Difference between revisions of "DynoPlot"

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m
Line 69: Line 69:
  
 
try:
 
try:
    import pymol
+
import pymol
    REAL_PYMOL = True
+
REAL_PYMOL = True
 
except ImportError:
 
except ImportError:
 
print "Nope"
 
print "Nope"
  
 
canvas = None
 
canvas = None
 +
rootframe = None
 
init = 0
 
init = 0
  
 
class SimplePlot(Tkinter.Canvas):
 
class SimplePlot(Tkinter.Canvas):
 
+
 
# Class variables
 
# Class variables
 
mark = 'Oval' # Only 'Oval' for now..
 
mark = 'Oval' # Only 'Oval' for now..
Line 93: Line 94:
 
item = (0,)    # items array used for clickable events
 
item = (0,)    # items array used for clickable events
 
shapes = {}    # store plot data, x,y etc..
 
shapes = {}    # store plot data, x,y etc..
 
+
 
def axis(self,xmin=40,xmax=300,ymin=10,ymax=290,xint=290,yint=40,xlabels=[],ylabels=[]):
 
def axis(self,xmin=40,xmax=300,ymin=10,ymax=290,xint=290,yint=40,xlabels=[],ylabels=[]):
 
+
 
# Store variables in self object
 
# Store variables in self object
 
self.xlabels = xlabels
 
self.xlabels = xlabels
Line 103: Line 104:
 
self.xmin = xmin
 
self.xmin = xmin
 
self.ymin = ymin
 
self.ymin = ymin
 
+
 
# Create axis lines
 
# Create axis lines
 
self.create_line((xmin,xint,xmax,xint),fill="black",width=3)
 
self.create_line((xmin,xint,xmax,xint),fill="black",width=3)
 
self.create_line((yint,ymin,yint,ymax),fill="black",width=3)
 
self.create_line((yint,ymin,yint,ymax),fill="black",width=3)
 
+
 
# Create tick marks and labels
 
# Create tick marks and labels
 
nextspot = xmin
 
nextspot = xmin
 
for label in xlabels:
 
for label in xlabels:
    self.create_line((nextspot, xint+5,nextspot, xint-5),fill="black",width=2)
+
self.create_line((nextspot, xint+5,nextspot, xint-5),fill="black",width=2)
    self.create_text(nextspot, xint-15, text=label)
+
self.create_text(nextspot, xint-15, text=label)
    if len(xlabels) == 1:
+
if len(xlabels) == 1:
nextspot = xmax
+
nextspot = xmax
    else:
+
else:
        nextspot += (xmax - xmin)/ (len(xlabels) - 1)
+
nextspot = nextspot + (xmax - xmin)/ (len(xlabels) - 1)
 
+
 
+
 
nextspot = ymax
 
nextspot = ymax
    for label in ylabels:
+
for label in ylabels:
    self.create_line((yint+5,nextspot,yint-5,nextspot),fill="black",width=2)
+
self.create_line((yint+5,nextspot,yint-5,nextspot),fill="black",width=2)
    self.create_text(yint-20,nextspot,text=label)
+
self.create_text(yint-20,nextspot,text=label)
    if len(ylabels) == 1:
+
if len(ylabels) == 1:
nextspot = ymin
+
nextspot = ymin
    else:
+
else:
        nextspot -= (ymax - ymin)/ (len(ylabels) - 1)
+
nextspot = nextspot - (ymax - ymin)/ (len(ylabels) - 1)
 
+
 
+
 
# Plot a point
 
# Plot a point
 
def plot(self,xp,yp,meta):
 
def plot(self,xp,yp,meta):
Line 135: Line 136:
 
x = self.convertToPixel("X",xp)
 
x = self.convertToPixel("X",xp)
 
y = self.convertToPixel("Y",yp)
 
y = self.convertToPixel("Y",yp)
 
+
 
if self.mark == "Oval":
 
if self.mark == "Oval":
    oval = self.create_oval(x-self.mark_size,y-self.mark_size,x+self.mark_size,y+self.mark_size,width=1,outline="black",fill="SkyBlue2")
+
oval = self.create_oval(x-self.mark_size,y-self.mark_size,x+self.mark_size,y+self.mark_size,width=1,outline="black",fill="SkyBlue2")
 
+
    self.shapes[oval] = [x,y,0,xp,yp,meta]
+
self.shapes[oval] = [x,y,0,xp,yp,meta]
 
