.set("bg_image_filename",None)
cmd.hide("")
cmd.set("fog", 0)
cmd.set("reflect", 0)
cmd.set("ambient",1)
cmd.set("ray_trace_mode", 0)
cmd.show("surface")
cmd.set("surface_color",color)
cmd.set("spec_reflect",0)
cmd.ray(width,height)
# I want below to work with tmpdir but, it fails. So this script makes unwanted tmpfile to dir named as dname
cmd.png(dname+"surf.png")
cmd.do("ls " + dname)
cmd.do("ls " + dname+"surf.png")
#cmd.load_png(dname+"surf.png")
time.sleep(0.01)
cmd.set("bg_image_filename",dname+"surf.png")
cmd.set("bg_image_mode",0)
if (showcartoon):
cmd.hide("")
cmd.show("cartoon")
cmd.color("white")
cmd.set("ray_trace_mode", 3)
cmd.set("ambient", 1)
cmd.set("reflect",0)
cmd.set("valence", 0)
cmd.set("spec_reflect",0)
cmd.set("ray_trace_color", "gray0")
#cmd.ray(n,n)
#cmd.png("/
print("Ray your image in the same aspect ratio as you specified in surfback")
def test(self):
cmd.fragment('ala')
cmd.ray(100, 100)
img = self.get_imagearray() # cmd.png without optional arguments
# bug was: ray tracing twice, second time would not be 100x100
self.assertEqual(img.shape[:2], (100, 100))
def take_screenshot(params, pdb_file_name, protein_number, step_number):
print("")
print("SCREENSHOT! protein #", protein_number, pdb_file_name, " step ", step_number, " with ", cmd.count_atoms("all"), " atoms")
screenshot_path = "./results/{}/screenshots/{}-{}/{}-{}.png".format(params.run_time_stamp, pdb_file_name, protein_number, pdb_file_name, step_number)
cmd.ray()
# cmd.zoom("all")
cmd.center("all")
cmd.png(screenshot_path)
def _test_recall(self):
cmd.scene('s1', 'recall')
cmd.ray(1, 1) # force scene update
self.assertEqual(['m3'], cmd.get_object_list('(visible)'))
self.assertEqual(['m3'], cmd.get_object_list('(enabled)'))
cmd.enable('g1')
cmd.ray(1, 1) # force scene update
self.assertEqual(['m1', 'm3'], cmd.get_object_list('(visible)'))
self.assertEqual(['m1', 'm3'], cmd.get_object_list('(enabled)'))
def _test_recall(self):
cmd.scene('s1', 'recall')
cmd.ray(1, 1) # force scene update
self.assertEqual(['m3'], cmd.get_object_list('(visible)'))
self.assertEqual(['m3'], cmd.get_object_list('(enabled)'))
cmd.enable('g1')
cmd.ray(1, 1) # force scene update
self.assertEqual(['m1', 'm3'], cmd.get_object_list('(visible)'))
self.assertEqual(['m1', 'm3'], cmd.get_object_list('(enabled)'))
def rotation_series(axis, increment, width, height, filename, with_centering):
if (increment == 0):
max_turns = 1
else:
max_turns = (360/increment) + 1
for x in range(max_turns):
if x > 0: cmd.rotate(axis, increment)
if with_centering: cmd.center("(all)")
cmd.ray(width, height)
cmd.png(filename + "_" + str(x * increment) + ".png", dpi=dpi())
return
def save_image(
width = 1920,
height = 1080,
selection = '(all)',
format = 'png',
state = -1,
prefix = os.path.join(Windows_Desktop() or _Nix_Desktop(), 'PyMOL'),
renderer = -1,
shift = 0.0):
cmd.ray(width, height, renderer, shift)
for path in pathes(prefix, format):
if not os.path.exists(path):
cmd.save(path, selection, state, format)
break
def test(self):
cmd.pseudoatom('m1')
cmd.pseudoatom('m2')
cmd.pseudoatom('m3')
cmd.group('g1', 'm1')
cmd.disable('g1')
cmd.disable('m2')
cmd.ray(1, 1) # force scene update
cmd.scene('s1', 'store')
self._test_recall()
cmd.disable('*')
self._test_recall()
cmd.enable('*')
self._test_recall()
def save_image(width=1920,
height=1080,
selection='(all)',
format='png',
state=-1,
prefix=os.path.join(Windows_Desktop() or _Nix_Desktop(),
'PyMOL'),
renderer=-1,
shift=0.0):
cmd.ray(width, height, renderer, shift)
for path in pathes(prefix, format):
if not os.path.exists(path):
cmd.save(path, selection, state, format)
break
def test(self):
cmd.pseudoatom('m1')
cmd.pseudoatom('m2')
cmd.pseudoatom('m3')
cmd.group('g1', 'm1')
cmd.disable('g1')
cmd.disable('m2')
cmd.ray(1, 1) # force scene update
cmd.scene('s1', 'store')
self._test_recall()
cmd.disable('*')
self._test_recall()
cmd.enable('*')
self._test_recall()
def makecartoon():
cmd.color('black', 'name C')
cmd.color('yellow', 'name S')
cmd.hide('lines', 'all')
cmd.set('stick_radius', 0.1)
cmd.set('sphere_scale', 0.25)
cmd.set('sphere_scale', 1, 'name au')
