def loadBR(pdb, saveName=None, color=None):
if not saveName:
saveName = pdb.split('.')[0]
cmd.load(pdb, saveName)
if color: cmd.color(color, saveName)
cmd.hide("lines")
cmd.hide("nonbonded")
# cmd.show("cartoon")
cmd.show("ribbon")
cmd.set("cartoon_transparency", 0.7)
keyResidues = ["ASPA0085", "ARGA0082", "GLUA0194", "GLUA0204", "LYSA0216", "RET", "ASPA0212"]
for eachRes in keyResidues:
# retinal's residue sequence id can vary in different pdbs.
selection = ""
if eachRes == "RET":
selection = "resn ret"
else:
selection = parseResidue(eachRes)
selection += " and not name c+o+n"
cmd.show("sticks", selection)
util.cbag(selection)
def DisplayLigand(self):
try:
cmd.set("auto_zoom", 0)
cmd.load(self.RefLigand, self.LigDisplay, state=self.State)
cmd.refresh()
# Display the atoms spheres
cmd.show('spheres', self.LigDisplay)
cmd.refresh()
cmd.alter(self.LigDisplay,'vdw=0.25')
cmd.rebuild(self.LigDisplay)
cmd.refresh()
util.cbag(self.LigDisplay)
cmd.refresh()
cmd.translate(self.Translation,self.LigDisplay)
cmd.refresh()
cmd.zoom(self.LigDisplay)
cmd.refresh()
except:
self.ErrorCode = 1
cmd.set("auto_zoom", self.auto_zoom)
return self.ErrorCode
def RefreshDisplay(self):
try:
# Display the atoms spheres
cmd.show('spheres', self.LigDisplay)
cmd.refresh()
cmd.alter(self.LigDisplay,'vdw=0.25')
cmd.rebuild(self.LigDisplay)
cmd.refresh()
util.cbag(self.LigDisplay)
cmd.refresh()
if self.AnchorAtom != -1:
AtomSel = self.LigDisplay + ' & id ' + str(self.AnchorAtom)
cmd.color('white',AtomSel)
cmd.refresh()
cmd.alter(AtomSel ,'vdw=0.30')
cmd.rebuild(AtomSel)
cmd.refresh()
except:
self.ErrorCode = 1
return self.ErrorCode
def RefreshDisplay(self):
try:
# Display the atoms spheres
cmd.show('spheres', self.LigDisplay)
cmd.refresh()
cmd.alter(self.LigDisplay, 'vdw=0.25')
cmd.rebuild(self.LigDisplay)
cmd.refresh()
util.cbag(self.LigDisplay)
cmd.refresh()
if self.AnchorAtom != -1:
AtomSel = self.LigDisplay + ' & id ' + str(self.AnchorAtom)
cmd.color('white', AtomSel)
cmd.refresh()
cmd.alter(AtomSel, 'vdw=0.30')
cmd.rebuild(AtomSel)
cmd.refresh()
except:
self.ErrorCode = 1
return self.ErrorCode
def show_ligand_interactions(recsel="not hetatm", ligsel="hetatm", cutoff=5):
"""
DESCRIPTION
Visualize interactions between receptor and ligand.