+
 
+
 
# Repaint all points
 
# Repaint all points
 
def repaint(self):
 
def repaint(self):
for value in self.shapes.values():
+
for key,value in self.shapes.items():
 
x = value[0]
 
x = value[0]
 
y = value[1]
 
y = value[1]
 
self.create_oval(x-self.mark_size,y-self.mark_size,x+self.mark_size,y+self.mark_size,width=1,outline="black",fill="SkyBlue2")
 
self.create_oval(x-self.mark_size,y-self.mark_size,x+self.mark_size,y+self.mark_size,width=1,outline="black",fill="SkyBlue2")
 
+
 
# Convert from pixel space to label space
 
# Convert from pixel space to label space
 
def convertToLabel(self,axis, value):
 
def convertToLabel(self,axis, value):
 
+
 
# Defaultly use X-axis info
 
# Defaultly use X-axis info
 
label0  = self.xlabels[0]
 
label0  = self.xlabels[0]
Line 157: Line 158:
 
spacing = self.spacingx
 
spacing = self.spacingx
 
min    = self.xmin
 
min    = self.xmin
 
+
 
# Set info for Y-axis use
 
# Set info for Y-axis use
 
if axis == "Y":
 
if axis == "Y":
      label0    = self.ylabels[0]
+
label0    = self.ylabels[0]
      label1    = self.ylabels[1]
+
label1    = self.ylabels[1]
    spacing  = self.spacingy
+
spacing  = self.spacingy
    min      = self.ymin
+
min      = self.ymin
 
+
 
pixel = value - min
 
pixel = value - min
 
label = pixel / spacing
 
label = pixel / spacing
 
label = label0 + label * abs(label1 - label0)
 
label = label0 + label * abs(label1 - label0)
 
+
 
if axis == "Y":
 
if axis == "Y":
 
label = - label
 
label = - label
 
+
 
return label
 
return label
 
+
 
# Converts value from 'label' space to 'pixel' space
 
# Converts value from 'label' space to 'pixel' space
 
def convertToPixel(self,axis, value):
 
def convertToPixel(self,axis, value):
 
+
 
# Defaultly use X-axis info
 
# Defaultly use X-axis info
 
label0  = self.xlabels[0]
 
label0  = self.xlabels[0]
Line 182: Line 183:
 
spacing = self.spacingx
 
spacing = self.spacingx
 
min    = self.xmin
 
min    = self.xmin
 
+
 
# Set info for Y-axis use
 
# Set info for Y-axis use
 
if axis == "Y":
 
if axis == "Y":
      label0    = self.ylabels[0]
+
label0    = self.ylabels[0]
      label1    = self.ylabels[1]
+
label1    = self.ylabels[1]
    spacing  = self.spacingy
+
spacing  = self.spacingy
    min      = self.ymin
+
min      = self.ymin
 
+
 
+
 
# Get axis increment in 'label' space
 
# Get axis increment in 'label' space
 
inc = abs(label1 - label0)
 
inc = abs(label1 - label0)
 
+
 
# 'Label' difference from value and smallest label (label0)
 
# 'Label' difference from value and smallest label (label0)
 
diff = float(value - label0)
 
diff = float(value - label0)
Line 199: Line 200:
 
# Get whole number in 'label' space
 
# Get whole number in 'label' space
 
whole = int(diff / inc)
 
whole = int(diff / inc)
 
+
 
# Get fraction number in 'label' space
 
# Get fraction number in 'label' space
 
part = float(float(diff/inc) - whole)
 
part = float(float(diff/inc) - whole)
 
+
 
# Return 'pixel' position value
 
# Return 'pixel' position value
 
pixel = whole * spacing + part * spacing
 
pixel = whole * spacing + part * spacing
 
+
# print "Pixel: %f * %f + %f * %f = %f" % (whole, spacing, part, spacing,pixel)
+
# print "Pixel: %f * %f + %f * %f = %f" % (whole, spacing, part, spacing,pixel)
 
+
 
# Reverse number by subtracting total number of pixels - value pixels
 
# Reverse number by subtracting total number of pixels - value pixels
 
if axis == "Y":
 
if axis == "Y":
  tot_label_diff = float(self.ylabels[len(self.ylabels)- 1] - label0)
+
tot_label_diff = float(self.ylabels[len(self.ylabels)- 1] - label0)
  tot_label_whole = int(tot_label_diff / inc)
+
tot_label_whole = int(tot_label_diff / inc)
  tot_label_part = float(float(tot_label_diff / inc) - tot_label_whole)
+
tot_label_part = float(float(tot_label_diff / inc) - tot_label_whole)
  tot_label_pix  = tot_label_whole * spacing + tot_label_part *spacing
+
tot_label_pix  = tot_label_whole * spacing + tot_label_part *spacing
 