cmd.set('sphere_scale', 1, 'name ag')
cmd.set('antialias', 2)
cmd.set('opaque_background', 0)
cmd.set('ray_trace_gain', 5)
cmd.set('depth_cue', 0)
cmd.show('sticks', 'all')
cmd.show('spheres', 'all')
cmd.ray(2400, 1800)
def load():
r = 0
rep = ["lines", "sticks", "spheres", "dots", "ribbon", "cartoon"]
list = glob("pdb/*/*")
list = map(lambda x: (random.random(), x), list)
list.sort()
list = map(lambda x: x[1], list)
# list = [ "pdb/rb/pdb0rbs.noc" ] + list
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
print file
cmd.delete('pdb')
cmd.load(file, 'pdb')
cmd.orient('pdb')
cmd.color('red', 'ss h')
cmd.color('yellow', 'ss s')
cmd.hide()
if cmd.count_atoms() < 15000:
cmd.show(rep[r], "all")
elif cmd.count_atoms() < 50000:
cmd.show("cartoon", "all")
else:
cmd.show("lines", "all")
r = r + 1
if r >= len(rep): r = 0
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
cmd.ray(160, 120)
cmd.dirty()
time.sleep(0.1)
if n > 1:
sys.__stderr__.write("\n")
sys.__stderr__.flush()
except:
traceback.print_exc()
def stereo_ray(output="", width="", height=""):
"""
DESCRIPTION
"stereo_ray" ray-traces the current scene twice (separated by
a six-degree rotation around the y axis)
and saves a pair of images that can be combined in any image
manipulation software to form a stereoimage.
The first argument, the output file name, is mandatory.
The second and third arguments, the size of the image, are not.
If the width is given, the height will be calculated.
USAGE
stereo_ray filename [, width [, height]]
EXAMPLE
stereo_ray output, 1000, 600
stereo_ray secondImage.png
"""
if output == "":
print "no output filename defined\n"
print "try: 'stereo_ray filename'"
return -1
# abort if no output file name given
if width == "":
width, height = cmd.get_session()["main"][0:2]
# get dimensions from viewer if not given
elif height == "":
oldWidth, oldHeight = cmd.get_session()["main"][0:2]
height = int(width) * oldHeight / oldWidth
# calculate height from proportions of viewer if
# only width is given
cmd.ray(width, height, angle=-3)
cmd.png(output + "_r")
cmd.ray(width, height, angle=3)
cmd.png(output + "_l")
def stereo_ray(output='', width='', height=''):
if output == '':
print 'no output filename defined\n'
print 'try: \'stereo_ray filename\''
return -1
# abort if no output file name given
if width == '':
width, height = cmd.get_session()['main'][0:2]
# get dimensions from viewer if not given
elif height == '':
oldWidth, oldHeight = cmd.get_session()['main'][0:2]
height = int(width) * oldHeight / oldWidth
# calculate height from proportions of viewer if
# only width is given
cmd.ray(width, height, angle=-3)
cmd.png(output + "_r")
cmd.ray(width, height, angle=3)
cmd.png(output + "_l")
def stereo_ray(output='', width='', height=''):
if output == '':
print 'no output filename defined\n'
print 'try: \'stereo_ray filename\''
return -1
# abort if no output file name given
if width == '':
width,height = cmd.get_session()['main'][0:2]
# get dimensions from viewer if not given
elif height == '':
oldWidth,oldHeight = cmd.get_session()['main'][0:2]
height = int(width)*oldHeight/oldWidth
# calculate height from proportions of viewer if
# only width is given
cmd.ray(width, height, angle=-3)
cmd.png(output+"_r")
cmd.ray(width, height, angle=3)
cmd.png(output+"_l")
def load():
r = 0
rep = [ "lines","sticks","spheres","dots","ribbon","cartoon" ]
list = glob("pdb/*/*")
list = map(lambda x:(random.random(),x),list)
list.sort()
list = map(lambda x:x[1],list)
# list = [ "pdb/rb/pdb0rbs.noc" ] + list
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
print file
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.orient('pdb')
cmd.color('red','ss h')
cmd.color('yellow','ss s')
cmd.hide()
if cmd.count_atoms()<15000:
cmd.show(rep[r],"all")
elif cmd.count_atoms()<50000:
cmd.show("cartoon","all")
else:
cmd.show("lines","all")
r = r + 1
if r>=len(rep): r=0;
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
cmd.ray(160,120)
cmd.dirty()
time.sleep(0.1)
if n>1:
sys.__stderr__.write("\n")
sys.__stderr__.flush()
except:
traceback.print_exc()
def images(B):
#cmd.do("cd {}".format(B))
pdb_list = glob.glob("*.pdb")
