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 ligand_sites_hq(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.set("surface_quality", "1", selection)
cmd.set("surface_type", 0, selection)
def ligand_sites_hq(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.set("surface_quality","1",selection)
cmd.set("surface_type",0,selection)
def _prepare(selection, polar_contacts=None, _self=cmd):
cmd = _self
# this function should undo everything that is done by any preset function in this module
# (except for coloring)
s = tmp_sele
cmd.select(s, selection)
cmd.cartoon("auto", s)
cmd.hide("everything", s)
cmd.set("two_sided_lighting", 0) # global
cmd.unset("transparency", s)
cmd.unset("dot_normals", s)
cmd.unset("mesh_normals", s)
cmd.unset("surface_quality", s)
cmd.unset("surface_type", selection)
cmd.unset("sphere_scale", selection)
cmd.unset_bond("stick_radius", s, s)
cmd.unset_bond("stick_color", s, s)
cmd.unset("cartoon_highlight_color", selection)
cmd.unset("cartoon_fancy_helices", selection)
cmd.unset("cartoon_smooth_loops", selection)
cmd.unset("cartoon_flat_sheets", selection)
cmd.unset("cartoon_side_chain_helper", selection)
cmd.unset("mesh_normals", s)
cmd.unset("dot_normals", s)
if polar_contacts == None:
polar_contacts = _get_polar_contacts_name(s, _self)
if polar_contacts in cmd.get_names('objects'):
cmd.delete(polar_contacts)
def _prepare(selection,polar_contacts=None,_self=cmd):
cmd=_self
# this function should undo everything that is done by any preset function in this module
# (except for coloring)
s = tmp_sele
cmd.select(s,selection)
cmd.cartoon("auto",s)
cmd.hide("everything",s)
cmd.set("two_sided_lighting",0) # global
cmd.unset("transparency",s)
cmd.unset("dot_normals",s)
cmd.unset("mesh_normals",s)
cmd.unset("surface_quality",s)
cmd.unset("surface_type",selection)
cmd.unset("sphere_scale",selection)
cmd.unset_bond("stick_radius",s,s)
cmd.unset_bond("stick_color",s,s)
cmd.unset("cartoon_highlight_color",selection)
cmd.unset("cartoon_fancy_helices",selection)
cmd.unset("cartoon_smooth_loops",selection)
cmd.unset("cartoon_flat_sheets",selection)
cmd.unset("cartoon_side_chain_helper",selection)
cmd.unset("mesh_normals",s)
cmd.unset("dot_normals",s)
if polar_contacts == None:
polar_contacts = _get_polar_contacts_name(s,_self)
if polar_contacts in cmd.get_names('objects'):
cmd.delete(polar_contacts)
def ligand_cartoon(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.set("cartoon_side_chain_helper", 1, selection)
cmd.show("cartoon", "rep ribbon")
cmd.hide("ribbon")
cmd.hide("surface")
def ligand_cartoon(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.set("cartoon_side_chain_helper",1,selection)
cmd.show("cartoon","rep ribbon")
cmd.hide("ribbon")
cmd.hide("surface")
def b_factor_putty(selection="(name ca or name p)",_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
_prepare(s,_self=cmd)
cmd.select(s,"(name ca or name p) and ("+selection+")")
cmd.show("cartoon",s)
cmd.set("cartoon_flat_sheets",0,selection)
cmd.cartoon("putty",s)
cmd.spectrum("b",selection=s)
def b_factor_putty(selection="(name ca or name p)", _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
_prepare(s, _self=cmd)
cmd.select(s, "(name ca or name p) and (" + selection + ")")
cmd.show("cartoon", s)
cmd.set("cartoon_flat_sheets", 0, selection)
cmd.cartoon("putty", s)
cmd.spectrum("b", selection=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 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 colors(scheme="",_self=cmd):
pymol=_self._pymol
cmd=_self
if scheme=="jmol":
cmd.set("auto_color",0)
cmd.set_color("hydrogen",[1.000,1.000,1.000])
cmd.set_color("carbon",[0.567,0.567,0.567])
cmd.set_color("nitrogen",[0.189,0.315,0.976])
cmd.set_color("oxygen",[1.000,0.051,0.051])
cmd.set_color("fluorine",[0.567,0.882,0.314])
cmd.set_color("sulfur",[1.000,1.000,0.189])
cmd.color("carbon","elem c")
cmd.recolor()
def x(st):
print st
cmd.set("raise_exceptions",0)
valu = eval(st)
print valu
if cmd.is_error(valu):
cmd.set("raise_exceptions",1)
try:
print eval(st)
except pymol.CmdException:
print "CmdException raised."