ARGUMENTS
recsel = string: atom selection of the receptor {default: "not hetatm"}
ligsel = string: atom selections of the ligand {default: "hetatm"}
cutoff = float: show as sticks all receptor residues within this distance from the ligand {default: 5.0}
"""
cmd.select('ligand', ligsel)
cmd.select('receptor', recsel)
cmd.bg_color('white')
cmd.show_as('cartoon')
cmd.show_as('sticks', 'hetatm')
cmd.set('cartoon_transparency', 0.2)
cmd.spectrum(selection=recsel+" or "+ligsel,byres=1)
util.cbag('not elem C')
cmd.set('cartoon_fancy_helices', 1);
cmd.show("sticks", "(hydro)");
cmd.select("pocket", "byres (receptor within %s of ligand)" % cutoff);
cmd.show("sticks", "pocket")
cmd.hide('(h. and (e. c extend 1))')
cmd.set('h_bond_max_angle', 30)
cmd.set('h_bond_cutoff_center', 3.6)
cmd.set('h_bond_cutoff_edge', 3.2)
cmd.dist('ligand_Hbonds', 'ligand', 'receptor', 3.5, mode=2)
cmd.set('dash_radius', 0.15)
# now set the label options
cmd.set('label_size', 20)
cmd.set('label_position', [0,0,10])
def clear(self):
self.cmd.unmask("all")
self.cmd.deprotect("all")
self.cmd.sculpt_deactivate("all")
if self.status == HAVE_SELECTIONS:
util.cbag("(byobj %s)" % cent_sele, _self=self.cmd)
self.cmd.flag("exclude", "(byobj %s)" % cent_sele, "clear")
self.status = NO_SELECTIONS
self.cmd.delete(sele_pre + "*")
self.cmd.refresh_wizard()
def clear(self):
self.cmd.unmask("all")
self.cmd.deprotect("all")
self.cmd.sculpt_deactivate("all")
if self.status == HAVE_SELECTIONS:
util.cbag("(byobj %s)"%cent_sele, _self=self.cmd)
self.cmd.flag("exclude","(byobj %s)"%cent_sele,"clear")
self.status = NO_SELECTIONS
self.cmd.delete(sele_pre+"*")
self.cmd.refresh_wizard()
def atomcolor(): """ atom coloring """ cmd.bg_color( "white" ) cmd.hide( "ev" ) cmd.show( "sticks", "not elem H" ) cmd.show( "lines", "elem H" ) util.cbag() cmd.color( "white", "elem C" )
def atomcolor():
"""
atom coloring
"""
cmd.bg_color("white")
cmd.hide("ev")
cmd.show("sticks", "not elem H")
cmd.show("lines", "elem H")
util.cbag()
cmd.color("white", "elem C")
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 DisplayLigand(self):
try:
cmd.load(self.pdbPath, self.LigDisplay, state=self.State)
# Display the atoms spheres
cmd.show('spheres', self.LigDisplay)
cmd.alter(self.LigDisplay,'vdw=0.25')
cmd.rebuild(self.LigDisplay)
util.cbag(self.LigDisplay)
cmd.translate(self.Translation,self.LigDisplay)
cmd.zoom(self.LigDisplay)
except:
return 1
return 0
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 showhbnet(hbFile="hb.txt"):
g = loadHbNet(hbFile)
cmd.set("sphere_transparency", 0.7)
cmd.set("line_width", 0.5)
for eachRes in g.nodes():
# only show the residues in the network that have connection with the key residues.
if not isShowing(g, eachRes): continue
resName = eachRes[:3]
chainId = eachRes[3]
resSeq = int(eachRes[4:])
# the schiff's base is specail, it's a combination of Lys216 and the retinal.
if eachRes == "RSBA0216":
selection = "(r. lys and c. a and i. 216) or (r. ret)"
cmd.show("lines", selection)
cmd.label("r. lys and c. a and i. 216 and name ca", '"RSB"')
util.cbag(selection)
continue
selection = "(r. %s and c. %c and i. %d)" % (resName, chainId, resSeq)
if resName == "HOH":
cmd.show("spheres", selection)
cmd.set("sphere_scale", 0.15)
cmd.label(selection, "chain+resi")
else:
cmd.show("lines", selection)
cmd.label(selection+" and name ca", "resn+resi")
util.cbag(selection)
# hide all the hydrogens.
cmd.hide("everything", "h.")