for pdb in pdb_list:
cmd.load(pdb)
cmd.run("/usr/local/bin/all_against_all.py")
cmd.select("all_ps", "name PS1+PS2+PS3")
cmd.do(
"align_all_to_all(selection='all_ps',cutoff=0,cycles=0,full_matrix=1,method='align')"
)
cmd.remove("het")
cmd.remove("all_ps")
cmd.show("sticks", "all")
cmd.hide("sticks", "all_ps")
cmd.hide("sphere", "all_ps")
cmd.set("sphere_scale", 0.30, "all_ps")
cmd.orient("all")
cmd.multisave("{}.pdb".format(B))
cmd.set("ray_opaque_background", 0)
cmd.ray(2400)
cmd.set("antialias", 1)
cmd.png("{}.png".format(B), 1200, 1200, 300)
cmd.quit()
def render_to_file(fname, top=True, side=True, vesicle=False, zoom_obj="pbcbox", zoom_distance=10):
fname = os.path.splitext(fname)[0]
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
if top:
cmd.ray("2048")
cmd.png("%s_top.png" % fname)
if side:
cmd.turn("x", -90)
if vesicle:
cmd.move("y", 150)
cmd.ray("2048")
cmd.png("%s_side.png" % fname)
cmd.reset()
cmd.zoom(zoom_obj, zoom_distance)
if vesicle:
cmd.turn("z", -90)
cmd.move("y", -50)
def run():
# get form data
height = form.input_height.value()
width = form.input_width.value()
dpi = form.input_dpi.value()
filename = form.input_filename.text()
units = form.input_units.currentText()
# calculate dots per centimeter or inch
if units == 'cm':
dots_per_unit = dpi * 2.54
else:
dots_per_unit = dpi
# convert image size to pixels
width *= dots_per_unit
height *= dots_per_unit
# render the image
if filename:
cmd.png(filename, width, height, dpi=dpi, ray=1, quiet=0)
else:
cmd.ray(width, height, quiet=0)
print('No filename selected, only rendering on display')
def test(self):
cmd.pseudoatom('m1')
cmd.mset('1x1')
cmd.create('m2', 'm1')
cmd.ray()
v = cmd.get_object_matrix('m2')
self.assertArrayEqual(v, [
1.,
0.,
0.,
0.,
0.,
1.,
0.,
0.,
0.,
0.,
1.,
0.,
0.,
0.,
0.,
1.,
], 0.001, 'object matrix not identity')
cmd.color("atomic", "not element C")
cmd.hide("licorice", "hydro")
# general settings
cmd.bg_colour("white")
cmd.set("ambient", 0.4)
cmd.set("antialias", 1)
cmd.set("ortho", 1)
cmd.set("sphere_mode", 5)
cmd.set("ray_trace_mode", 1)
cmd.set("cartoon_fancy_helices", 1)
cmd.set("cartoon_highlight_color", "grey30")
# draw the grid
## select the range
cmd.select('20A', 'ROCK1_ligand expand 20')
cmd.load('drawgridbox.pml')
# view
cmd.set_view ((
0.003532045, -0.998905182, -0.046578705,
0.942174196, -0.012283626, 0.334894955,
-0.335102588, -0.045066781, 0.941101432,
-0.000204355, 0.000496300, -208.231918335,
53.537849426, 102.745925903, 29.107488632,
130.434631348, 285.912689209, -20.000000000 ))
# save pymol session
cmd.save(HERE / "pymol_3d_grid_encoding.pse")
cmd.ray(800, 800)
cmd.png(DATA / "pymol_3d_grid_encoding.png")
def make_figure(output='', mode='',size=900,opaque='transparent'):
"""
AUTHOR
Martin Christen
DESCRIPTION
"make_figure" creates publication-quality figures of the current scene.
It understands several predefined "modes" and sizes.
USAGE
make_figure filename [, mode] [, size (default=900 pixels)] [,opaque]
ARGUMENTS
mode = string: type of desired figure (single, fb, sides, stereo or -nothing-)
size = integer: size of the figure in pixels OR # panels (if <= 12)
opaque = specify an opaque background.
By default, the script makes the background transparent.
EXAMPLES
make_figure output
make_figure output, single, 975, opaque
make_figure output, fb, 2
make_figure output, sides,4
make_figure output, stereo
NOTES
"single" mode makes a single 300 dpi figure
"fb" mode makes TWO 300 dpi figure
("front" and "back", rotating by 180 degrees about y)
"sides" mode makes FOUR 300 dpi figures
("front" "left" "right" and back, rotating by 90 degrees clockwise about y)
"stereo" generates two 300 dpi, 750 px figures
("L" and "R", to be combined as a stereo image)
If you specify the stereo mode, the size argument is IGNORED.
If no mode argument is given, the script generates quick figures
for general use: TWO figures (front and back) at 300 x 300 px, 72 dpi.
Size is interpreted as pixels, except if the number is ridiculously small
(<=12), in which case the script as "number of panels" to make.
Edit the script manually to define corresponding values.
