def anime(self, cleanup=0):
self.interrupt = cleanup
suspend_undo = self.cmd.get("suspend_undo")
self.cmd.set("suspend_undo", 1, updates=0)
if not cleanup:
try:
self.cmd.set("suspend_updates", 1, quiet=1)
self.cmd.disable()
self.cmd.load("$TUT/1hpv.pdb")
util.chainbow("1hpv", _self=self.cmd)
self.cmd.hide("everything", "1hpv")
self.cmd.show("cartoon", "1hpv")
self.cmd.show("sticks", "1hpv///200/")
self.cmd.create("1hpv_a", "1hpv//A//")
self.cmd.set("cartoon_smooth_loops", 0, "1hpv_a")
self.cmd.create("1hpv_b", "1hpv//B//")
self.cmd.set("cartoon_smooth_loops", 0, "1hpv_b")
self.cmd.create("1hpv_l", "1hpv///200/")
util.cbay("1hpv_l", _self=self.cmd)
self.cmd.delete("1hpv")
self.cmd.set_view ((\
0.374249548, -0.517475128, 0.769516647,\
-0.214397043, -0.855623126, -0.471108317,\
0.902203023, 0.011330833, -0.431161582,\
-0.000023194, -0.000007302, -125.089942932,\
11.953758240, 20.323493958, 8.406080246,\
75.304412842, 189.396347046, 0.000000000 ))
self.cmd.translate([-20, 0, 0], object="1hpv_a")
self.cmd.translate([20, 0, 0], object="1hpv_b")
self.cmd.zoom("center", 30)
self.cmd.translate([0, 10, 00], object="1hpv_l")
finally:
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.refresh()
for a in range(1, 21):
if self.interrupt:
break
try:
self.cmd.set("suspend_updates", 1, quiet=1)
self.cmd.translate([1, 0, 0], object="1hpv_a")
self.cmd.translate([-1, 0, 0], object="1hpv_b")
self.cmd.translate([0, -0.5, 0], object="1hpv_l")
finally:
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.refresh()
for a in range(1, 62):
if self.interrupt:
break
self.cmd.turn("y", 6)
self.cmd.move('z', 2)
self.cmd.move('y', -0.12)
self.cmd.refresh()
else:
self.cmd.delete("1hpv_*")
self.cmd.set("suspend_undo", suspend_undo, updates=0)
def anime(self,cleanup=0):
if not cleanup:
try:
self.cmd.set("suspend_updates",1,quiet=1)
self.cmd.disable()
self.cmd.load("$TUT/1hpv.pdb")
util.chainbow("1hpv",_self=self.cmd)
self.cmd.hide("everything","1hpv")
self.cmd.show("cartoon","1hpv")
self.cmd.show("sticks","1hpv///200/")
self.cmd.create("1hpv_a","1hpv//A//")
self.cmd.set("cartoon_smooth_loops",0,"1hpv_a")
self.cmd.create("1hpv_b","1hpv//B//")
self.cmd.set("cartoon_smooth_loops",0,"1hpv_b")
self.cmd.create("1hpv_l","1hpv///200/")
util.cbay("1hpv_l",_self=self.cmd)
self.cmd.delete("1hpv")
self.cmd.set_view ((\
0.374249548, -0.517475128, 0.769516647,\
-0.214397043, -0.855623126, -0.471108317,\
0.902203023, 0.011330833, -0.431161582,\
-0.000023194, -0.000007302, -125.089942932,\
11.953758240, 20.323493958, 8.406080246,\
75.304412842, 189.396347046, 0.000000000 ))
self.cmd.translate([-20,0,0],object="1hpv_a")
self.cmd.translate([20,0,0],object="1hpv_b")
self.cmd.zoom("center",30)
self.cmd.translate([0,10,00],object="1hpv_l")
finally:
self.cmd.set("suspend_updates",0,quiet=1)
self.cmd.refresh()
for a in range(1,21):
try:
self.cmd.set("suspend_updates",1,quiet=1)
self.cmd.translate([1,0,0],object="1hpv_a")
self.cmd.translate([-1,0,0],object="1hpv_b")
self.cmd.translate([0,-0.5,0],object="1hpv_l")
finally:
self.cmd.set("suspend_updates",0,quiet=1)
self.cmd.refresh()
for a in range(1,62):
self.cmd.turn("y",6)
self.cmd.move('z',2)
self.cmd.move('y',-0.12)
self.cmd.refresh()
else:
self.cmd.delete("1hpv_*")