+
  pixel = tot_label_pix - pixel
+
pixel = tot_label_pix - pixel
 
+
 
# Add min edge pixels
 
# Add min edge pixels
 
pixel = pixel + min
 
pixel = pixel + min
 
 
 
return pixel
 
return pixel
 
+
 
 
 
# Print out which data point you just clicked on..
 
# Print out which data point you just clicked on..
 
def pickWhich(self,event):
 
def pickWhich(self,event):
+
    # Find closest data point      
+
# Find closest data point      
    x = event.widget.canvasx(event.x)
+
x = event.widget.canvasx(event.x)
            y = event.widget.canvasx(event.y)
+
y = event.widget.canvasx(event.y)
    spot = event.widget.find_closest(x,y)
+
spot = event.widget.find_closest(x,y)
 
+
    # Print the shape's meta information corresponding with the shape that was picked
+
# Print the shape's meta information corresponding with the shape that was picked
    if spot[0] in self.shapes:
+
if self.shapes.has_key(spot[0]):
print "Residue(Ca): %s\n" % self.shapes[spot[0]][5][2]
+
print "Residue(Ca): %s\n" % str(self.shapes[spot[0]][5][2])
 
+
 
+
        # Mouse Down Event
+
# Mouse Down Event
 
def down(self,event):
 
def down(self,event):
 
+
    # Store x,y position
+
# Store x,y position
    self.lastx = event.x
+
self.lastx = event.x
    self.lasty = event.y
+
self.lasty = event.y
 
+
    # Find the currently selected item
+
# Find the currently selected item
    x = event.widget.canvasx(event.x)
+
x = event.widget.canvasx(event.x)
            y = event.widget.canvasx(event.y)
+
y = event.widget.canvasx(event.y)
    self.item = event.widget.find_closest(x,y)
+
self.item = event.widget.find_closest(x,y)
 +
 +
# Identify that the mouse is down
 +
self.down  = 1
 
 
    # Identify that the mouse is down
 
    self.down  = 1
 
 
 
# Mouse Up Event
 
# Mouse Up Event
 
def up(self,event):
 
def up(self,event):
 
+
    # Get label space version of x,y
+
# Get label space version of x,y
    labelx = self.convertToLabel("X",event.x)
+
labelx = self.convertToLabel("X",event.x)
    labely = self.convertToLabel("Y",event.y)
+
labely = self.convertToLabel("Y",event.y)
 
+
    # Convert new position into label space..
+
# Convert new position into label space..
    if self.item[0] in self.shapes:
+
if self.shapes.has_key(self.item[0]):
        self.shapes[self.item[0]][0] = event.x
+
self.shapes[self.item[0]][0] = event.x
        self.shapes[self.item[0]][1] = event.y
+
self.shapes[self.item[0]][1] = event.y
        self.shapes[self.item[0]][2] =  1
+
self.shapes[self.item[0]][2] =  1
        self.shapes[self.item[0]][3] = labelx
+
self.shapes[self.item[0]][3] = labelx
        self.shapes[self.item[0]][4] = labely
+
self.shapes[self.item[0]][4] = labely
 
+
    # Reset Flags
+
# Reset Flags
    self.item = (0,)
+
self.item = (0,)
            self.down = 0
+
self.down = 0
 
+
 
+
 
# Mouse Drag(Move) Event
 
# Mouse Drag(Move) Event
 
def drag(self,event):
 
def drag(self,event):
 
 
# Check that mouse is down and item clicked is a valid data point
+
# Check that mouse is down and item clicked is a valid data point
if self.down and self.item[0] in self.shapes:
+
if self.down and self.shapes.has_key(self.item[0]):
 +
 +
self.move(self.item, event.x - self.lastx, event.y - self.lasty)
 
 
    self.move(self.item, event.x - self.lastx, event.y - self.lasty)
+
self.lastx = event.x
 
+
self.lasty = event.y
    self.lastx = event.x
 
    self.lasty = event.y
 
  
  
 
def __init__(self):
 
def __init__(self):
 
