# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------------
# bp_surface.py - Binding pocket surface generator for Pymol version 2.0
# -------------------------------------------------------------------------------
# Copyright (C) 2008 by Lightnir - lightnir@gmail.com
# This script is free software; you can redistribute it and#or modify
# it under the terms of the GNU Library General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later version.
# This script is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU Library General Public
# License along with this program; if not, write to the
# Free Software Foundation, Inc.,
# 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
from pymol import cmd
from Tkinter import *
from pymol.cgo import *
from math import *
import Pmw
import tkColorChooser
BPSFrame = None
def __init__(self):
self.menuBar.addcascademenu('Plugin', 'LightnirsPlugins', 'Lightnirs Plugins',
label='Lightnirs Plugins')
self.menuBar.addmenuitem('LightnirsPlugins', 'command',
'BPsurface',
label='BP surface',
command = lambda s=self: BPSurface(s))
class BPSurface:
# Class variables
selections = []
cv = IntVar()
pp = IntVar()
cp = IntVar()
rv = IntVar()
colorize = IntVar()
Default_Color = None
res_states = [['Hydrophobic','Gray',0], ['Aromatic','White',0], ['Polar','Green',0], ['Positive','Red',0], ['Negative','Blue',0], ['Cysteine','Yellow',0], ['Proline','Magenta',0]]
def __init__(self,app):
global BPSFrame
if BPSFrame==None:
BPSFrame = Toplevel(width=400, height=300) # create a root window
BPSFrame.title("BP surface editor") # Set window title
BPSFrame.resizable(0, 0) # Disable window resize
BPSFrame.geometry('-40+40') # Set window placement
self.get_selections()
self.Default_Color = BPSFrame.cget("bg")
# Create Ligand selection Combobox
BPSFrame.cb1 = Pmw.ComboBox(BPSFrame,
label_text = 'Ligand:',
labelpos = 'nw',
scrolledlist_items = BPSurface.selections
)
BPSFrame.cb1.grid(row=0, column=0,columnspan=2)
# Create binding pocket Combobox
BPSFrame.cb2 = Pmw.ComboBox(BPSFrame,
label_text = 'Binding pocket:',
labelpos = 'nw',
scrolledlist_items = BPSurface.selections
)
BPSFrame.cb2.grid(row=1, column=0,columnspan=2)
# Create Z axis Slider
BPSFrame.slider1 = Scale(BPSFrame, from_=-20, to=20, command=self.scaling, tickinterval=10, resolution=0.5, label='Z axis cutoff', orient=HORIZONTAL)
BPSFrame.slider1.grid(row=2, column=0, columnspan=2, sticky=N+W+S+E,)
# Create X axis Slider
BPSFrame.slider2 = Scale(BPSFrame, from_=-90, to=90, command=self.scaling, tickinterval=30, resolution=1, label='X axis rotation',orient=HORIZONTAL)
# Create Y axis Slider
BPSFrame.slider3 = Scale(BPSFrame, from_=-90, to=90, command=self.scaling, tickinterval=30, resolution=1, label='Y axis rotation', orient=HORIZONTAL)
# Add Checkboxes
BPSurface.cv.set(1)
cbx = Checkbutton(BPSFrame, text="Create new object", command=None, variable=BPSurface.cv, onvalue="1", offvalue="0")
cbx.grid(row=5,column=0, columnspan=2, sticky=W)