except cmd.QuietException:
print "QuietException raised."
def protein_vacuum_esp(selection, mode=2, border=10.0, quiet = 1, _self=cmd):
pymol=_self._pymol
cmd=_self
if ((string.split(selection)!=[selection]) or
selection not in cmd.get_names('objects')):
print " Error: must provide an object name"
raise cmd.QuietException
obj_name = selection + "_e_chg"
map_name = selection + "_e_map"
pot_name = selection + "_e_pot"
cmd.disable(selection)
cmd.delete(obj_name)
cmd.delete(map_name)
cmd.delete(pot_name)
cmd.create(obj_name,"((polymer and ("+selection+
") and (not resn A+C+T+G+U)) or ((bymol (polymer and ("+
selection+"))) and resn NME+NHE+ACE)) and (not hydro)")
# try to just get protein...
protein_assign_charges_and_radii(obj_name,_self=_self)
ext = cmd.get_extent(obj_name)
max_length = max(abs(ext[0][0] - ext[1][0]),abs(ext[0][1] - ext[1][1]),abs(ext[0][2]-ext[1][2])) + 2*border
# compute an grid with a maximum dimension of 50, with 10 A borders around molecule, and a 1.0 A minimum grid
sep = max_length/50.0
if sep<1.0: sep = 1.0
print " Util: Calculating electrostatic potential..."
if mode==0: # absolute, no cutoff
cmd.map_new(map_name,"coulomb",sep,obj_name,border)
elif mode==1: # neutral, no cutoff
cmd.map_new(map_name,"coulomb_neutral",sep,obj_name,border)
else: # local, with cutoff
cmd.map_new(map_name,"coulomb_local",sep,obj_name,border)
cmd.ramp_new(pot_name, map_name, selection=obj_name,zero=1)
cmd.hide("everything",obj_name)
cmd.show("surface",obj_name)
cmd.set("surface_color",pot_name,obj_name)
cmd.set("surface_ramp_above_mode",1,obj_name)
def technical(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)
util.chainbow(s,_self=cmd)
util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)
util.cbac("(("+s+") and not elem c)",_self=cmd)
cmd.show("nonbonded",s)
cmd.show("lines","((("+s+") and not "+lig_sele+") extend 1)")
cmd.show("sticks","("+lig_sele+" and ("+s+"))")
cmd.show("ribbon",s)
cmd.dist(polar_contacts,s,s,mode=2,label=0,reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.set("dash_width",1.5,polar_contacts)
cmd.hide("labels",polar_contacts)
cmd.show("dashes",polar_contacts)
cmd.show("nonbonded","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))")
def technical(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)
util.chainbow(s, _self=cmd)
util.cbc("(" + lig_sele + " and (" + s + "))", _self=cmd)
util.cbac("((" + s + ") and not elem c)", _self=cmd)
cmd.show("nonbonded", s)
cmd.show("lines", "(((" + s + ") and not " + lig_sele + ") extend 1)")
cmd.show("sticks", "(" + lig_sele + " and (" + s + "))")
cmd.show("ribbon", s)
cmd.dist(polar_contacts, s, s, mode=2, label=0, reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.set("dash_width", 1.5, polar_contacts)
cmd.hide("labels", polar_contacts)
cmd.show("dashes", polar_contacts)
cmd.show("nonbonded",
"((" + lig_sele + "|resn hoh+wat+h2o) and (" + 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 ligand_sites_dots(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("surface_type","1",selection)
cmd.set("surface_quality","1",selection)