"""
#define sizes here (in pixels)
panel1 = 1800
panel2 = 1350
panel3 = 900
panel4 = 900
panel5 = 750
panel6 = 750
panel7 = 675
panel8 = 675
panel9 = 600
panel10 = 585
panel11 = 585
panel12 = 585
#verify size is an integer number and convert to pixels
size = int(size)
if size > 12:
pixels = size
elif size == 1:
pixels = panel1
elif size == 2:
pixels = panel2
elif size == 3:
pixels = panel3
elif size == 4:
pixels = panel4
elif size == 5:
pixels = panel5
elif size == 6:
pixels = panel6
elif size == 7:
pixels = panel7
elif size == 8:
pixels = panel8
elif size == 9:
pixels = panel9
elif size == 10:
pixels = panel10
elif size == 11:
pixels = panel11
elif size == 3:
pixels = panel12
#change background
cmd.unset('opaque_background')
if opaque == 'opaque':
cmd.set('opaque_background')
#apply mode
if output == '':
print 'no output filename defined\n'
print 'try: \'make_figure filename\''
return -1
# abort if no output file name given
if mode =='':
cmd.set('surface_quality',1)
cmd.set('opaque_background')
cmd.png(output+"_back_quick",300,300,dpi=72)
cmd.turn('y',180)
cmd.png(output+"_front_quick",300,300,dpi=72)
cmd.turn('y',180)
cmd.set('surface_quality',0)
# make front and back figures for quick mode
elif mode == 'single':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output, dpi=300)
cmd.set('surface_quality',0)
# make a figure for single mode
elif mode == 'fb':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output+"_front", dpi=300)
cmd.turn('y',180)
cmd.ray(pixels, pixels)
cmd.png(output+"_back", dpi=300)
cmd.turn('y',180)
cmd.set('surface_quality',0)
# make front and back figures for single mode
elif mode == 'sides':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output+"_1", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_2", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_3", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_4", dpi=300)
cmd.turn('y',90)
cmd.set('surface_quality',0)
# make front and back figures for single mode
elif mode == 'stereo':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(750, 750, angle=-3)
cmd.png(output+"_R", dpi=300)
cmd.ray(750, 750, angle=3)
cmd.png(output+"_L", dpi=300)
with open(edgepath,'r') as fin :
data = fin.readlines();
edges = [line.strip().split() for line in data]
for n,e in enumerate(edges) :
t = cmd.dist('dist'+str(n),'3H4E//A/'+e[0]+'/CA',\
'3H4E//A/'+e[1]+'/CA')
if t < cutoff :
cmd.delete('dist'+str(n))
else :
cmd.color('blue','dist'+str(n))
cmd.hide('labels','dist'+str(n))
cmd.show('spheres','3H4E//A/'+e[0]+'/CA')
cmd.show('spheres','3H4E//A/'+e[1]+'/CA')
cmd.color('yellow','3H4E//A/'+e[0]+'/CA')
cmd.color('yellow','3H4E//A/'+e[1]+'/CA')
cmd.set('dash_radius','0.2');
cmd.set('dash_gap','0.0');
cmd.set('sphere_scale','0.3')
#cmd.set('sphere_scale','0.8','retinal');
cmd.ray()
print('*'*5+'Image:%s'%os.path.abspath(outfp)+'*'*5)
cmd.png(os.path.abspath(outfp))
print '-------Completed Call--------';
cmd.color('_colorm', 'sm')
#cmd.set ('label_font_id', 16)
#cmd.set ('label_size', 24)
#cmd.pseudoatom('xatom', pos=[1,0,0], label="x")
#cmd.pseudoatom('yatom', pos=[0,1,0], label="y")
#cmd.pseudoatom('zatom', pos=[0,0,2], label="z")
cmd.set('label_font_id', 16)
cmd.set('label_size', 20)
cmd.pseudoatom('xatom', pos=[2.5, 0, 0], label="x")
cmd.pseudoatom('yatom', pos=[0, 2.5, 0], label="y")
cmd.pseudoatom('zatom', pos=[0, 0, 5.5], label="z")
cmd.set('ray_opaque_background', 'on')
cmd.set('transparency', 0.50)
cmd.set_view('\
-0.086753346, 0.836276770, 0.541441798,\
0.670052588, -0.353231400, 0.652936995,\
0.737265468, 0.419426382, -0.529700875,\
0.000000000, 0.000000000, -34.167503357,\
0.108778238, 0.131587982, 2.662951946,\
26.937919617, 41.397087097, -20.000000000')
cmd.pseudoatom('latom', pos=[3.5, -2.5, 0], label="_label")
cmd.ray(1024, 1024)
cmd.png('this.png', dpi=600)
cmd.quit()
def FocalBlur(aperture=2.0, samples=10, ray=0, width=0, height=0):
'''
DESCRIPTION
Creates fancy figures by introducing a focal blur to the image. The object
at the origin will be in focus.