def on_pdbentry_pressed(self):
pdb = self.pdbloc.getvalue()
if self.check_exist(pdb) == Pmw.OK:
cmd.load(pdb, 'original', format='pdb', quiet=0)
util.cbag()
self.pmobj.append('original')
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')
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)
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)
def update_plot_multiple(self, source=0, to_display=set(), canvas=None):
""" Check for updated selections data in all plots simultaneously"""
start_time = time.time()
if source == 1:
# Check mulltiple selection by dragging rectangle
if self.scale == "Model":
logging.info("Display models sent by OnDrag: ")
logging.info(to_display)
self.models_to_display = to_display.intersection(
self.all_models)
logging.info(self.models_to_display)
#if self.correlate.get():
for m in self.all_models:
if m in self.models_to_display:
logging.debug("Color: %04d" % m)
#cmd.select('sele', '%04d' % s[5][1])
#cmd.show('cartoon', 'name CA and %04d' % s[5][1])
cmd.show('line', '%04d' % m)
#cmd.disable('sele')
elif m in self.models_shown:
cmd.hide('line', '%04d' % m)
self.models_shown = self.models_to_display
# elif s[5][1] not in self.models_to_display and s[5][1] in self.models_shown:
# canvas.itemconfig(k, fill='grey')
# cpt=0
# for it in canvas.ids_ext[k]:
# if self.canvas[cpt] != canvas:
# self.canvas[cpt].itemconfig(it, fill='grey')
# else:
# cpt+=1
# self.canvas[cpt].itemconfig(it, fill='grey')
# cpt+=1
# logging.debug("Hide: %04d" % s[5][1])
# #cmd.select('sele', '%04d' % s[5][1])
# cmd.hide('everything', '%04d' % s[5][1])
# #cmd.disable('sele')
# self.models_shown = self.models_to_display
# else:
# for k,s in canvas.shapes.iteritems():
# if s[5][1] in canvas.selected:
# canvas.itemconfig(k, fill=self.color_selection[self.canvas.index(canvas)])
# elif s[5][1] not in self.models_to_display:
# canvas.itemconfig(k, fill='grey')
# show = canvas.selected
# tmp = []
# for canv in self.canvas:
# if len(canv.selected) > 0 and canv != canvas:
# tmp = [val for val in show if val in canv.selected]
# show = tmp
# for model in self.models_shown:
# if model in show:
# cmd.show('line', '%04d' % model)
# else:
# cmd.hide('everything', '%04d' % model)
# self.models_shown = show
#
# elif self.scale == "Residue":
# logging.info("Display residues sent by OnDrag: ")
# logging.info(to_display)
# self.residues_to_display = to_display.intersection(self.all_residues)
# logging.info(self.residues_to_display)
# for k,s in canvas.shapes.iteritems():
# if s[5][1] in self.residues_to_display and s[5][1] not in self.residues_shown:
# canvas.itemconfig(k, fill='blue')
# cpt = 0
# for it in canvas.ids_ext[k]:
# if self.canvas[cpt] != canvas:
# self.canvas[cpt].itemconfig(it, fill='blue')
# else:
# cpt+=1
# self.canvas[cpt].itemconfig(it, fill='blue')
# cpt+=1
# logging.debug("Stick: %04d" % s[5][1])
# #cmd.select('sele', '%04d' % s[5][1])
# #cmd.show('cartoon', 'name CA and %04d' % s[5][1])
# cmd.show('sticks', 'resid %d and model %04d' % (s[5][1], self.model_selected))
# #cmd.disable('sele')
# elif s[5][1] not in self.residues_to_display and s[5][1] in self.residues_shown:
# canvas.itemconfig(k, fill='grey')
# cpt=0
# for it in canvas.ids_ext[k]:
# if self.canvas[cpt] != canvas:
# self.canvas[cpt].itemconfig(it, fill='grey')
# else:
# cpt+=1
# self.canvas[cpt].itemconfig(it, fill='grey')
# cpt+=1
# logging.debug("Line: %04d" % s[5][1])
# #cmd.select('sele', '%04d' % s[5][1])
# cmd.hide('sticks', 'resid %d and model %04d' % (s[5][1], self.model_selected))
# # cmd.show('line', 'resid %d and model %04d' % (s[5][1], self.model_selected))
# #cmd.disable('sele')
# self.residues_shown = self.residues_to_display
elif source == 0:
# Check single picking items
for canv in self.canvas:
if canv.picked != 0 and canv.picked != canv.previous:
logging.info("Something has been picked")
canv.itemconfig(canv.picked, fill='blue')
cpt = 0
for it in canv.ids_ext[canv.picked]:
if self.canvas[cpt] != canv:
self.canvas[cpt].itemconfig(it, fill='blue')
else:
cpt += 1
self.canvas[cpt].itemconfig(it, fill='blue')
cpt += 1
if self.scale == "Model":
cmd.show(
'cartoon', 'name CA and %04d' %
canv.shapes[canv.picked][5][1])
cmd.show('lines',
'%04d' % canv.shapes[canv.picked][5][1])
logging.info(
"You selected item %d corresponding to model %d" %
(canv.picked, canv.shapes[canv.picked][5][1]))
elif self.scale == "Residue":
cmd.show(
'sticks', 'resid %d and model %04d' %
(canv.shapes[canv.picked][5][1],
self.model_selected))
logging.info(
"You selected item %d corresponding to model %d" %
(canv.picked, canv.shapes[canv.picked][5][1]))
if canv.previous != 0:
canv.itemconfig(canv.previous, fill='grey')
cpt = 0
for it in canv.ids_ext[canv.previous]:
if self.canvas[cpt] != canv:
self.canvas[cpt].itemconfig(it, fill='grey')
else:
cpt += 1
self.canvas[cpt].itemconfig(it, fill='grey')
cpt += 1
if self.scale == "Model":
cmd.hide('everything',
'%04d' % canv.shapes[canv.previous][5][1])
elif self.scale == "Residue":
cmd.hide(
'sticks', 'resid %d and model %04d' %
(canv.shapes[canv.previous][5][1],
self.model_selected))
canv.previous = canv.picked
break # We can pick only one item among all canvas
# Check selection from PyMol viewer
try:
items = self.queue.get_nowait()
logging.info("Items from user selection in the viewer: " +
str(items))
logging.info("Current state: %s / Scale: %s" %
(self.current_state, self.scale))
# Automatic checking of model selection by the user
if self.current_state == "default" and self.scale == "Model":
self.models_to_display = items.intersection(
self.all_models)
if len(self.models_to_display) > 0:
for k, s in canvas.shapes.iteritems():
if s[5][1] in self.models_to_display:
logging.info("Color red -> %04d" % s[5][1])
canvas.itemconfig(k, fill='blue')
cpt = 0
for it in canvas.ids_ext[k]:
if self.canvas[cpt] != canvas:
self.canvas[cpt].itemconfig(
it, fill='blue')
else:
cpt += 1
self.canvas[cpt].itemconfig(
it, fill='blue')
cpt += 1
cmd.color('red', '%04d' % s[5][1])
else:
logging.info("Color default -> %04d" % s[5][1])
canvas.itemconfig(k, fill='grey')
cpt = 0
for it in canvas.ids_ext[k]:
if self.canvas[cpt] != canvas:
self.canvas[cpt].itemconfig(
it, fill='grey')
else:
cpt += 1
self.canvas[cpt].itemconfig(
it, fill='grey')
cpt += 1
util.cbag('%04d' % s[5][1])
# cmd.select('sele', '%04d' % s[5][1])
# cmd.hide('line', '(sele)')
cmd.disable('lb')
# We wait for user selection to trigger next steps
elif self.current_state == "selection":
# Model selection
if int(cmd.get("mouse_selection_mode")) == 5:
try:
logging.info("Model selected for analyses: %d " %
list(items)[0])
self.model_selected = list(items)[0]
cmd.hide('everything', 'all')
cmd.show('cartoon', '%04d' % self.model_selected)
cmd.show('lines', '%04d' % self.model_selected)
color_by_residue.color_by_restype()
for k, s in canvas.shapes.iteritems():
if s[5][1] == self.model_selected:
canvas.itemconfig(k, fill='blue')
cpt = 0
for it in canvas.ids_ext[k]:
if self.canvas[cpt] != canvas:
self.canvas[cpt].itemconfig(
it, fill='blue')
else:
cpt += 1
self.canvas[cpt].itemconfig(
it, fill='blue')
cpt += 1
else:
logging.info("Color default -> %04d" %
s[5][1])
canvas.itemconfig(k, fill='grey')
cpt = 0
for it in canvas.ids_ext[k]:
if self.canvas[cpt] != canvas:
self.canvas[cpt].itemconfig(
it, fill='grey')
else:
cpt += 1
self.canvas[cpt].itemconfig(
it, fill='grey')
cpt += 1
# cmd.select('sele', '%04d' % s[5][1])
#cmd.disable('lb')
self.current_state = "default"
self.on_model_selected(evt=None)
items = set()
except IndexError:
logging.info("No model selected in the viewer")
pass
# Residue selection
elif int(cmd.get("mouse_selection_mode")) == 1:
try:
logging.info(
"Residue selection for analyses: %d " %
list(items)[0])
self.item_selected = list(items)[0]
items = set()
self.current_state = "default"
self.on_reference_selected_for_distance(evt=None)
except IndexError:
logging.info("No residue selected in the viewer")
pass
except Queue.Empty:
pass
# Reset plot and viewer
elif source == 2:
logging.info("RESET")
for canv in self.canvas:
for k, s in canv.shapes.iteritems():
canv.itemconfig(k, fill='grey')
cpt = 0
for it in canvas.ids_ext[k]:
if self.canvas[cpt] != canvas:
self.canvas[cpt].itemconfig(it, fill='grey')
else:
cpt += 1
self.canvas[cpt].itemconfig(it, fill='grey')
cpt += 1
self.models_to_display.clear()
self.models_shown.clear()
canv.previous = 0
canv.picked = 0
cmd.hide('everything', 'all')
# "Selection mode"
elif source == 3:
logging.info("SELECTION MODE")
for canv in self.canvas:
for k, s in canv.shapes.iteritems():
canv.itemconfig(k, fill='grey')
cpt = 0
for it in canv.ids_ext[k]:
if self.canvas[cpt] != canv:
self.canvas[cpt].itemconfig(it, fill='grey')
else:
cpt += 1
self.canvas[cpt].itemconfig(it, fill='grey')
cpt += 1
self.models_to_display.add(s[5][1])
self.models_shown.add(s[5][1])
cmd.show('cartoon', 'name CA')
cmd.show('lines', 'all')
logging.debug("---- %s seconds ----" % str(time.time() - start_time))
print time.time()
try:
self.rootframe.after(500, self.update_plot_multiple)
except:
pass
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)
def on_execute_button_clicked(self):
if not _HAS_LIB:
tkMessageBox.showerror(
'ERROR',
'Please install EMDY before launch the plugin',
parent=self.parent)
return
if self.notebook.getcurselection() == 'Preparation':
if self.mod is None or self.top is None or self.prm is None:
failed = self.load_input()
if failed:
return
try:
self.mod = add_atoms(self.mod, self.top, self.prm)
except Exception:
tkMessageBox.showerror(
'ERROR',
'Failed',
parent=self.parent)
else:
tkMessageBox.showinfo(
'INFO',
'Successfully completed',
parent=self.parent)
elif self.notebook.getcurselection() == 'Solvation':
if self.mod is None or self.top is None or self.prm is None:
failed = self.load_input()
if failed:
return
try:
self.mod = add_solvents(self.mod, self.watmod.getvalue(),
self.watseg.getvalue(),
self.boxshape.get(),
float(self.pad.getvalue()),
float(self.cut.getvalue()))
except Exception:
tkMessageBox.showerror(
'ERROR',
'Failed',
parent=self.parent)
else:
tkMessageBox.showinfo(
'INFO',
'Successfully completed',
parent=self.parent)
elif self.notebook.getcurselection() == 'Ionization':
if self.mod is None or self.top is None or self.prm is None:
failed = self.load_input()
if failed:
return
if self.do_neutral.get():
catnum = aninum = 0
else:
catnum = int(self.catnum.getvalue())
aninum = int(self.aninum.getvalue())
if catnum == aninum == 0:
return
catmod = IONS[self.catmod.getvalue()]
animod = IONS[self.animod.getvalue()]
try:
self.mod = add_ions(self.mod, catmod, catnum, animod, aninum,
float(self.salcon.getvalue()),
float(self.ionsol.getvalue()),
float(self.ionion.getvalue()), None,
self.ionseg.getvalue(), self.ionmeth.get())
except Exception:
tkMessageBox.showerror(
'ERROR',
'Failed',
parent=self.parent)
else:
tkMessageBox.showinfo(
'INFO',
'Successfully completed',
parent=self.parent)
else:
if self.mod is None or self.top is None or self.prm is None:
self.load_input()
return
# generate a tmp file for view
objname = {'Preparation': 'modified', 'Solvation': 'solvated',
'Ionization': 'ionized'}[self.notebook.getcurselection()]
tmpfp = StringIO()
with PdbFile(tmpfp, 'w') as f:
f.write(self.mod)
for obj in self.pmobj:
cmd.delete(obj)
cmd.read_pdbstr(tmpfp.getvalue(), objname)
util.cbag()
self.pmobj = [objname]
if self.notebook.getcurselection() == 'Ionization':
cmd.show('spheres', 'segi %s'%self.ionseg.getvalue())