cmd.set("dot_normals",0,s)
def ligand_sites_dots(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.show("sticks", s + " and rep lines")
cmd.hide("lines", s + " and rep lines")
cmd.set("surface_type", "1", selection)
cmd.set("surface_quality", "1", selection)
cmd.set("dot_normals", 0, s)
def ligand_sites_trans_hq(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("transparency","0.33",s)
cmd.set("surface_type",0,selection)
cmd.set("surface_quality",1,selection)
def ligand_sites_trans_hq(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.show("sticks", s + " and rep lines")
cmd.hide("lines", s + " and rep lines")
cmd.set("transparency", "0.33", s)
cmd.set("surface_type", 0, selection)
cmd.set("surface_quality", 1, selection)
def ligand_sites_mesh(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("surface_type","2",selection)
cmd.set("surface_quality","0",selection)
cmd.set("mesh_normals",0,s)
cmd.delete(s)
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 ball_and_stick(selection="(all)",mode=1,_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
_prepare(s,_self=cmd)
if mode == 1:
cmd.hide("everything",s)
cmd.set_bond("stick_color","white",s,s)
cmd.set_bond("stick_radius","0.14",s,s)
cmd.set("sphere_scale","0.25",s)
cmd.show("sticks",s)
cmd.show("spheres",s)
elif mode == 2:
cmd.hide("everything",s)
cmd.set_bond("stick_color","white",s,s)
cmd.set_bond("stick_radius","-0.14",s,s)
cmd.set("stick_ball","1")
cmd.set("stick_ball_ratio",-1.0)
cmd.set("stick_ball_color","atomic")
cmd.show("sticks",s)
def ball_and_stick(selection="(all)", mode=1, _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
_prepare(s, _self=cmd)
if mode == 1:
cmd.hide("everything", s)
cmd.set_bond("stick_color", "white", s, s)
cmd.set_bond("stick_radius", "0.14", s, s)
cmd.set("sphere_scale", "0.25", s)
cmd.show("sticks", s)
cmd.show("spheres", s)
elif mode == 2:
cmd.hide("everything", s)
cmd.set_bond("stick_color", "white", s, s)
cmd.set_bond("stick_radius", "-0.14", s, s)
cmd.set("stick_ball", "1")
cmd.set("stick_ball_ratio", -1.0)
cmd.set("stick_ball_color", "atomic")
cmd.show("sticks", s)
def performance(mode,_self=cmd):
pymol=_self._pymol
cmd=_self
mode = int(mode)
if mode==0: # maximum quality
cmd.set('line_smooth',1)
cmd.set('depth_cue',1)
cmd.set('specular',1)
cmd.set('surface_quality',1)
cmd.set('stick_quality',15)
cmd.set('sphere_quality',2)
cmd.set('cartoon_sampling',14)
cmd.set('ribbon_sampling',10)
cmd.set('transparency_mode',2)
cmd.set('stick_ball',1)
cmd.do("rebuild")
elif mode==33:
cmd.set('line_smooth',1)
cmd.set('depth_cue',1)
cmd.set('specular',1)
cmd.set('surface_quality',0)
cmd.set('stick_quality',8)
cmd.set('sphere_quality',1)
cmd.set('cartoon_sampling',7)
cmd.set('ribbon_sampling',1)
cmd.set('transparency_mode',2)
cmd.set('stick_ball',0)
cmd.do("rebuild")
elif mode==66: # good perfomance
cmd.set('line_smooth',0)
cmd.set('depth_cue',0)
cmd.set('specular',1)
cmd.set('surface_quality',0)
cmd.set('stick_quality',8)
cmd.set('sphere_quality',1)
cmd.set('cartoon_sampling',6)
cmd.set('ribbon_sampling',1)