AUTHOR
Jarl Underhaug
University of Bergen
jarl_dot_underhaug_at_gmail_dot_com
Updates by Jason Vertrees and Thomas Holder
USAGE
FocalBlur aperture=float, samples=int, ray=0/1, width=int, height=int
EXAMPELS
FocalBlur aperture=1, samples=100
FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
'''
# Formalize the parameter types
ray = (ray in ("True", "true", 1, "1"))
aperture, samples = float(aperture), int(samples)
width, height = int(width), int(height)
# Create a temporary directory
tmpdir = mkdtemp()
# Get the orientation of the protein and the light
light = cmd.get('light')[1:-1]
light = [float(s) for s in light.split(',')]
view = cmd.get_view()
# Rotate the protein and the light in order to create the blur
for frame in range(samples):
# Angles to rotate protein and light
# Populate angles as Fermat's spiral
theta = frame * pi * 110.0 / 144.0
radius = 0.5 * aperture * sqrt(frame / float(samples - 1))
x = cos(theta) * radius
y = sin(theta) * radius
xr = x / 180.0 * pi
yr = y / 180.0 * pi
# Rotate the protein
cmd.turn('x', x)
cmd.turn('y', y)
# Rotate the light
ly = light[1] * cos(xr) - light[2] * sin(xr)
lz = light[2] * cos(xr) + light[1] * sin(xr)
lx = light[0] * cos(yr) + lz * sin(yr)
lz = lz * cos(yr) - lx * sin(yr)
cmd.set('light', [lx, ly, lz])
curFile = "%s/frame-%04d.png" % (tmpdir, frame)
print("Created frame %i/%i (%0.0f%%)" % (frame + 1, samples, 100 * (frame + 1) / samples))
# Save the image to temporary directory
if ray:
cmd.ray(width, height)
cmd.png(curFile)
else:
cmd.png(curFile, quiet=1)
# Create the average/blured image
try:
avg = Image.blend(avg, Image.open(curFile), 1.0 / (frame + 1))
except:
avg = Image.open(curFile)
# Return the protein and the light to the original orientation
cmd.set('light', light)
cmd.set_view(view)
# Load the blured image
avg.save('%s/avg.png' % (tmpdir))
cmd.load('%s/avg.png' % (tmpdir))
# Delete the temporary files
rmtree(tmpdir)
cmd.pseudoatom('yatom', pos=[0, 2.5, 0], label="y")
cmd.pseudoatom('zatom', pos=[0, 0, 4.0], label="z")
cmd.set('ray_opaque_background', 'off')
cmd.set('transparency', 0.30)
#cmd.set_view ('\
# -0.086753346, 0.836276770, 0.541441798,\
# 0.670052588, -0.353231400, 0.652936995,\
# 0.737265468, 0.419426382, -0.529700875,\
# 0.000000000, 0.000000000, -34.167503357,\
# 0.108778238, 0.131587982, 1.662951946,\
# 26.937919617, 41.397087097, -20.000000000' )
#
cmd.set_view('\
-0.036295272, 0.997309446, 0.063655443,\
-0.180431277, -0.069193237, 0.981151760,\
0.982915938, 0.024127077, 0.182457983,\
0.000000000, 0.000000000, -42.977798462,\
0.235994816, 0.235994816, 0.235994816,\
33.884025574, 52.071571350, -20.000000000')
#cmd.pseudoatom('latom', pos=[3.5,-2.5,0], label="_label")
#cmd.pseudoatom('latom', pos=[-3,0,0], label=u"\u0394\u03C1'\u2081".encode('utf-8'))
cmd.pseudoatom('latom', pos=[-3, 0, 0], label=u"_label".encode('utf-8'))
cmd.ray(1200, 1200)
cmd.png('this.png', dpi=600)
cmd.quit()
lines = f.readlines()[1:]
for line in lines:
line_elements = line.strip().split(',')
site = int(line_elements[0])
neff = float(line_elements[-1])
neffs[site] = neff
# Determine the min and max entropy to set the range of the color scale
min_neff = min(neffs.values())
max_neff = max(neffs.values())
# Change each residue's B factor to its entropy value
for site in neffs:
cmd.alter("resi %d" % site, "b = %g" % neffs[site])
# Color the structure by B-factor values
cmd.spectrum('b', 'yellow_red', structure, minimum=min_neff, maximum=max_neff)
# set up view
cmd.set_view('-0.722045004, -0.058464222, -0.689368665, '
'0.598552346, 0.446926057, -0.664827526, '
'0.346962959, -0.892658830, -0.287708551, '
'0.000000000, 0.000000000, -119.305297852, '
'16.283113480, 28.784046173, 25.007221222, '
'91.323577881, 147.287002563, -20.000000000')
cmd.select('none')
cmd.ray(1600, 1200)
cmd.png('./results/prefs/structure_by_neff.png')
"""
A script that will execute a 360 degree spin of the structure, ray-tracing the
structure at each interval and saving the image.