+
        self.menuBar.addcascademenu('Plugin', 'PlotTools', 'Plot Tools',
+
self.menuBar.addcascademenu('Plugin', 'PlotTools', 'Plot Tools',
                                    label='Plot Tools')
+
label='Plot Tools')
        self.menuBar.addmenuitem('PlotTools', 'command',
+
self.menuBar.addmenuitem('PlotTools', 'command',
                                'Launch Rama Plot',
+
'Launch Rama Plot',
                                label='Rama Plot',
+
label='Rama Plot',
                                command = lambda s=self: ramaplot())
+
command = lambda s=self: ramaplot())
  
  
 
def ramaplot(x=0,y=0,meta=[],clear=0):
 
def ramaplot(x=0,y=0,meta=[],clear=0):
    global canvas
+
global canvas
    global init
+
global rootframe
 +
global init
 +
 +
# If no window is open
 +
if init == 0:
 +
rootframe=Tk()
 +
rootframe.title(' Dynamic Angle Plotting ')
 +
rootframe.protocol("WM_DELETE_WINDOW", close_callback)
 +
 +
canvas = SimplePlot(rootframe,width=320,height=320)
 +
canvas.bind("<Button-2>",canvas.pickWhich)
 +
canvas.bind("<Button-3>",canvas.pickWhich)
 +
canvas.bind("<ButtonPress-1>",canvas.down)
 +
canvas.bind("<ButtonRelease-1>",canvas.up)
 +
canvas.bind("<Motion>",canvas.drag)
 +
canvas.pack(side=Tkinter.LEFT,fill="both",expand=1)
 +
canvas.axis(xint=150,xlabels=range(-180,181,30),ylabels=range(-180,181, 30))
 +
canvas.update()
 +
init = 1
 +
else:
 +
canvas.plot(int(x), int(y),meta)
  
    # If no window is open
+
def close_callback():
    if init == 0:
+
global init
        rootframe=Tk()
+
global rootframe
        rootframe.title(' Dynamic Angle Plotting ')
+
init=0
 +
rootframe.destroy()
  
        canvas = SimplePlot(rootframe,width=320,height=320)
 
        canvas.bind("<Button-2>",canvas.pickWhich)
 
        canvas.bind("<Button-3>",canvas.pickWhich)
 
        canvas.bind("<ButtonPress-1>",canvas.down)
 
        canvas.bind("<ButtonRelease-1>",canvas.up)
 
        canvas.bind("<Motion>",canvas.drag)
 
        canvas.pack(side=Tkinter.LEFT,fill="both",expand=1)
 
        canvas.axis(xint=150,xlabels=[-180,-150,-120,-90,-60,-30,0,30,60,90,120,150,180],ylabels=[-180,-150,-120,-90,-60,-30,0,30,60,90,120,150,180])
 
        canvas.update()
 
init = 1
 
    else:
 
      canvas.plot(int(x), int(y),meta)
 
  
  
Line 319: Line 329:
 
class DynoRamaObject:
 
class DynoRamaObject:
 
global canvas
 
global canvas
 
+
 
def start(self,sel):
 
def start(self,sel):
 
+
    # Get selection model
+
# Get selection model
      model = cmd.get_model(sel)
+
model = cmd.get_model(sel)
    residues = ['dummy']
+
residues = ['dummy']
    resnames = ['dummy']
+
resnames = ['dummy']
    phi = []
+
phi = []
    psi = []
+
psi = []
    dummy = []
+
dummy = []
    i = 0
+
i = 0
 
+
            # Loop through each atom
+
# Loop through each atom
    for at in model.atom:
+
for at in model.atom:
 
 
# Only plot once per residue
 
    if at.chain+":"+at.resn+":"+at.resi not in residues:
 
        residues.append(at.chain+":"+at.resn+":"+at.resi)
 
        resnames.append(at.resn+at.resi)
 
        dummy.append(i)
 
        i += 1
 
 
 
            # Check for a null chain id (some PDBs contain this)
 
        unit_select = ""
 
        if at.chain != "":
 
    unit_select = "chain "+str(at.chain)+" and "
 
 
 
        # Define selections for residue i-1, i and i+1   
 
    residue_def = unit_select+'resi '+str(at.resi)
 
      residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
 
    residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
 
 
 
    try:
 
# Store phi,psi residue definitions to pass on to plot routine
 
phi_psi = [
 
# Phi angles
 
  residue_def_prev+' and name C',
 
  residue_def+' and name N',
 
  residue_def+' and name CA',
 
  residue_def+' and name C',
 
# Psi angles
 
  residue_def+' and name N',
 
  residue_def+' and name CA',
 
  residue_def+' and name C',
 
    residue_def_next+' and name N']
 