cmd.set('transparency_mode',2)
cmd.set('stick_ball',0.0)
cmd.do("rebuild")
else: # maximum performance
cmd.set('line_smooth',0)
cmd.set('depth_cue',0)
cmd.set('specular',0)
cmd.set('surface_quality',-1) # new
cmd.set('stick_quality',5)
cmd.set('sphere_quality',0)
cmd.set('ribbon_sampling',1)
cmd.set('cartoon_sampling',3)
cmd.set('transparency_mode',0)
cmd.set('stick_ball',0.0)
cmd.do("rebuild")
def ray_shadows(mode,_self=cmd):
pymol=_self._pymol
cmd=_self
# adjustment factors for new lighting model in 0.99
reflect_scale = 0.5
direct_scale = 1.8
gamma_scale = 1/1.3
ambient_scale = 1.16
if mode=='none':
cmd.set('ray_shadows',0)
else:
cmd.set('ray_shadows',1)
if mode=='light':
cmd.set('light_count',2)
cmd.set("light","[-0.4,-0.4,-1.0]")
cmd.set('ambient',0.14)
cmd.set('direct',0.65)
cmd.set('reflect',0.25)
cmd.set('shininess',40)
cmd.set('power',1.0)
cmd.set('specular_intensity',0.5)
cmd.set('spec_direct',0)
cmd.set('spec_count',-1)
cmd.set('ray_shadow_decay_factor',0)
elif mode=='matte':
cmd.set('light_count',4)
cmd.set("light","[-0.4,-0.4,-1.0]")
cmd.set("light2","[-0.3,-0.4,-1.0]")
cmd.set("light3","[-0.3,-0.3,-1.0]")
cmd.set("light4","[-0.4,-0.3,-1.0]")
cmd.set('ambient',0.14)
cmd.set('direct',0.45)
cmd.set('reflect',0.45)
cmd.set('shininess',25)
cmd.set('power',1.25)
cmd.set('spec_count',-1)
cmd.set('specular_intensity',0.2)
cmd.set('spec_direct',0)
cmd.set('ray_shadow_decay_factor',0)
elif mode=='soft':
cmd.set('light_count',10)
cmd.set("light","[-0.4,-0.4,-1.0]")
cmd.set("light2","[-0.3,-0.4,-1.0]")
cmd.set("light3","[-0.3,-0.3,-1.0]")
cmd.set("light4","[-0.4,-0.3,-1.0]")
cmd.set("light5","[-0.4,-0.5,-1.0]")
cmd.set("light6","[-0.5,-0.5,-1.0]")
cmd.set("light7","[-0.5,-0.4,-1.0]")
cmd.set("light8","[-0.5,-0.3,-1.0]")
cmd.set("light9","[-0.3,-0.5,-1.0]")
cmd.set('ambient',0.14)
cmd.set('direct',0.40)
cmd.set('reflect',0.50)
cmd.set('specular_intensity',0.5)
cmd.set('spec_count',1)
cmd.set('shininess',55)
cmd.set('power',1.0)
cmd.set('spec_direct',0)
cmd.set('ray_shadow_decay_factor',0.1)
cmd.set('ray_shadow_decay_range',1.8)
elif mode=='occlusion':
cmd.set('light_count',9)
cmd.set("light" ,"[-0.2,-0.2,-1.0]")
cmd.set("light2","[-0.2, 0.0,-1.0]")
cmd.set("light3","[-0.2, 0.2,-1.0]")
cmd.set("light4","[ 0.0, 0.2,-1.0]")
cmd.set("light5","[ 0.2, 0.2,-1.0]")
cmd.set("light6","[ 0.2, 0.0,-1.0]")
cmd.set("light7","[ 0.2,-0.2,-1.0]")
cmd.set("light8","[ 0.0,-0.2,-1.0]")
cmd.set('ambient',0.18)
cmd.set('direct',0.10)
cmd.set('reflect',0.80)
cmd.set('shininess',10)
cmd.set('spec_count',-1)
cmd.set('power',1.0)
cmd.set('specular_intensity',0)
cmd.set('spec_direct',0.25)
cmd.set('ray_shadow_decay_factor',0.1)
cmd.set('ray_shadow_decay_range',5.0)
elif mode=='medium':
cmd.set('light_count',2)
cmd.set("light","[-0.4,-0.4,-1.0]")
cmd.set('ambient',0.14)
cmd.set('direct',0.45)
cmd.set('reflect',0.45)
cmd.set('shininess',55)
cmd.set('spec_count',-1)
cmd.set('power',1.0)
cmd.set('specular_intensity',0.5)
cmd.set('spec_direct',0)
cmd.set('ray_shadow_decay_factor',0)
elif mode=='heavy':
cmd.set('light_count',2)
cmd.set("light","[-0.4,-0.4,-1.0]")