"""
from pymol import cmd
import os.path
FRAMES = 360 # How many frames to spread the spin over
AXIS = 'y' # The axis about which to spin
OUTPUT = 'turn_ray_images' # The output directory for images
RAY_X = 1920 # The x-dimension of the image, 0 will use current window size
RAY_Y = 1080 # The y-dimension of the image, 0 will use current window size
os.mkdir(OUTPUT)
for i in xrange(FRAMES):
cmd.turn(AXIS, 360.0 / FRAMES)
cmd.ray(width=RAY_X, height=RAY_Y)
frame_name = '{0}.png'.format(str(i).zfill(4))
cmd.png(os.path.join(os.getcwd(), OUTPUT, frame_name))
def compare_10gs_11gs():
# it is possible to download proteins from RCSB (Protein Data Bank) to fetch_path, which is current working
# directory by default
cmd.set('fetch_path', cmd.exp_path(PATH_data))
cmd.fetch('10gs')
cmd.fetch('11gs')
cmd.load('{0}10gs.cif'.format(PATH_data), '10gs')
cmd.load('{0}11gs.cif'.format(PATH_data), '11gs')
# proteins
# pymol has several options for proteins alignment, align is better for proteins with high homology
align_command = cmd.align # or super, or cealign
align_res = align_command('10gs', '11gs')
if align_command == cmd.align:
print('aligned with rmsd {0}'.format(align_res[0]))
# cmd.create creates a separate object (copies everything to it)
# het stands for heteroatoms (non-protein)
cmd.create('10gs_protein', '10gs and not het')
cmd.create('11gs_protein', '11gs and not het')
# print protein sequences for fun
fasta_10gs = cmd.get_fastastr(selection='10gs_protein')
fasta_11gs = cmd.get_fastastr(selection='11gs_protein')
print('10gs sequence:{0}'.format(fasta_10gs))
print('11gs sequence:{0}'.format(fasta_11gs))
cmd.delete('*_protein') # delete objects
# ligands
cmd.select('10gs_ligands', '10gs and not resname HOH and het')
cmd.select('11gs_ligands', '11gs and not resname HOH and het')
space_10gs = {'lig_names': []} # or simpy lig_names = []
space_11gs = {'lig_names': []}
# strange pymol interface to iterate over atoms
cmd.iterate('10gs_ligands', 'lig_names.append(resn)', space=space_10gs)
cmd.iterate('11gs_ligands', 'lig_names.append(resn)', space=space_11gs)
ligs_10gs = set(space_10gs['lig_names'])
ligs_11gs = set(space_11gs['lig_names'])
# by the way, in both 10gs and 11gs we have MSE, which is actually a modified residue and not a ligand
print('ligands found in 10gs: {0}'.format(ligs_10gs))
print('ligands found in 11gs: {0}'.format(ligs_11gs))
for ligand_unique in ligs_10gs.symmetric_difference(ligs_11gs):
cmd.save(
'{0}{1}_{2}_ligand.sdf'.format(
PATH_data, '10gs' if ligand_unique in ligs_10gs else '11gs',
ligand_unique), 'resname {0}'.format(ligand_unique))
# deleting selection, objects remain unchanged
cmd.delete('ligs*')
print('drawing a figure (this will take some time)')
cmd.set('transparency_mode', 1)
cmd.bg_color('white')
cmd.show('sticks', 'het and not resname HOH')
cmd.color('white', 'not het')
cmd.show('surface', 'not het')
cmd.hide('lines')
cmd.set('transparency', '0.7')
cmd.show('spheres', 'resname HOH')
cmd.color('palecyan', 'resname HOH')
cmd.hide('nonbonded', 'resname HOH')
cmd.set('sphere_transparency', '0.7')
cmd.ray()
cmd.png('{0}fig.png'.format(PATH_data))
cutoff = 2
# Load the edges from file
with open(edgepath, 'r') as fin:
data = fin.readlines()
edges = [line.strip().split() for line in data]
for n, e in enumerate(edges):
t = cmd.dist('dist'+str(n),'3H4E//A/'+e[0]+'/CA',\
'3H4E//A/'+e[1]+'/CA')
if t < cutoff:
cmd.delete('dist' + str(n))
else:
cmd.color('blue', 'dist' + str(n))
cmd.hide('labels', 'dist' + str(n))
cmd.show('spheres', '3H4E//A/' + e[0] + '/CA')
cmd.show('spheres', '3H4E//A/' + e[1] + '/CA')
cmd.color('yellow', '3H4E//A/' + e[0] + '/CA')
cmd.color('yellow', '3H4E//A/' + e[1] + '/CA')
cmd.set('dash_radius', '0.2')
cmd.set('dash_gap', '0.0')
cmd.set('sphere_scale', '0.3')
#cmd.set('sphere_scale','0.8','retinal');
cmd.ray()
print('*' * 5 + 'Image:%s' % os.path.abspath(outfp) + '*' * 5)
cmd.png(os.path.abspath(outfp))
print '-------Completed Call--------'
def cheese(render_type,
savefile=None,
duration=5,
mode='ray',
width=1920,
height=1080):
"""
DESCRIPTION
loads nice settings for rendering and take a picture or records a movie of the trajectory.
Before running, position the camera to have a good point of view.
