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()
print "done"
# Align all states
cmd.intra_fit('all')
cmd.hide('all')
#cmd.rewind()
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('spheres', 'receptor')
util.cbaw('receptor')
cmd.show('spheres', 'ligand')
cmd.show('spheres', 'ions')
util.cbay('ligand')
cmd.color('green', 'receptor')
#cmd.show('surface', 'receptor')
#cmd.set('transparency', 0.65)
#cmd.set('surface_mode', 3)
#cmd.set('surface_color', 'white')
# QuteMol-like
cmd.bg_color('white')
cmd.set('light_count', 8)
cmd.set('spec_count', 1)
# Load PDB file into PyMOL
cmd.set('suspend_updates', 'on')
cmd.set('retain_order', 1)
cmd.load(pdb_temporary_filename, object='system')
cmd.hide('all')
print('selecting solute...')
print(cmd.select('solute', '(not resn WAT) and (not resn HOH) and (not hydrogen)'))
cmd.select('water', 'resn WAT')
cmd.deselect()
#cmd.show('cartoon', 'solute')
#cmd.color('white', 'solute')
cmd.orient('solute')
util.cbaw('solute')
if solute == 'dna':
cmd.show('sticks', 'solute') # DNA
else:
cmd.show('cartoon', 'solute') # DNA
# speed up builds
cmd.set('defer_builds_mode', 3)
cmd.set('cache_frames', 0)
cmd.cache('disable')
cmd.set('async_builds', 1)
cmd.set('ray_transparency_contrast', 3.0)
cmd.set('ray_transparency_shadows', 0)
model = cmd.get_model('system')
# Aim 3 : benzotriazoles (green)
fragments = ['x10820', 'x10871', 'x10876']
for fragment in fragments:
cmd.load(path + f'Mpro-{fragment}_0A_bound-ligand.mol2',
f'benzotriazoles-{fragment}-ligand')
cmd.load(path + f'Mpro-{fragment}_0A_bound-protein.pdb',
f'benzotriazoles-{fragment}-protein')
util.cbag(f'benzotriazoles-*')
# N3 ligand (white)
cmd.load('6lu7.pdb')
cmd.align('(6lu7 and chain A)', 'aminopyridines-x10237-protein')
cmd.select('N3-ligand', '6lu7 and chain C')
cmd.select('N3-protein', '6lu7 and (chain A or chain B)')
util.cbaw('N3-ligand')
# All fragments
show_fragments = False
if show_fragments:
files = glob(f'{path}/Mpro-x*.mol2')
for filename in files:
print(filename)
match = re.search('Mpro-(?P<fragment>x\d+)_', filename)
fragment = match.group('fragment')
cmd.load(filename, f'fragment-{fragment}')
cmd.select('fragments', 'fragments-*')
# remove waters
cmd.remove('resn HOH')
cmd.deselect()
print "done"
# Align all states
cmd.intra_fit('all')
cmd.hide('all')
#cmd.rewind()
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('spheres', 'receptor')
util.cbaw('receptor')
cmd.show('spheres', 'ligand')
cmd.show('spheres', 'ions')
util.cbay('ligand')
cmd.color('green', 'receptor')
#cmd.show('surface', 'receptor')
#cmd.set('transparency', 0.65)
#cmd.set('surface_mode', 3)
#cmd.set('surface_color', 'white')
# QuteMol-like
cmd.bg_color('white')
cmd.set('light_count',8)
cmd.set('spec_count',1)
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)