# Load PDB file.
cmd.rewind()
cmd.delete('all')
cmd.reset()
cmd.load(reference_pdbfile, 'complex')
cmd.remove('resn WAT') # remove waters
cmd.select('receptor', '(not resn MOL) and (not resn WAT) and (not hydrogen)')
cmd.select('ligand', 'resn MOL and not hydrogen')
cmd.select('ions', 'resn Na\+ or resn Cl\-')
cmd.deselect()
cmd.hide('all')
cmd.show('cartoon', 'receptor')
cmd.show('spheres', 'ligand')
cmd.show('spheres', 'ions')
util.cbay('ligand')
cmd.color('green', 'receptor')
# speed up builds
cmd.set('defer_builds_mode', 3)
cmd.set('cache_frames', 0)
cmd.set('ray_transparency_contrast', 3.0)
cmd.set('ray_transparency_shadows', 0)
model = cmd.get_model('complex')
#for atom in model.atom:
# print "%8d %4s %3s %5d %8.3f %8.3f %8.3f" % (atom.index, atom.name, atom.resn, int(atom.resi), atom.coord[0], atom.coord[1], atom.coord[2])
#pymol.finish_launching()
phase = 'complex-implicit'
replica = 0 # replica index to render
#replica = 15 # replica index to render
# Load PDB file.
cmd.rewind()
cmd.delete('all')
cmd.reset()
cmd.load(reference_pdbfile, 'complex')
cmd.select('receptor', 'not chain C and not hydrogen')
cmd.select('ligand', 'chain C and not hydrogen')
cmd.deselect()
cmd.hide('all')
cmd.show('cartoon', 'receptor')
cmd.show('sticks', 'ligand')
util.cbay('ligand')
cmd.color('green', 'receptor')
# speed up builds
cmd.set('defer_builds_mode', 3)
cmd.set('cache_frames', 0)
model = cmd.get_model('complex')
#for atom in model.atom:
# print "%8d %4s %3s %5d %8.3f %8.3f %8.3f" % (atom.index, atom.name, atom.resn, int(atom.resi), atom.coord[0], atom.coord[1], atom.coord[2])
# Read atoms from PDB
pdbatoms = readAtomsFromPDB(reference_pdbfile)
# Build mappings.
pdb_indices = dict()
def reps(self, cleanup=0):
rep_list = [
"lines", "sticks", "spheres", "surface", "mesh", "dots", "ribbon",
"cartoon"
]
try:
if not cleanup:
self.cmd.disable()
self.cmd.set("suspend_updates", 1, quiet=1)
self.cmd.mset()
self.cmd.set("movie_panel", 0)
self.cmd.load("$PYMOL_DATA/demo/pept.pdb", "rep1")
self.cmd.alter("rep1///1-5+8-13/", "ss='S'")
self.cmd.cartoon("auto")
self.cmd.hide("everything", "rep1")
for a in range(2, 9):
self.cmd.create("rep%d" % a, "rep1")
for y, x in enumerate(rep_list, 1):
self.cmd.show(x, "rep%d" % y)
self.cmd.reset()
self.cmd.zoom("rep1", 24)
util.cbay("rep2", _self=self.cmd)
util.cbac("rep3", _self=self.cmd)
util.cbas("rep4", _self=self.cmd)
util.cbab("rep5", _self=self.cmd)
util.cbaw("rep6", _self=self.cmd)
util.cbay("rep8", _self=self.cmd)
self.cmd.set("suspend_updates", 0, quiet=1)
scale = 0.5
for b in range(1, 20):
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.refresh()
self.cmd.set("suspend_updates", 1, quiet=1)
xt = -3.2
yt = 1.6
for a in range(1, 5):
self.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):
self.cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
for a in range(1, 9):
self.cmd.origin("rep%d" % a, object="rep%d" % a)
self.cmd.mset("1")
st = ' '.join("rotate angle=-3,object=rep%d,axis=%s;" %
(x, 'yx'[x % 2]) for x in range(1, 9))
self.cmd.mdo(1, st)
self.cmd.set("suspend_updates", 0, quiet=1)
self.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 = self.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)
self.cmd.set("cgo_line_width", 1.5)
self.cmd.set("auto_zoom", 0)
self.cmd.load_cgo(cgo, 'reps')
self.cmd.set("auto_zoom", 1)
else:
self.cmd.delete("rep*")
self.cmd.mset()
self.cmd.mstop()
self.cmd.set("movie_panel", 1)
except:
traceback.print_exc()
def reps(self,cleanup=0):
rep_list = [ "lines","sticks","spheres","surface","mesh","dots","ribbon","cartoon" ]
try:
if not cleanup:
self.cmd.disable()
self.cmd.set("suspend_updates",1,quiet=1)
self.cmd.mset()
self.cmd.unset("movie_panel")
self.cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
self.cmd.alter("rep1///1-5+8-13/","ss='S'")
self.cmd.cartoon("auto")
self.cmd.hide("everything","rep1")
for a in range(2,9):
self.cmd.create("rep%d"%a,"rep1")
map(lambda x,y,s=self:s.cmd.show(x,"rep%d"%y),
rep_list,
range(1,9))
self.cmd.reset()
self.cmd.zoom("rep1",24)
util.cbay("rep2",_self=self.cmd)