self.CreatePlane()
BPSurface.pp.set(1)
cbx2 = Checkbutton(BPSFrame, text="Plane preview", command=self.TogglePlane, variable=BPSurface.pp, onvalue="1", offvalue="0")
cbx2.grid(row=6,column=0, columnspan=2, sticky=W)
BPSurface.cp.set(0)
cbx3 = Checkbutton(BPSFrame, text="Use custom plane", command=self.ToggleCustomPlane, variable=BPSurface.cp, onvalue="1", offvalue="0")
cbx3.grid(row=7,column=0, columnspan=2, sticky=W)
BPSurface.rv.set(0)
cbx4 = Checkbutton(BPSFrame, text="Make residue selections", command=self.ToggleResidueSelect, variable=BPSurface.rv, onvalue="1", offvalue="0")
cbx4.grid(row=8,column=0, columnspan=2, sticky=W)
# Add some buttons
btn1=Button(BPSFrame, text='Refresh', padx=0, pady=0, command = self.refresh_list)
btn1.grid(row=9, column=0, sticky=N+W+S+E, padx=0, pady=0,ipadx=0,ipady=0)
btn2=Button(BPSFrame, text='Clear', padx=0, pady=0, command = lambda r=1,d=1: self.clear_flags(r,d))
btn2.grid(row=9, column=1, sticky=N+W+S+E, padx=0, pady=0,ipadx=0,ipady=0)
btn3=Button(BPSFrame, text='Apply', padx=0, pady=0, command = self.ok)
btn3.grid(row=10, column=0, sticky=N+W+S+E,)
btn4=Button(BPSFrame, text='Close', padx=0, pady=0, command = self.myHide)
btn4.grid(row=10, column=1, sticky=N+W+S+E)
# Residue selection column
# Create frame for residue content
BPSFrame.Res = Frame(BPSFrame)
# Create Colorize button
self.colorize.set(1)
col_cbx = Checkbutton(BPSFrame.Res, text="Colorize residues", command=self.ToggleColor, variable=self.colorize, onvalue=1, offvalue=0)
col_cbx.grid(row=0,column=0, sticky=N+W)
# Create group widget
BPSFrame.gr = Pmw.Group(BPSFrame.Res, tag_text='Residues')
BPSFrame.gr.grid(row=1, column=0, padx=3, pady=3, sticky=N+W+E)
# Create residues buttons and checkboxes
BPSFrame.ccb = []
for i in range(0,len(self.res_states)):
var = IntVar()
var.set(1)
BPSFrame.ccb.append(Button(BPSFrame.gr.interior(), text='', bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED, height=1, width=2, padx=0, pady=0, command=lambda nr=i: self.changecolor(nr)))
BPSFrame.ccb[i].grid(row=i,column=0, sticky=N+W)
rs_cbx = Checkbutton(BPSFrame.gr.interior(), text=self.res_states[i][0], variable=var, onvalue="1", offvalue="0")
rs_cbx.grid(row=i,column=1, sticky=N+W)
self.res_states[i][2]=var
undo1 = Button(BPSFrame.Res, text='Undo all', padx=0, pady=0, command = lambda u="all":self.undo(u))
undo1.grid(row=2,column=0, sticky=N+W+E)
undo2 = Button(BPSFrame.Res, text='Undo last', padx=0, pady=0, command = lambda u="last":self.undo(u))
undo2.grid(row=3,column=0, sticky=N+W+E)
# Define own colors
self.create_bp_colors()
# Make a backup session
cmd.save('bp_undoall.pse', '(all)')
# create callback to prevent window kill
BPSFrame.protocol("WM_DELETE_WINDOW", self.myHide)
BPSFrame.mainloop()
else:
if BPSFrame.state() == "normal":
self.myHide()
elif BPSFrame.state() == "withdrawn":
self.myShow()
def ToggleColor(self):
if self.colorize.get()==1:
for i in range(0,len(self.res_states)):
