def pretty_solv(selection="(all)", _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
polar_contacts = _get_polar_contacts_name(s, _self)
_prepare(s, polar_contacts, _self=cmd)
cmd.dss(s, preserve=1)
cmd.cartoon("auto", s)
cmd.show("cartoon", s)
cmd.show("sticks", "(" + lig_sele + " and (" + s + "))")
cmd.show("nb_spheres",
"((" + lig_sele + "|resn hoh+wat+h2o) and (" + s + "))")
util.cbc("(" + lig_sele + " and (" + s + "))", _self=cmd)
util.cbac("(" + lig_sele + " and (" + s + ") and not elem c)", _self=cmd)
cmd.spectrum("count",
selection="(elem c and (" + s + ") and not " + lig_sele + ")")
cmd.set("cartoon_highlight_color", -1, selection)
cmd.set("cartoon_fancy_helices", 0, selection)
cmd.set("cartoon_smooth_loops", 0, selection)
cmd.set("cartoon_flat_sheets", 1, selection)
cmd.set("cartoon_side_chain_helper", 0, selection)
if polar_contacts in cmd.get_names():
cmd.disable(polar_contacts)
if cmd.count_atoms(s):
cmd.zoom(s)
def simple(selection="(all)", _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
_prepare(s, _self=cmd)
util.cbc(s, _self=cmd)
cmd.show("ribbon", s)
cmd.show(
"lines", "(byres ((" + s + " & r. CYS+CYX & n. SG) & bound_to (" + s +
" & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
# try to show what covalent ligands are connected to...
cmd.show("sticks", "(" + lig_sele + " and (" + s + ")) extend 2")
cmd.show(
"sticks", "byres ((" + lig_sele + " and (" + s +
") and not resn ACE+NAC+NME+NH2) extend 1)")
cmd.hide("sticks", "(" + s + ") and ((not rep sticks) extend 1)")
cmd.show("sticks", "(" + lig_sele + " and (" + s + ")) extend 2")
# color by atom if lines or sticks are shown
util.cnc("(( rep lines or rep sticks or (" + lig_and_solv_sele +
")) and (" + s + "))",
_self=cmd)
cmd.show("nonbonded", "(" + lig_and_solv_sele + " and (" + s + "))")
cmd.show("lines", "(" + lig_and_solv_sele + " and (" + s + "))")
if cmd.count_atoms(s):
cmd.zoom(s)
cmd.delete(s)
def toggle_zooms(mode=-1):
global zooms
if mode<0:
zooms = not zooms
else:
zooms = mode
if zooms:
cmd.zoom(m4x_ligands,2)
else:
cmd.zoom("m4x_aligned")
def toggle_zooms(mode=-1):
global zooms
if mode < 0:
zooms = not zooms
else:
zooms = mode
if zooms:
cmd.zoom(m4x_ligands, 2)
else:
cmd.zoom("m4x_aligned")
def pub_solv(selection="(all)",_self=cmd):
cmd=_self
pretty_solv(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.set("cartoon_smooth_loops",1,selection)
cmd.set("cartoon_highlight_color","grey50",selection)
cmd.set("cartoon_fancy_helices",1,selection)
cmd.set("cartoon_flat_sheets",1,selection)
cmd.set("cartoon_side_chain_helper",0,selection)
if cmd.count_atoms(s):
cmd.zoom(s)
def pub_solv(selection="(all)", _self=cmd):
cmd = _self
pretty_solv(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.set("cartoon_smooth_loops", 1, selection)
cmd.set("cartoon_highlight_color", "grey50", selection)
cmd.set("cartoon_fancy_helices", 1, selection)
cmd.set("cartoon_flat_sheets", 1, selection)
cmd.set("cartoon_side_chain_helper", 0, selection)
if cmd.count_atoms(s):
cmd.zoom(s)
def ligands(selection="(all)", _self=cmd):
cmd = _self
try:
s = tmp_sele
cmd.select(s, selection)
polar_contacts = _get_polar_contacts_name(s, _self)
_prepare(s, polar_contacts, _self=cmd)
host = "_preset_host"
solvent = "_preset_solvent"
near_solvent = "_preset_solvent"
lig = "_preset_lig"
cmd.select(host, s + " and " + prot_and_dna_sele)
cmd.select(solvent, s + " and " + solv_sele)
cmd.select(lig, s + " and " + lig_sele)
cmd.select(near_solvent,
s + " and (" + solvent + " within 4 of " + lig + ")")
util.chainbow(host, _self=cmd)
util.cbc(lig, _self=cmd)
util.cbac("((" + s + ") and not elem c)", _self=cmd)
cmd.hide("everything", s)
cmd.show("ribbon", host)
cmd.show(
"lines",
"(" + s + " and byres (" + host + " within 5 of " + lig + "))")
cmd.show("sticks", lig)
cmd.show("sticks", solvent + " and neighbor " + lig)
cmd.show("lines",
"(" + s + " and (rep lines extend 1) and " + lig + ")")
if cmd.count_atoms(lig):
