from pymol.wizard import Wizard
from pymol import cmd
import pymol
import types
saved = {}
class Demo(Wizard):
def launch(self,name):
return None
def __init__(self,*arg):
self.message = []
self.last = None
if saved.has_key('last'):
self.last = saved['last']
if len(arg):
demo = DemoInfo()
name = arg[0]
if self.last:
if hasattr(demo,self.last):
getattr(demo,self.last)(cleanup=1)
if hasattr(demo,name):
self.last = name
demo_fn = getattr(demo,name)
t = threading.Thread(target=demo_fn)
t.setDaemon(1)
t.start()
self.message = demo.message_dict.get(name,None)
else:
self.last = None
saved['last']=self.last
def get_prompt(self):
saved['last']=self.last
self.prompt = self.message
return self.prompt
def get_panel(self):
return [
[ 1, 'Demonstrations', '' ],
[ 2, 'Representations', 'replace_wizard demo,reps'],
[ 2, 'Cartoon Ribbons', 'replace_wizard demo,cartoon'],
[ 2, 'Roving Detail', 'replace_wizard demo,roving'],
[ 2, 'Roving Density', 'replace_wizard demo,roving_density'],
[ 2, 'Transparency', 'replace_wizard demo,trans'],
[ 2, 'Ray Tracing', 'replace_wizard demo,ray'],
[ 2, 'Sculpting', 'replace_wizard demo,sculpt'],
[ 2, 'Scripted Animation', 'replace_wizard demo,anime'],
[ 2, 'Electrostatics', 'replace_wizard demo,elec'],
[ 2, 'CGOs', 'replace_wizard demo,cgo'],
[ 2, 'Molscript/R3D Input', 'replace_wizard demo,raster3d'],
[ 2, 'End Demonstration', 'replace_wizard demo,finish' ]
]
from pymol.vfont import plain
from pymol.cgo import *
import string
import traceback
from pymol import util
import threading
class DemoInfo:
message_dict = {
'roving' : [
"Middle-Click to rove... CTRL-SHIFT-Middle-Click to center...",],
'roving_density' : [
"Middle-Click to rove... CTRL-SHIFT-Middle-Click to center...",],
'elec' : [
"CTRL-Middle-Click on color bar to change levels...",],
'sculpt' : [
"CTRL-Left-Click to drag atoms... CTRL-Right-Click to rotate bonds...",],
}
def rep_old(self,cleanup=0):
if not cleanup:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("pept")
cmd.delete("pept_dist")
cmd.load("$PYMOL_DATA/demo/pept.pdb")
cmd.show("sticks","(pept and not i;5:7)")
cmd.show("surface","(pept and i;5,6)")
cmd.show("mesh","(pept and i;1,11,12,13)")
cmd.show("spheres","(pept and i;2,12,9,4 and not n;c,n,o,ca)")
cmd.show("dots","(i;8)")
cmd.dist("pept_dist","(pept and i;1&n;OD2)","(pept and i;13&n;OG1)")
cmd.set("dot_width","2");
finally:
cmd.set("suspend_updates",0,quiet=1)
else:
cmd.delete("pept")
cmd.delete("pept_dist")
def reps(self,cleanup=0):
rep_list = [ "lines","sticks","spheres","surface","mesh","dots","ribbon","cartoon" ]
try:
if not cleanup:
cmd.disable()
cmd.set("suspend_updates",1,quiet=1)
cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
cmd.alter("rep1///1-5+8-13/","ss='S'")
cmd.cartoon("auto")
cmd.hide("everything","rep1")
for a in range(2,9):
cmd.create("rep%d"%a,"rep1")
map(lambda x,y:cmd.show(x,"rep%d"%y),
rep_list,
range(1,9))
cmd.reset()
cmd.zoom("rep1",24)
util.cbay("rep2")
util.cbac("rep3")
util.cbas("rep4")
util.cbab("rep5")
util.cbaw("rep6")
util.cbay("rep8")
cmd.set("suspend_updates",0,quiet=1)
scale=0.5
for b in range(1,20):
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.set("suspend_updates",1,quiet=1)
xt=-3.2
yt=1.6
for a in range(1,5):
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):
cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
for a in range(1,9):