cmd.set('ambient',0.05)
cmd.set('direct',0.20)
cmd.set('reflect',0.85)
cmd.set('spec_count',-1)
cmd.set('shininess',90)
cmd.set('power',1.0)
cmd.set('specular_intensity',0.5)
cmd.set('spec_direct',0)
cmd.set('ray_shadow_decay_factor',0)
elif mode=='black': # best for light backgrounds
cmd.set('light_count',2)
cmd.set("light","[-0.4,-0.4,-1.0]")
cmd.set('ambient',0.001)
cmd.set('direct',0.0)
cmd.set('reflect',1.1)
cmd.set('spec_count',-1)
cmd.set('power',1.0)
cmd.set('shininess',90)
cmd.set('specular_intensity',0.5)
cmd.set('spec_direct',0)
cmd.set('ray_shadow_decay_factor',0)
def setup_alignment_contexts(context_info): # Author: Warren DeLano
(list,dict) = context_info[0:2]
doc_list = ['\888Legend:']
obj_name_dict = {}
for a in list:
sf = string.find(a,"_")
if sf>=0:
object_name = a[0:sf]
if not obj_name_dict.has_key(object_name):
obj_name_dict[object_name] = 1
col_index = cmd.get_object_color_index(object_name)
if col_index>=0:
col_tup = cmd.get_color_tuple(col_index)
if is_tuple(col_tup):
col_int = map(lambda x:int(x*9+0.49999),col_tup)
col_str = string.join(map(lambda x:chr(ord('0')+x),col_int),'')
doc_list.append("\\"+col_str+object_name+"\\---")
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.append("")
doc_list.append("\\888Toggles:")
zoom_context = 1
global labels,ligands,waters,sites,cgos,zooms,dashes
labels = 1
ligands = 1
waters = 1
sites = 1
cgos = 0
zooms = 0
dashes = 1
global m4x_sites,m4x_ligands,m4x_waters
m4x_sites = "m4x_sites"
m4x_ligands = "m4x_ligands"
m4x_waters = "m4x_waters"
cmd.select(m4x_sites,"none")
cmd.select(m4x_ligands,"none")
cmd.select(m4x_waters,"none")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_zooms)
doc_list.append(key+": Zoom")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_sites)
doc_list.append(key+": Sites")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_waters)
doc_list.append(key+": Waters")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_dashes)
doc_list.append(key+": H-Bonds")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_cgos)
doc_list.append(key+": Fits")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_ligands)
doc_list.append(key+": Ligands")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": HB-Dists")
for a in list:
include_flag = 0
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
if cmd.count_atoms(site):
if cmd.count_atoms(site+" & m4x_aligned"):
include_flag = 1
if cmd.count_atoms(ligand):
if cmd.count_atoms(ligand+" & m4x_nearby"):
include_flag = 1
if include_flag:
name_list = dict[a]
if water in name_list:
cmd.select(m4x_waters,m4x_waters+"|"+water)
if ligand in name_list:
cmd.select(m4x_ligands,m4x_ligands+"|"+ligand)
if site in name_list:
cmd.select(m4x_sites,m4x_sites+"|"+site+
"|((byres (neighbor ("+site+" and name c))) and name n+ca)"+
"|((byres (neighbor ("+site+" and name n))) and name c+ca+o)")
cmd.wizard("fedora",doc_list)
toggle_cgos(1)
toggle_labels(0)
toggle_dashes(0)
toggle_ligands(1)
toggle_sites(0)
toggle_waters(0)
toggle_cgos(1)
cmd.deselect()