cmd.dist(polar_contacts,
host + "|" + near_solvent,
lig + "|" + near_solvent,
mode=2,
quiet=1,
label=0,
reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.hide("labels", polar_contacts)
cmd.show("dashes", polar_contacts)
else:
cmd.delete(polar_contacts)
cmd.show("nonbonded", lig + "|" + host + "|" + near_solvent)
if cmd.count_atoms(lig):
cmd.zoom(lig, 3)
cmd.delete(host)
cmd.delete(solvent)
cmd.delete(near_solvent)
cmd.delete(lig)
except:
traceback.print_exc()
def ligand_sites(selection="(all)",_self=cmd):
cmd=_self
try:
s = tmp_sele
cmd.select(s,selection)
polar_contacts = _get_polar_contacts_name(s,_self)
_prepare(s,polar_contacts,_self=cmd)
host = "_preset_host"
solvent = "_preset_solvent"
near_solvent = "_preset_solvent"
lig = "_preset_lig"
cmd.select(host,s+" and "+prot_and_dna_sele)
cmd.select(solvent,s+" and "+solv_sele)
cmd.select(lig,s+" and "+lig_sele)
cmd.select(near_solvent,s+" and ("+solvent+" within 4 of "+lig+")")
cmd.flag("ignore",host,"clear")
cmd.flag("ignore",lig+"|"+solvent,"set")
util.chainbow(host,_self=cmd)
util.cbc(lig,_self=cmd)
util.cbac("(("+s+") and not elem c)",_self=cmd)
cmd.hide("everything",s)
cmd.show("ribbon",host)
cmd.show("lines","("+s+" and byres ("+host+" within 5 of "+lig+"))")
cmd.show("surface","("+s+" and ((rep lines expand 4) within 6 of "+lig+"))")
cmd.set("two_sided_lighting",1) # global setting
cmd.set("transparency",0,s)
cmd.set("surface_quality",0,s)
cmd.show("sticks",lig)
cmd.show("sticks",solvent+" and neighbor "+lig)
cmd.show("lines","("+s+" and (rep lines extend 1) and "+lig+")")
if cmd.count_atoms(lig):
cmd.dist(polar_contacts,host+"|"+near_solvent,lig+"|"+near_solvent,mode=2,quiet=1,label=0,reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.hide("labels",polar_contacts)
cmd.show("dashes",polar_contacts)
else:
cmd.delete(polar_contacts)
cmd.show("nb_spheres",lig+"|"+host+"|"+near_solvent)
if cmd.count_atoms(lig):
cmd.zoom(lig,3)
cmd.delete(host)
cmd.delete(solvent)
cmd.delete(near_solvent)
cmd.delete(lig)
except:
traceback.print_exc()
cmd.delete(s)
def simple(selection="(all)",_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
_prepare(s,_self=cmd)
util.cbc(s,_self=cmd)
cmd.show("ribbon",s)
cmd.show("lines","(byres (("+s+" & r. CYS+CYX & n. SG) & bound_to ("+s+" & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
# try to show what covalent ligands are connected to...
cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
cmd.show("sticks","byres (("+lig_sele+" and ("+s+") and not resn ACE+NAC+NME+NH2) extend 1)")
cmd.hide("sticks","("+s+") and ((not rep sticks) extend 1)")
cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
# color by atom if lines or sticks are shown
util.cnc("(( rep lines or rep sticks or ("+lig_and_solv_sele+")) and ("+s+"))",_self=cmd)
cmd.show("nonbonded","("+lig_and_solv_sele+" and ("+s+"))")
cmd.show("lines","("+lig_and_solv_sele+" and ("+s+"))")
if cmd.count_atoms(s):
cmd.zoom(s)
cmd.delete(s)
def pretty_solv(selection="(all)",_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
polar_contacts = _get_polar_contacts_name(s,_self)
_prepare(s,polar_contacts,_self=cmd)
cmd.dss(s,preserve=1)
cmd.cartoon("auto",s)
cmd.show("cartoon",s)
cmd.show("sticks","("+lig_sele+" and ("+s+"))")
cmd.show("nb_spheres","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))")
util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)
util.cbac("("+lig_sele+" and ("+s+") and not elem c)",_self=cmd)
cmd.spectrum("count",selection="(elem c and ("+s+") and not "+lig_sele+")")
cmd.set("cartoon_highlight_color",-1,selection)
cmd.set("cartoon_fancy_helices",0,selection)
cmd.set("cartoon_smooth_loops",0,selection)
cmd.set("cartoon_flat_sheets",1,selection)
cmd.set("cartoon_side_chain_helper",0,selection)
if polar_contacts in cmd.get_names():
cmd.disable(polar_contacts)
if cmd.count_atoms(s):
cmd.zoom(s)
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 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)