cmd.origin("rep%d"%a,object="rep%d"%a)
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']))
cmd.mdo(1,st)
cmd.set("suspend_updates",0,quiet=1)
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 = 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)
cmd.set("cgo_line_width",1.5)
cmd.set("auto_zoom",0)
cmd.load_cgo(cgo,'reps')
cmd.set("auto_zoom",1)
else:
cmd.delete("rep*")
cmd.mset()
cmd.mstop()
except:
traceback.print_exc()
def raster3d(self,cleanup=0):
if not cleanup:
cmd.disable()
cmd.set_view( (\
0.269525230, -0.492282957, 0.827655137,\
-0.158114254, -0.870419860, -0.466229916,\
0.949923635, -0.005200397, -0.312437057,\
-0.000086844, 0.000019042, -133.217041016,\
11.377667427, 21.768899918, 9.270449638,\
105.029335022, 169.626159668, 0.000000000 ))
cmd.load("$PYMOL_DATA/demo/1hpv.r3d","cgo1")
cmd.zoom("cgo1")
else:
cmd.delete("cgo1")
def cgo(self,cleanup=0):
if not cleanup:
cmd.disable()
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.do("run $PYMOL_DATA/demo/cgo03.py")
finally:
cmd.set("suspend_updates",0,quiet=1)
else:
cmd.delete("cgo03")
cmd.mset()
cmd.mstop()
cmd.rewind()
def anime_old(self,cleanup=0):
if not cleanup:
cmd.disable()
cmd.delete("arg")
cmd.fragment("arg")
cmd.zoom("arg",2)
cmd.show("sticks","arg")
cmd.feedback('dis','sel','res')
for a in xrange(1,181):
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.edit("(arg and n;cd)","(arg and n;cg)",quiet=1)
cmd.torsion("6")
cmd.unpick()
cmd.edit("(arg and n;cb)","(arg and n;ca)",quiet=1)
cmd.torsion("2")
cmd.unpick()
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.feedback('ena','sel','res')
else:
cmd.delete("arg")
def anime(self,cleanup=0):
if not cleanup:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.load("$TUT/1hpv.pdb")
util.chainbow("1hpv")
cmd.hide("everything","1hpv")
cmd.show("cartoon","1hpv")
cmd.show("sticks","1hpv///200/")
cmd.create("1hpv_a","1hpv//A//")
cmd.set("cartoon_smooth_loops",0,"1hpv_a")
cmd.create("1hpv_b","1hpv//B//")
cmd.set("cartoon_smooth_loops",0,"1hpv_b")
cmd.create("1hpv_l","1hpv///200/")
util.cbay("1hpv_l")
cmd.delete("1hpv")
cmd.set_view ((\
0.374249548, -0.517475128, 0.769516647,\
-0.214397043, -0.855623126, -0.471108317,\
0.902203023, 0.011330833, -0.431161582,\
-0.000023194, -0.000007302, -125.089942932,\
11.953758240, 20.323493958, 8.406080246,\
75.304412842, 189.396347046, 0.000000000 ))
cmd.translate([-20,0,0],object="1hpv_a")
cmd.translate([20,0,0],object="1hpv_b")
cmd.zoom("center",30)
cmd.translate([0,10,00],object="1hpv_l")
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
for a in range(1,21):
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.translate([1,0,0],object="1hpv_a")
cmd.translate([-1,0,0],object="1hpv_b")
cmd.translate([0,-0.5,0],object="1hpv_l")
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
for a in range(1,62):
cmd.turn("y",6)
cmd.move('z',2)
cmd.move('y',-0.12)
cmd.refresh()
else:
cmd.delete("1hpv_*")
def roving(self,cleanup=0):
if not cleanup:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.set("ribbon_color","blue","il2")
cmd.set("roving_detail",1)
cmd.set("roving_origin",1)
cmd.set("stick_radius",0.12,"il2")
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
else:
cmd.delete("il2")
cmd.set("roving_detail",0)
cmd.refresh()
cmd.delete("rov_*")
def roving_density(self,cleanup=0):
if not cleanup:
try:
cmd.load("$PYMOL_DATA/demo/il2.pdb")