 
 
          # Compute phi/psi angle
 
        phi = cmd.get_dihedral(phi_psi[0],phi_psi[1],phi_psi[2],phi_psi[3])
 
        psi = cmd.get_dihedral(phi_psi[4],phi_psi[5],phi_psi[6],phi_psi[7])
 
 
 
print "Plotting Phi,Psi: "+str(phi)+","+str(psi)     
+
# Only plot once per residue
        ramaplot(phi,psi,meta=phi_psi)
+
if not at.chain+":"+at.resn+":"+at.resi in residues:
    except:
+
residues.append(at.chain+":"+at.resn+":"+at.resi)
continue
+
resnames.append(at.resn+at.resi)
 
+
dummy.append(i)
 
+
i += 1
 +
 +
# Check for a null chain id (some PDBs contain this)
 +
unit_select = ""
 +
if not at.chain == "":
 +
unit_select = "chain "+str(at.chain)+" and "
 +
 +
# Define selections for residue i-1, i and i+1   
 +
residue_def = unit_select+'resi '+str(at.resi)
 +
residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
 +
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
 +
 +
try:
 +
# Store phi,psi residue definitions to pass on to plot routine
 +
phi_psi = [
 +
# Phi angles
 +
residue_def_prev+' and name C',
 +
residue_def+' and name N',
 +
residue_def+' and name CA',
 +
residue_def+' and name C',
 +
# Psi angles
 +
residue_def+' and name N',
 +
residue_def+' and name CA',
 +
residue_def+' and name C',
 +
residue_def_next+' and name N']
 +
 +
# Compute phi/psi angle
 +
phi = cmd.get_dihedral(phi_psi[0],phi_psi[1],phi_psi[2],phi_psi[3])
 +
psi = cmd.get_dihedral(phi_psi[4],phi_psi[5],phi_psi[6],phi_psi[7])
 +
 +
print "Plotting Phi,Psi: "+str(phi)+","+str(psi)     
 +
ramaplot(phi,psi,meta=phi_psi)
 +
except:
 +
continue
 +
 +
 
def __call__(self):
 
def __call__(self):
 +
 +
# Loop through each item on plot to see if updated
 +
for key,value in canvas.shapes.items():
 +
dihedrals = value[5]
 +
 +
# Look for update flag...
 +
if value[2]:
 +
 +
# Set residue's phi,psi to new values
 +
print "Re-setting Phi,Psi: "+str(value[3])+","+str(value[4])   
 +
cmd.set_dihedral(dihedrals[0],dihedrals[1],dihedrals[2],dihedrals[3],value[3])    
 +
cmd.set_dihedral(dihedrals[4],dihedrals[5],dihedrals[6],dihedrals[7],value[4])    
 +
 +
value[2] = 0
  
    # Loop through each item on plot to see if updated
 
    for key,value in canvas.shapes.items():
 
dihedrals = value[5]
 
 
# Look for update flag...
 
if value[2]:
 
  
    # Set residue's phi,psi to new values
 
    print "Re-setting Phi,Psi: %s,%s" % (value[3],value[4])   
 
    cmd.set_dihedral(dihedrals[0],dihedrals[1],dihedrals[2],dihedrals[3],value[3])    
 
    cmd.set_dihedral(dihedrals[4],dihedrals[5],dihedrals[6],dihedrals[7],value[4])    
 
  
    value[2] = 0
 
 
 
 
 
# The wrapper function, used to create the Ploting window and the PyMol callback object    
 
# The wrapper function, used to create the Ploting window and the PyMol callback object    
 
def rama(sel):
 
def rama(sel):
Line 404: Line 414:
 
cmd.extend('rama',rama)    
 
cmd.extend('rama',rama)    
 
cmd.extend('ramaplot',ramaplot)
 
cmd.extend('ramaplot',ramaplot)
 
 
</source>
 
</source>
  

Revision as of 07:55, 2 February 2010

DESCRIPTION

This script was setup to do generic plotting, that is given a set of data and axis labels it would create a plot. Initially, I had it setup to draw the plot directly in the PyMol window (allowing for both 2D and 3D style plots), but because I couldn't figure out how to billboard CGO objects (Warren told me at the time that it couldn't be done) I took a different approach. The plot now exists in it's own window and can only do 2D plots. It is however interactive. I only have here a Rama.(phi,psi) plot, but the code can be easily extended to other types of data. For instance, I had this working for an energy vs distance data that I had generated by another script.