USAGE
cheese render_type [, savefile [, duration [, mode [, width [, height]]]]]
ARGUMENTS
render_type = one of:
- set: only load render settings
- snap: take a snapshot of the current view
- traj: record the whole trajectory
- bullettime: make a whole revolution around the z axis
savefile = file name to use to save the movie, without extension. If not given,
the movie won't be save but only shown (default=None)
duration = duration in seconds of the final movie (default=5)
mode = set to 'draw' to disable ray tracing (default='ray')
width = width of the movie in pixel (default=1920)
height = height of the movie in pixel (default=1080)
"""
duration = int(duration)
# # store settings for later restoration
# store_settings.load()
# cmd.sync()
# settings_file = '/tmp/stir_settings.py'
# cmd.do(f'store_settings {settings_file}')
# load nice settings for rendering
config.rendering()
cmd.sync()
def init_movie():
cmd.mdelete()
cmd.mview('reset')
frames = duration * 30
cmd.mset(f'1x{frames}')
return frames
# only load settings
if render_type == 'set':
return
# take a simple picture
elif render_type == 'snap':
cmd.ray(width=width, height=height)
# make a still movie of the whole trajectory
elif render_type == 'traj':
frames = init_movie()
cmd.mview('store', 1, state=1)
cmd.sync()
states = cmd.count_states()
cmd.mview('store', frames, state=states)
cmd.sync()
cmd.mview('reinterpolate')
cmd.sync()
# make a movie rotating 360 around the z axis
elif render_type == 'bullettime':
frames = init_movie()
cmd.mview('store', 1)
cmd.mview('store', frames)
# TODO: moving objects seems a bit hacky. Any better solution?
for obj in cmd.get_object_list():
cmd.mview('store', object=obj)
cmd.sync()
for i in range(4):
frame = int(frames * (i + 1) / 4)
cmd.frame(frame)
cmd.sync()
for obj in cmd.get_object_list():
cmd.rotate('z', angle=-90, camera=0, object=obj)
cmd.sync()
cmd.mview('store', object=obj)
cmd.sync()
cmd.mview('reinterpolate', object=obj, power=1)
cmd.sync()
cmd.mview('reinterpolate')
cmd.sync()
else:
raise ValueError(
f'{render_type} is not a valid argument. See `help cheese`.')
# save if required, otherwise just play it
if savefile:
if render_type in (
'traj',
'bullettime',
):
cmd.viewport(width, height)
movie.produce(f'{savefile}.mp4',
mode=mode,
encoder='ffmpeg',
quality=100)
elif render_type in ('snap', ):
cmd.png(f'{savefile}.png', dpi=300)
cmd.sync()
else:
if render_type in (
'traj',
'bullettime',
):
cmd.mplay()
elif render_type in ('snap', ):
pass
def save_image_default(filename):
cmd.bg_color("white")
cmd.ray(default_image_size(), default_image_size())
cmd.png("./output/" + filename + ".png", dpi=dpi())
cmd.bg_color("black")
return
values = inFile.readlines()
print values
# create the global, stored array
stored = []
# read the new B factors from file
for line in values: stored.append( float(line) )
print stored
max_b = max(stored)
min_b = min(stored)
cmd.bg_color("white")
print min_b
print max_b
# close the input file
inFile.close()
# clear out the old B Factors
cmd.alter("%s and n. CA"%pdb, "b=0.0")
# update the B Factors with new properties
cmd.alter("%s and n. CA"%pdb, "b=stored.pop(0)")
# color the protein based on the new B Factors of the alpha carbons
cmd.spectrum("b", "rainbow", "%s and n. CA"%pdb, minimum=min_b, maximum=max_b)
cmd.ray("775", "2400")
cmd.png("unscaled%s.png"%infilename.split("_")[0])
A = AggregatTransferFromFile(fname)
cmd.set_view ([
-0.480811268, 0.603387773, 0.636203885,
0.675508440, 0.717507422, -0.169974893,
-0.559037924, 0.348030269, -0.752567112,
-0.000127681, 0.000030167, -122.974456787,
13.921709061, -7.469791889, -4.264435768,
-1086.176879883, 1332.132446289, -20.000000000])
# select only a few sample points
indices = [0, 250, 500, 1000, 1999]
t = np.linspace(0, A._tLength, A._tSteps)[indices]
# Get values ordered by time in first index
values = np.swapaxes(A.get(), 0, 1)[indices]
selections = ['lab{}'.format(i + 1) for i in range(8)]
for lab in selections:
cmd.label(lab, '')
selections = ['bcl{}'.format(i + 1) for i in range(7)]
for i, val in enumerate(values):
alpha = p_to_alpha(val)
for n, bcl in enumerate(selections):
cmd.set_bond('stick_transparency', alpha[n], bcl)
cmd.refresh()
cmd.ray(width, height)
print('Belongs to time {}'.format(t[i] * 5.20883746))
cmd.png('../fmo_transfer_{}.png'.format(i), dpi=DPI, ray=1)
def save_image_filament(filename):
cmd.bg_color("white")
