def update_selections(self):
if self.status == HAVE_SELECTIONS:
if self.mode == 'by_resi':
self.cmd.select(
free_sele, "((byobj %s) and byres ((%s) x; %8.3f))" %
(cent_sele, cent_sele, self.radius))
self.cmd.select(
fix_sele,
"((byobj %s) and (not %s) and byres ((%s) x; %8.3f))" %
(cent_sele, free_sele, cent_sele,
self.radius + self.cushion))
self.cmd.select(
excl_sele, "((byobj %s) and (not (%s|%s)))" %
(cent_sele, free_sele, fix_sele))
elif self.mode == 'ligand_rx':
self.cmd.select(
free_sele,
"((byobj %s) and byres (%s))" % (cent_sele, cent_sele))
self.cmd.select(
fix_sele,
"((byobj %s) and (not %s) and byres ((%s) x; %8.3f))" %
(cent_sele, free_sele, free_sele, self.cushion))
self.cmd.select(
excl_sele, "((byobj %s) and (not (%s|%s)))" %
(cent_sele, free_sele, fix_sele))
self.cmd.protect("(byobj %s)" % cent_sele)
self.cmd.deprotect(free_sele)
self.cmd.flag('exclude', "(byobj %s)" % cent_sele, "clear")
self.cmd.flag('exclude', excl_sele, "set")
self.cmd.color('grey', excl_sele)
self.cmd.unmask("(byobj %s)" % cent_sele)
self.cmd.mask(excl_sele)
self.cmd.mask(fix_sele)
self.cmd.zoom(free_sele, 3, animate=1)
util.cbac(fix_sele, _self=self.cmd)
util.cbag(free_sele, _self=self.cmd)
self.cmd.disable('indicate')
self.cmd.disable(cent_sele)
self.cmd.disable(free_sele)
self.cmd.disable(fix_sele)
self.cmd.disable(excl_sele)
self.cmd.unpick()
for obj in self.cmd.get_names(selection=cent_sele):
self.cmd.push_undo(obj)
self.cmd.sculpt_activate(obj)
def update_selections(self):
if self.status == HAVE_SELECTIONS:
if self.mode=='by_resi':
self.cmd.select(free_sele,"((byobj %s) and byres ((%s) x; %8.3f))"%
(cent_sele,cent_sele,self.radius))
self.cmd.select(fix_sele,"((byobj %s) and (not %s) and byres ((%s) x; %8.3f))"%
(cent_sele,free_sele,cent_sele,self.radius+self.cushion))
self.cmd.select(excl_sele,"((byobj %s) and (not (%s|%s)))"%
(cent_sele,free_sele,fix_sele))
elif self.mode=='ligand_rx':
self.cmd.select(free_sele,"((byobj %s) and byres (%s))"%
(cent_sele,cent_sele))
self.cmd.select(fix_sele,"((byobj %s) and (not %s) and byres ((%s) x; %8.3f))"%
(cent_sele,free_sele,free_sele,self.cushion))
self.cmd.select(excl_sele,"((byobj %s) and (not (%s|%s)))"%
(cent_sele,free_sele,fix_sele))
self.cmd.protect("(byobj %s)"%cent_sele)
self.cmd.deprotect(free_sele)
self.cmd.flag('exclude',"(byobj %s)"%cent_sele,"clear")
self.cmd.flag('exclude',excl_sele,"set")
self.cmd.color('grey',excl_sele)
self.cmd.unmask("(byobj %s)"%cent_sele)
self.cmd.mask(excl_sele)
self.cmd.mask(fix_sele)
self.cmd.zoom(free_sele,3,animate=1)
util.cbac(fix_sele,_self=self.cmd)
util.cbag(free_sele,_self=self.cmd)
self.cmd.disable('indicate')
self.cmd.disable(cent_sele)
self.cmd.disable(free_sele)
self.cmd.disable(fix_sele)
self.cmd.disable(excl_sele)
self.cmd.unpick()
for obj in self.cmd.get_names(selection=cent_sele):
self.cmd.push_undo(obj)
self.cmd.sculpt_activate(obj)
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 setup_contexts(context_info): # Author: Warren DeLano
(list, dict) = context_info[0:2]
key_list = [
'F1',
'F2',
'F3',
'F4',
'F5',
'F6',
'F7',
'F8',
'F9',
'F10', #,'F11','F12',
'SHFT-F1',
'SHFT-F2',
'SHFT-F3',
'SHFT-F4',
'SHFT-F5',
'SHFT-F6',
'SHFT-F7',
'SHFT-F8',
'SHFT-F9',
'SHFT-F10'
] # ,'SHFT-F11','SHFT-F12']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_labels)
doc_list.append(key + ": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, lambda: (cmd.zoom(), toggle_labels(0)))
doc_list.append(key + ": Zoom All")
for a in list:
water = a + "_water"
ligand = a + "_ligand"
site = a + "_site"