BPSFrame.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
else:
for i in range(0,len(self.res_states)):
BPSFrame.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
def changecolor(self,nr):
new_color = tkColorChooser.askcolor(self.res_states[nr][1])
rgb_color = map(lambda color: '%.4f'%float(color/float(65536)) ,new_color[0])
self.res_states[nr][1]=new_color[1]
print rgb_color,new_color[1]
cmd.set_color('bp_plugin_color_'+str(nr),new_color[0],0)
BPSFrame.ccb[nr].config(bg=new_color[1], activebackground=new_color[1])
def create_bp_colors(self):
for i in range(0,len(self.res_states)):
rgb_color = map(lambda color: '%.4f'%float(color/float(65536)) ,BPSFrame.winfo_rgb(self.res_states[i][1]))
cmd.set_color('bp_plugin_color_'+str(i),rgb_color)
def state(self):
return map(lambda var: var[2].get(), self.res_states)
def undo(self,u):
if u=="all":
cmd.load('bp_undoall.pse')
if u=="last":
cmd.load('bp_undolast.pse')
self.TogglePlane()
def scaling(self,v):
self.TogglePlane()
def myShow(self):
self.refresh_list()
BPSFrame.deiconify()
def myHide(self):
cmd.delete("plane_preview")
BPSFrame.withdraw()
def get_selections(self):
BPSurface.selections = []
for item in cmd.get_names("all"):
if cmd.get_type(item)=="object:molecule":
BPSurface.selections.append(item)
if cmd.get_type(item)=="selection":
if item[0]<>"_":
BPSurface.selections.append(item)
def refresh_list(self):
if BPSurface.pp.get()==1:
self.CreatePlane()
# Save old values
old = BPSurface.selections
try:
old_cb1=BPSFrame.cb1.getvalue()[0]
except:
old_cb1=''
try:
old_cb2=BPSFrame.cb2.getvalue()[0]
except:
old_cb2=''
self.get_selections()
# Update selectionlist if needed
if not(old==BPSurface.selections):
BPSFrame.cb1.setlist(BPSurface.selections)
BPSFrame.cb2.setlist(BPSurface.selections)
# Is ligand selection still available?
if not(old_cb1 in BPSurface.selections):
# No - clear the combobox entry
BPSFrame.cb1.component('entryfield').clear()
else:
# Yes - set the old value
BPSFrame.cb1.selectitem(old_cb1,setentry=1)
# Is binding pocket selection still available?
if not(old_cb2 in BPSurface.selections):
# No - clear the combobox entry
BPSFrame.cb2.component('entryfield').clear()
else:
# Yes - set the old value
BPSFrame.cb2.selectitem(old_cb2,setentry=1)
def clear_flags(self,r,d):
cmd.flag('ignore','all','clear')
if r==1:
cmd.rebuild('all')
if d==1:
cmd.delete('bp_cutoff')
cmd.delete('bp_surface')
cmd.delete('bp_hydrophobic')
cmd.delete('bp_aromatic')
cmd.delete('bp_negative')
cmd.delete('bp_positive')
cmd.delete('bp_proline')
cmd.delete('bp_cysteine')
cmd.delete('bp_polar')
def CreatePlane(self):
view = cmd.get_view()
# choose the size of the plane
plane_size = abs(view[11])/4.0
obj = []
# Create a plane in camera space
plane = [
[ -plane_size, plane_size, BPSFrame.slider1.get() ],
[ plane_size, plane_size, BPSFrame.slider1.get() ],
[ -plane_size, -plane_size, BPSFrame.slider1.get() ],
[ plane_size, -plane_size, BPSFrame.slider1.get() ]]