cmd.ray(ray_width_filament(), ray_height_filament())
cmd.png("./output/" + filename + ".png", dpi=dpi())
cmd.bg_color("black")
return
def setray0():
cmd.set("ray_trace_mode", "0")
cmd.ray()
def setray2():
cmd.set("ray_trace_mode", "2")
cmd.bg_color('white')
cmd.ray()
def setray3():
cmd.set("ray_trace_mode", "3")
cmd.ray()
for i in range(5):
cmd.load("./PDBs-%d/State%d-%d.pdb" % (p_id, stateid, i))
for i in range(5):
cmd.align("State%d-%d" % (stateid, i),
"State%d-%d" % (stateid, ref_state_id))
#alignto does the same thing as the above loop, but it sometimes could cause problem
#cmd.alignto("State%d-0"%stateid)
cmd.show("cartoon")
cmd.hide("lines", "!State%d-%d" % (stateid, ref_state_id))
cmd.center("all")
cmd.set("cartoon_transparency", 0.7, "all")
cmd.set("cartoon_transparency", 0, "State%d-%d" % (stateid, ref_state_id))
cmd.util.chainbow("all")
cmd.util.cnc("all")
cmd.orient()
cmd.util.performance(0)
cmd.set("ray_opaque_background", "off")
cmd.ray()
png_fn = os.path.join(outdir, "image-p%d-state-%d.png" % (p_id, stateid))
high_res_state = [0, 1, 2, 4, 11, 12, 13, 20, 28, 30]
if stateid in high_res_state:
png_fn = os.path.join(outdir,
"image-p%d-state-%d-highres.png" % (p_id, stateid))
cmd.ray(2400, 1800)
cmd.png(png_fn, dpi=300)
else:
cmd.png(png_fn)
cmd.quit()
def pubimage_tmblr(*argumenthere, **kwd):
'''Takes an image with the specified properties. The properties should be entered in the following order:
ray_trace_mode, antialias, ray width, ray height, bg_color
If not specified, then the properties default to
ray_trace_mode (int 1-3) --> 3
antialias (int 0-2) --> 2
raynum1, raynum2 (int) --> ray 1200, 1200
bg_color (string) --> white
'''
# The following is for debugging:
# argumenthere[0] (int 1-3) --> ray_trace_mode (int)
# argumenthere[1] (int 0-2) --> antialias (int)
# argumenthere[2], argumenthere[3] (int) --> ray num1, num2 (int)
# argumenthere[4] (string) --> bg_color (string)
global iternum
#Setting ray_trace_mode
try:
cmd.set('ray_trace_mode',
value=int(argumenthere[0]),
selection='',
state=0,
updates=1,
log=0,
quiet=1)
except IndexError:
cmd.set('ray_trace_mode', 3)
#Setting antialias
try:
cmd.set('antialias',
int(argumenthere[1]),
selection='',
state=0,
updates=1,
log=0,
quiet=1)
except IndexError:
cmd.set('antialias', 2)
#Setting bg_color
try:
cmd.bg_color(argumenthere[4])
except IndexError:
cmd.bg_color('white')
#CENTER IMAGE TAKING AND ROTATION
#Ray the image
try:
cmd.ray(width=int(argumenthere[2]),
height=int(argumenthere[3]),
antialias=-1,
angle=0.0,
shift=0.0,
renderer=-1,
quiet=1,
async=0)
except IndexError:
cmd.ray(width=1200, height=1200)
#Save the Image
try:
cmd.png('molecule' + str(iternum) + 'center.png')
except IndexError:
cmd.png('molecule' + str(iternum) + 'center.png')
cmd.turn('x', 90.0)
#TOP-DOWN IMAGE TAKING AND ROTATION
#Ray the image
try:
cmd.ray(width=int(argumenthere[2]),
height=int(argumenthere[3]),
antialias=-1,
angle=0.0,
shift=0.0,
renderer=-1,
quiet=1,
async=0)
except IndexError:
cmd.ray(width=1200, height=1200)
#Save the Image
try:
cmd.png('molecule' + str(iternum) + 'topdown.png')
except IndexError:
cmd.png('molecule' + str(iternum) + 'topdown.png')
cmd.turn('x', -180.0)
#BOTTOM-UP IMAGE TAKING AND ROTATION
#Ray the image
try:
cmd.ray(width=int(argumenthere[2]),
height=int(argumenthere[3]),
antialias=-1,
angle=0.0,
shift=0.0,
renderer=-1,
quiet=1,
async=0)
except IndexError:
cmd.ray(width=1200, height=1200)
#Save the Image
try:
cmd.png('molecule' + str(iternum) + 'bottomup.png')
except IndexError:
cmd.png('molecule' + str(iternum) + 'bottomup.png')
cmd.turn('x', 90.0)
cmd.turn('y', 90.0)
#LEFT IMAGE TAKING AND ROTATION
#Ray the image
try:
cmd.ray(width=int(argumenthere[2]),
height=int(argumenthere[3]),
antialias=-1,
angle=0.0,
shift=0.0,
renderer=-1,
quiet=1,
async=0)
except IndexError:
cmd.ray(width=1200, height=1200)
#Save the Image
try:
cmd.png('molecule' + str(iternum) + 'left.png')
except IndexError:
cmd.png('molecule' + str(iternum) + 'left.png')
cmd.turn('y', -180.0)
#RIGHT IMAGE TAKING AND ROTATION
#Ray the image
try:
cmd.ray(width=int(argumenthere[2]),
height=int(argumenthere[3]),
antialias=-1,
angle=0.0,
shift=0.0,
renderer=-1,
quiet=1,
async=0)
except IndexError:
cmd.ray(width=1200, height=1200)
#Save the Image
try:
cmd.png('molecule' + str(iternum) + 'right.png')
except IndexError:
cmd.png('molecule' + str(iternum) + 'right.png')
cmd.turn('y', 90.0)
iternum += 1