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.disable()
cmd.enable("il2")
cmd.map_new("map","gaussian","0.75","il2")
cmd.set("ribbon_color","purple","il2")
cmd.set("roving_detail",1)
cmd.set("roving_origin",1)
cmd.set("stick_radius",0.12,"il2")
cmd.set("roving_sticks",0)
cmd.set("roving_polar_contacts",0)
cmd.set("line_width","3")
cmd.set("roving_map1_name","map")
cmd.isomesh("rov_m1","map",9999.0,"il2")
cmd.color("density","rov_m1")
cmd.set_view ((\
0.132852688, -0.729740858, 0.670686543,\
-0.228543565, 0.635894477, 0.737154961,\
-0.964425683, -0.251212329, -0.082298420,\
0.000062190, 0.000183226, -58.861488342,\
13.349151611, -1.565427899, 22.383148193,\
55.259441376, 63.259449005, 0.000000000 ))
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
else:
cmd.set("roving_detail",0)
cmd.set("roving_map1_name","")
cmd.set("roving_polar_contacts",7)
cmd.set("roving_sticks",6)
cmd.delete("il2")
cmd.delete("map")
cmd.set("line_width",1.5)
cmd.refresh()
cmd.set("roving_detail",0)
cmd.delete("rov_*")
cmd.sync()
def cartoon(self,cleanup=0):
if not cleanup:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("1tii")
cmd.load("$PYMOL_DATA/demo/1tii.pdb")
cmd.hide("(1tii)")
cmd.show("cartoon","1tii")
cmd.zoom("1tii")
cmd.spectrum("count","rainbow","1tii////ca")
cmd.set("cartoon_highlight_color","grey50","1tii")
cmd.set("cartoon_fancy_helices",1,"1tii")
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
else:
cmd.delete("1tii")
def elec(self,cleanup=0):
if not cleanup:
cmd.disable()
cmd.delete("pept")
cmd.delete("e_pot")
cmd.delete("e_lvl")
cmd.load("$PYMOL_DATA/demo/pept.pkl")
cmd.hide("(pept)")
cmd.show("surface","pept")
cmd.set("coulomb_dielectric",80.0)
cmd.map_new("e_pot","coulomb",1.0,"pept",5)
cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
cmd.set("surface_color","e_lvl","pept")
cmd.refresh()
else:
cmd.delete("pept")
cmd.delete("e_pot")
cmd.delete("e_lvl")
def trans(self,cleanup=0):
if not cleanup:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("trans")
cmd.load("$PYMOL_DATA/demo/pept.pdb","trans")
cmd.hide("(trans)")
cmd.show("surface","trans")
cmd.show("sticks","trans")
cmd.set("surface_color","white","trans")
cmd.set("transparency",0.5,"trans")
cmd.zoom("trans")
finally:
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
else:
cmd.delete("trans")
def ray(self,cleanup=0):
if not cleanup:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("ray")
cmd.load("$PYMOL_DATA/demo/il2.pdb","ray")
cmd.remove("(ray and hydro)")
cmd.hide("lines","ray")
cmd.show("spheres","ray")
cmd.orient("ray")
cmd.turn("x",90)
util.ray_shadows('heavy')
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.do("ray")
else:
cmd.delete("ray")
def finish(self,cleanup=0):
cmd.do("_ wizard")
def sculpt(self,cleanup=0):
if not cleanup:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("sculpt")
cmd.load("$PYMOL_DATA/demo/pept.pdb","sculpt")
cmd.hide("lines","sculpt")
cmd.show("sticks","sculpt")
cmd.show("spheres","sculpt")
cmd.set("sphere_transparency","0.75","sculpt")
cmd.set("sphere_color","grey","sculpt")
cmd.frame(1)
cmd.set("auto_sculpt",1)
cmd.set("sculpting",1)
cmd.sculpt_activate("sculpt")
cmd.do("edit_mode")
cmd.set("valence","0.05")
cmd.set("suspend_updates",0,quiet=0)
cmd.unpick()
else:
cmd.set("valence","0")
cmd.set("sculpting",0)
cmd.set("auto_sculpt",0)
cmd.delete("sculpt")
cmd.mouse()