# cmd.feedback("enable","python","output")
cmd.feedback("enable","objectmolecule","results")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",0)
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")
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()
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)
def setup_alignment_contexts(context_info): # Author: Warren DeLano
(list, dict) = context_info[0:2]
doc_list = ['\888Legend:']
obj_name_dict = {}
for a in list:
sf = string.find(a, "_")
if sf >= 0:
object_name = a[0:sf]
if not obj_name_dict.has_key(object_name):
obj_name_dict[object_name] = 1
col_index = cmd.get_object_color_index(object_name)
if col_index >= 0:
col_tup = cmd.get_color_tuple(col_index)
if is_tuple(col_tup):
col_int = map(lambda x: int(x * 9 + 0.49999), col_tup)
col_str = string.join(
map(lambda x: chr(ord('0') + x), col_int), '')
doc_list.append("\\" + col_str + object_name + "\\---")
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.append("")
doc_list.append("\\888Toggles:")
zoom_context = 1
global labels, ligands, waters, sites, cgos, zooms, dashes
labels = 1
ligands = 1
waters = 1
sites = 1
cgos = 0
zooms = 0
dashes = 1
global m4x_sites, m4x_ligands, m4x_waters
m4x_sites = "m4x_sites"
m4x_ligands = "m4x_ligands"
m4x_waters = "m4x_waters"
cmd.select(m4x_sites, "none")
cmd.select(m4x_ligands, "none")
cmd.select(m4x_waters, "none")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_zooms)
doc_list.append(key + ": Zoom")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_sites)
doc_list.append(key + ": Sites")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_waters)
doc_list.append(key + ": Waters")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_dashes)
doc_list.append(key + ": H-Bonds")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_cgos)
doc_list.append(key + ": Fits")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_ligands)
doc_list.append(key + ": Ligands")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_labels)
doc_list.append(key + ": HB-Dists")
for a in list:
include_flag = 0
water = a + "_water"
ligand = a + "_ligand"
site = a + "_site"
hbond = a + "_hbond"
if cmd.count_atoms(site):
if cmd.count_atoms(site + " & m4x_aligned"):
include_flag = 1
if cmd.count_atoms(ligand):
if cmd.count_atoms(ligand + " & m4x_nearby"):
include_flag = 1
if include_flag:
name_list = dict[a]
if water in name_list:
cmd.select(m4x_waters, m4x_waters + "|" + water)
if ligand in name_list:
cmd.select(m4x_ligands, m4x_ligands + "|" + ligand)
if site in name_list:
cmd.select(
m4x_sites,
m4x_sites + "|" + site + "|((byres (neighbor (" + site +
" and name c))) and name n+ca)" + "|((byres (neighbor (" +
site + " and name n))) and name c+ca+o)")
cmd.wizard("fedora", doc_list)
toggle_cgos(1)
toggle_labels(0)
toggle_dashes(0)
toggle_ligands(1)
toggle_sites(0)
toggle_waters(0)
toggle_cgos(1)
cmd.deselect()
# cmd.feedback("enable","python","output")
cmd.feedback("enable", "objectmolecule", "results")
cmd.set("internal_feedback", 1)
cmd.set("internal_prompt", 0)
cmd.feedback("disable", "selector", "actions")
cmd.feedback("disable", "scene", "actions")