hbond = a + "_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded", water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks", ligand)
cmd.hide("cartoon", ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks", site)
util.cbac(site)
zoom_list.append(site)
# replace cartoon with explicit atoms for "site" atoms
cmd.hide("cartoon", site)
cmd.show(
"sticks",
"(byres (neighbor (" + site + " and name C))) and name N+CA")
cmd.show(
"sticks",
"(byres (neighbor (" + site + " and name N))) and name C+CA+O")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = ' or '.join(zoom_list)
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0, 1):
zoom_context = 0
cmd.set_key(key, lambda x=zoom_str: (cmd.zoom(x)))
mo = re.search("_([^_]+)$", a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key + ": Zoom " + cont_name)
if hbond in name_list:
cmd.show("dashes", hbond)
cmd.show("labels", hbond)
cmd.wizard("fedora", doc_list)
if zoom_context not in (0, 1):
cmd.zoom(zoom_context)
toggle_labels(0)
# cmd.feedback("enable","python","output")
cmd.feedback("enable", "objectmolecule", "results")
cmd.feedback("disable", "selector", "actions")
cmd.feedback("disable", "scene", "actions")
cmd.set("internal_feedback", 1)
cmd.set("internal_prompt", 0)
cmd.reset()
cmd.delete('all')
path = "/Users/choderaj/github/foldingathome/covid-moonshot/receptors/monomer/"
# Aim 1 : 3-aminopyridines (cyan)
fragments = [
'x2646', 'x10201', 'x10387', 'x10789', 'x10019', 'x10236', 'x10237',
'x10959'
]
for fragment in fragments:
cmd.load(path + f'Mpro-{fragment}_0A_bound-ligand.mol2',
f'aminopyridines-{fragment}-ligand')
cmd.load(path + f'Mpro-{fragment}_0A_bound-protein.pdb',
f'aminopyridines-{fragment}-protein')
util.cbac(f'aminopyridines-*')
# Aim 2 : quinolones (magenta)
fragments = ['x2910', 'x3080', 'x3303']
for fragment in fragments:
cmd.load(path + f'Mpro-{fragment}_0A_bound-ligand.mol2',
f'quinolones-{fragment}-ligand')
cmd.load(path + f'Mpro-{fragment}_0A_bound-protein.pdb',
f'quinolones-{fragment}-protein')
util.cbam(f'quinolones-*')
# 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')
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)
def setup_contexts(context_info): # Author: Warren DeLano
(list,dict) = context_info[0:2]
key_list = [
'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12',
'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,lambda :(cmd.zoom(),toggle_labels(0)))
doc_list.append(key+": Zoom All")
for a in list:
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded",water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks",ligand)
cmd.hide("cartoon",ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks",site)
util.cbac(site)
zoom_list.append(site)
# replace cartoon with explicit atoms for "site" atoms
cmd.hide("cartoon",site)
cmd.show("sticks","(byres (neighbor ("+site+" and name c))) and name n+ca")
cmd.show("sticks","(byres (neighbor ("+site+" and name n))) and name c+ca+o")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = string.join(zoom_list,' or ')
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0,1):
zoom_context = 0
cmd.set_key(key,lambda x=zoom_str:(cmd.zoom(x)))
mo = re.search("_([^_]+)$",a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key+": Zoom "+cont_name)
if hbond in name_list:
cmd.show("dashes",hbond)
cmd.show("labels",hbond)
cmd.wizard("fedora",doc_list)
if zoom_context not in (0,1):
cmd.zoom(zoom_context)
toggle_labels(0)
# cmd.feedback("enable","python","output")
cmd.feedback("enable","objectmolecule","results")
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",0)