# Using custom plane?
if BPSurface.cp.get()==1:
sinx = sin(pi*BPSFrame.slider2.get()/180)
siny = sin(pi*BPSFrame.slider3.get()/180)
cosx = cos(pi*BPSFrame.slider2.get()/180)
cosy = cos(pi*BPSFrame.slider3.get()/180)
# Map XY axis rotation
# cosY sinX*sinY -cosX*sinY
# 0 cosX sinX
# sinY -sinX*cosY cosX*cosY
plane = map( lambda p: [
cosy*p[0] + sinx*siny*p[1] + (-cosx*siny*p[2]),
cosx * p[1] + sinx* p[2],
siny * p[0] + (-sinx*cosy*p[1]) + cosx*cosy*p[2]
], plane )
normal = [ 0.0, 0.0, 1.0 ]
# Transform plane coordinates into model space
plane = map( lambda p,v=view: [
v[0] * p[0] + v[1] * p[1] + v[2]* p[2],
v[3] * p[0] + v[4] * p[1] + v[5]* p[2],
v[6] * p[0] + v[7] * p[1] + v[8]* p[2]
], plane )
normal = apply( lambda p,v=view:[
v[0] * p[0] + v[1] * p[1] + v[2]* p[2],
v[3] * p[0] + v[4] * p[1] + v[5]* p[2],
v[6] * p[0] + v[7] * p[1] + v[8]* p[2]
], (normal,) )
# Transform position relative to the camera
plane = map( lambda p,v=view: [
p[0] + v[9 ] + v[12],
p[1] + v[10] + v[13],
p[2] + + v[14],
], plane )
obj.extend( [ COLOR, 0.5, 0.5, 1.0 ] ) # blueish
obj.extend( [ BEGIN, TRIANGLE_STRIP ] )
obj.append( NORMAL )
obj.extend( normal )
# draw the plane
for a in plane:
obj.append( VERTEX)
obj.extend(a)
obj.append( END )
# delete existing object (if any)
cmd.delete("plane_preview")
# now load the new object without zooming
cmd.set('auto_zoom', 0, quiet=1)
auto_zoom = cmd.get('auto_zoom')
cmd.load_cgo(obj,'plane_preview')
cmd.set('auto_zoom', auto_zoom, quiet=1)
def TogglePlane(self):
if BPSurface.pp.get()==0:
cmd.delete("plane_preview")
if BPSurface.pp.get()==1:
self.CreatePlane()
def ToggleCustomPlane(self):
self.TogglePlane()
if BPSurface.cp.get()==0:
BPSFrame.slider2.grid_remove()
BPSFrame.slider3.grid_remove()
if BPSurface.cp.get()==1:
BPSFrame.slider2.grid(row=3, column=0, columnspan=2, sticky=N+W+S+E,)
BPSFrame.slider3.grid(row=4, column=0, columnspan=2, sticky=N+W+S+E,)
def ToggleResidueSelect(self):
if BPSurface.rv.get()==1:
BPSFrame.Res.grid(row=0, column=2, rowspan=10, sticky=N+W+E)
if BPSurface.rv.get()==0:
BPSFrame.Res.grid_remove()
def ok(self):
# Has cb1 a value?
sel1 = BPSFrame.cb1.getvalue()
if len(sel1) == 0:
dialog = Pmw.MessageDialog(BPSFrame,
title = 'Error',
defaultbutton = 0,
buttons = ('OK',),
message_text = 'ERROR: No ligand selection. Please\n choose one from the dropdownlist.'
)
dialog.iconname('Selection Error')
dialog.bell()
dialog.activate()
return 0
# Has cb2 a value?
sel2 = BPSFrame.cb2.getvalue()
if len(sel2) == 0:
dialog = Pmw.MessageDialog(BPSFrame,
title = 'Error',
defaultbutton = 0,
buttons = ('OK',),
message_text = 'ERROR: No binding pocket selection. Please\n choose one from the dropdownlist.'
)
dialog.iconname('Selection Error')
dialog.bell()
dialog.activate()
return 0
# Are cb1 and cb2 the same?
if sel1[0]==sel2[0]:
dialog = Pmw.MessageDialog(BPSFrame,
title = 'Error',
defaultbutton = 0,
buttons = ('OK',),
message_text = 'ERROR: Ligand and binding pocket must have different selections'
)
dialog.iconname('Selection Error')
dialog.bell()
dialog.activate()
return 0
# Set orgin and normal vector
cmd.origin(sel1[0])
vector = [[ 0, 0, 1]]