util.cbac("rep3",_self=self.cmd)
util.cbas("rep4",_self=self.cmd)
util.cbab("rep5",_self=self.cmd)
util.cbaw("rep6",_self=self.cmd)
util.cbay("rep8",_self=self.cmd)
self.cmd.set("suspend_updates",0,quiet=1)
scale=0.5
for b in range(1,20):
self.cmd.set("suspend_updates",0,quiet=1)
self.cmd.refresh()
self.cmd.set("suspend_updates",1,quiet=1)
xt=-3.2
yt=1.6
for a in range(1,5):
self.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):
self.cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
for a in range(1,9):
self.cmd.origin("rep%d"%a,object="rep%d"%a)
self.cmd.mset("1")
st = string.join(map(lambda x,y:"rotate angle=-3,object=rep%d,axis=%s;"%(x,y),range(1,9),
['x','y','x','y','x','y','x','y']))
self.cmd.mdo(1,st)
self.cmd.set("suspend_updates",0,quiet=1)
self.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 = self.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)
self.cmd.set("cgo_line_width",1.5)
self.cmd.set("auto_zoom",0)
self.cmd.load_cgo(cgo,'reps')
self.cmd.set("auto_zoom",1)
else:
self.cmd.delete("rep*")
self.cmd.mset()
self.cmd.mstop()
self.cmd.set("movie_panel",1)
except:
traceback.print_exc()
def reps(self, cleanup=0):
rep_list = [
"lines", "sticks", "spheres", "surface", "mesh", "dots", "ribbon",
"cartoon"
]
suspend_undo = self.cmd.get("suspend_undo")
self.cmd.set("suspend_undo", 1, updates=0)
try:
if not cleanup:
self.cmd.disable()
self.cmd.set("suspend_updates", 1, quiet=1)
self.cmd.mset()
self.cmd.set("movie_panel", 0)
self.cmd.load("$PYMOL_DATA/demo/pept.pdb", "rep1")
self.cmd.alter("rep1///1-5+8-13/", "ss='S'")
self.cmd.cartoon("auto")
self.cmd.hide("everything", "rep1")
for a in range(2, 9):
self.cmd.create("rep%d" % a, "rep1")
for y, x in enumerate(rep_list, 1):
self.cmd.show(x, "rep%d" % y)
self.cmd.reset()
self.cmd.zoom("rep1", 24)
util.cbay("rep2", _self=self.cmd)
util.cbac("rep3", _self=self.cmd)
util.cbas("rep4", _self=self.cmd)
util.cbab("rep5", _self=self.cmd)
util.cbaw("rep6", _self=self.cmd)
util.cbay("rep8", _self=self.cmd)
self.cmd.set("suspend_updates", 0, quiet=1)
scale = 0.5
for b in range(1, 20):
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.refresh()
self.cmd.set("suspend_updates", 1, quiet=1)
xt = -3.2
yt = 1.4
for a in range(1, 5):
self.cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
yt = -2.
xt = -3.2
for a in range(5, 9):
self.cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
for a in range(1, 9):
self.cmd.origin("rep%d" % a, object="rep%d" % a)
self.cmd.mset("1")
st = ' '.join("rotate angle=-3,object=rep%d,axis=%s;" %
(x, 'yx'[x % 2]) for x in range(1, 9))
self.cmd.mdo(1, st)
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.mplay()
axes = [[4.5, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]
c = 1
self.cmd.set("suspend_updates", 1, quiet=1)
for a in rep_list:
ext = self.cmd.get_extent("rep%d" % c)
pos = [(ext[0][0] + ext[1][0]) / 2,
(ext[0][1] + ext[1][1]) / 2 + 16,
(ext[0][2] + ext[1][2]) / 2]
c = c + 1
self.cmd.pseudoatom("reps", label=str(a), pos=pos)
self.cmd.set("label_size", 24, "reps")
self.cmd.set("suspend_updates", 0, quiet=1)
else:
self.cmd.delete("rep*")
self.cmd.mset()
self.cmd.mstop()
self.cmd.set("movie_panel", 1)
except cmd.QuietException:
# in case of hopping to the next demo
pass
except:
traceback.print_exc()
finally:
self.cmd.set("suspend_updates", 0, quiet=1)
self.cmd.set("suspend_undo", suspend_undo, updates=0)
# Recognize helices and sheets
cmd.dss()
# Align everything
cmd.intra_fit("all")
# Set up display
cmd.remove("resn WAT") # remove waters
cmd.select("receptor", "(not resn MOL) and (not resn WAT) and (not hydrogen)")
cmd.select("ligand", "resn MOL")
cmd.deselect()
cmd.hide("all")
cmd.show("cartoon", "receptor")
cmd.show("spheres", "ligand")
util.cbay("ligand")
cmd.color("green", "receptor")
# Show surface
# cmd.show('surface', 'receptor')
# cmd.set('surface_color', 'white')
# cmd.set('surface_mode', 3)
# cmd.set('transparency', 0.65)
# cmd.set('surface_quality', 1)
# speed up builds
cmd.set("defer_builds_mode", 3)
cmd.set("cache_frames", 0)
cmd.set("antialias", 2)
# Rewind