# Using custom plane?
if BPSurface.cp.get()==1:
sinx = sin(pi*BPSFrame.slider2.get()/180)
siny = sin(pi*BPSFrame.slider3.get()/180)
cosx = cos(pi*BPSFrame.slider2.get()/180)
cosy = cos(pi*BPSFrame.slider3.get()/180)
# Remap the normal vector to custom
vector = map( lambda p: [
cosy*p[0] + sinx*siny*p[1] + (-cosx*siny*p[2]),
cosx * p[1] + sinx* p[2],
siny * p[0] + (-sinx*cosy*p[1]) + cosx*cosy*p[2]
], vector )
# Remap the normal vector to the model space
d=cmd.get_view(0)
vector = map( lambda p,v=d: [
v[0] * p[0] + v[1] * p[1] + v[2]* p[2],
v[3] * p[0] + v[4] * p[1] + v[5]* p[2],
v[6] * p[0] + v[7] * p[1] + v[8]* p[2]
], vector )
# Calculate plane coefficients
# Ax + By + Cz + D = 0
# D = -Ax -By -Cz
A = vector[0][0]
B = vector[0][1]
C = vector[0][2]
D = -vector[0][0]*d[12] - vector[0][1]*d[13] - vector[0][2]*d[14]
atoms = cmd.get_model(sel2[0])
# Surface stuff
self.clear_flags(0,1)
for at in atoms.atom:
if (A*(at.coord[0])+B*at.coord[1]+C*at.coord[2]+D-BPSFrame.slider1.get()>0):
if not('bp_cutoff' in cmd.get_names("selections")):
cmd.select('bp_cutoff','index '+str(at.index))
else:
cmd.select('bp_cutoff','bp_cutoff or index '+str(at.index))
if ('bp_cutoff' in cmd.get_names("selections")):
if BPSurface.cv.get()==0:
cmd.flag('ignore','bp_cutoff','reset')
cmd.delete('indicate')
cmd.deselect()
cmd.show('surface',sel2[0])
else:
self.clear_flags(0,0)
cmd.hide('surface',sel2[0])
cmd.set('auto_zoom','off')
cmd.create('bp_surface',sel2[0]+' and not bp_cutoff')
cmd.set('auto_zoom','on')
cmd.show('surface','bp_surface')
cmd.rebuild(sel2[0])
# Selections stuff
if BPSurface.rv.get()==1: # make residue selections
if self.state()[0]==1: # select hydrophobic
cmd.select('bp_hydrophobic', 'byres ('+sel2[0]+' and resn ala+gly+ile+leu+met+val)')
if self.state()[1]==1: # select aromatic
cmd.select('bp_aromatic', 'byres ('+sel2[0]+' and resn phe+trp+tyr)')
if self.state()[2]==1: # select polar
cmd.select('bp_polar', 'byres ('+sel2[0]+' and resn his+asn+gln+ser+thr)')
if self.state()[3]==1: # select positive
cmd.select('bp_positive', 'byres ('+sel2[0]+' and resn lys+arg)')
if self.state()[4]==1: # select negative
cmd.select('bp_negative', 'byres ('+sel2[0]+' and resn asp+glu)')
if self.state()[5]==1: # select cysteine
cmd.select('bp_cysteine', 'byres ('+sel2[0]+' and resn cys)')
if self.state()[6]==1: # select proline
cmd.select('bp_proline', 'byres ('+sel2[0]+' and resn pro)')
cmd.deselect()
cmd.save('bp_undolast.pse', '(all)')
if (BPSurface.rv.get()==1 and BPSurface.colorize.get()==1): # colorize?
if self.state()[0]==1: # hydrophobic
cmd.color('bp_plugin_color_0','bp_hydrophobic')
if self.state()[1]==1: # select aromatic
cmd.color('bp_plugin_color_1','bp_aromatic')
if self.state()[2]==1: # select polar
cmd.color('bp_plugin_color_2','bp_polar')
if self.state()[3]==1: # select positive
cmd.color('bp_plugin_color_3','bp_positive')
if self.state()[4]==1: # select negative
cmd.color('bp_plugin_color_4','bp_negative')
if self.state()[5]==1: # select cysteine
cmd.color('bp_plugin_color_5','bp_cysteine')
if self.state()[6]==1: # select proline
cmd.color('bp_plugin_color_6','bp_proline')
After a month when I went to work a package was lying at my desk. Containing this magazine. The scan below does not reflect the actual appearance because of the print on a semi gloss paper. It looks more darker then it is. Neither the less it feels really good to see my own work in print.