This script will create a Phi vs Psi(Ramachandran) plot of the selection given. The plot will display data points which can be dragged around Phi,Psi space with the corresponding residue's Phi,Psi angles changing in the structure (PyMol window).

IMAGES

SETUP

place the DynoPlot.py script into the appropriate startup directory then restart PyMol

LINUX old-style installation

$PYMOL_PATH/modules/pmg_tk/startup/

LINUX distutils installation

/usr/lib/pythonX.X/site-packages/pmg_tk/startup/

Windows

PYMOL_PATH/modules/pmg_tk/startup/ , where PYMOL_PATH on Windows is defaulted to C:/Program Files/DeLano Scientific/PyMol/start/

NOTES / STATUS

  • Tested on Windows, PyMol version 0.97
  • This is an initial version, which needs some work.
  • Left, Right mouse buttons do different things; Right = identify data point, Left = drag data point around
  • Post comments/questions or send them to: dwkulp@mail.med.upenn.edu

USAGE

rama SELECTION

EXAMPLES

  • load pdb file 1ENV (download it or use the PDB loader plugin)
  • select resi 129-136
  • rama sel01
  • rock # the object needs to be moving in order for the angles to be updated.

REFERENCES

SCRIPTS (DynoPlot.py)

DynoPlot.py

#!/usr/bin/env python
###############################################
#  File:          DynoPlot.py
#  Author:        Dan Kulp
#  Creation Date: 8/29/05
#
#  Notes:
#  Draw plots that display interactive data. 
#   Phi,Psi plot shown.
###############################################


from __future__ import division
from __future__ import generators

import os,math
import Tkinter
from Tkinter import *
import Pmw
import distutils.spawn # used for find_executable
import random
from pymol import cmd

try:
	import pymol
	REAL_PYMOL = True
except ImportError:
	print "Nope"

canvas = None
rootframe = None
init = 0

class SimplePlot(Tkinter.Canvas):
	
	# Class variables
	mark = 'Oval' # Only 'Oval' for now..
	mark_size = 5
	xlabels = []   # axis labels
	ylabels = []
	spacingx = 0   # spacing in x direction
	spacingy = 0    
	xmin = 0       # min value from each axis
	ymin = 0
	lastx = 0      # previous x,y pos of mouse   
	lasty = 0
	down  = 0      # flag for mouse pressed
	item = (0,)    # items array used for clickable events
	shapes = {}    # store plot data, x,y etc..
	
	def axis(self,xmin=40,xmax=300,ymin=10,ymax=290,xint=290,yint=40,xlabels=[],ylabels=[]):
		
		# Store variables in self object
		self.xlabels = xlabels
		self.ylabels = ylabels
		self.spacingx = (xmax-xmin) / (len(xlabels) - 1)
		self.spacingy = (ymax-ymin) / (len(ylabels) - 1)
		self.xmin = xmin
		self.ymin = ymin
		
		# Create axis lines
		self.create_line((xmin,xint,xmax,xint),fill="black",width=3)
		self.create_line((yint,ymin,yint,ymax),fill="black",width=3)
		
		# Create tick marks and labels
		nextspot = xmin
		for label in xlabels:
			self.create_line((nextspot, xint+5,nextspot, xint-5),fill="black",width=2)
			self.create_text(nextspot, xint-15, text=label)
			if len(xlabels) == 1:
				nextspot = xmax
			else:
				nextspot = nextspot + (xmax - xmin)/ (len(xlabels) - 1)
		
		
		nextspot = ymax
		for label in ylabels:
			self.create_line((yint+5,nextspot,yint-5,nextspot),fill="black",width=2)
			self.create_text(yint-20,nextspot,text=label)
			if len(ylabels) == 1:
				nextspot = ymin
			else:
				nextspot = nextspot - (ymax - ymin)/ (len(ylabels) - 1)
	
	
	# Plot a point
	def plot(self,xp,yp,meta):
		
		# Convert from 'label' space to 'pixel' space
		x = self.convertToPixel("X",xp)
		y = self.convertToPixel("Y",yp)
		
		if self.mark == "Oval":
			oval = self.create_oval(x-self.mark_size,y-self.mark_size,x+self.mark_size,y+self.mark_size,width=1,outline="black",fill="SkyBlue2")
			
			self.shapes[oval] = [x,y,0,xp,yp,meta]
	
	
	# Repaint all points		
	def repaint(self):
		for key,value in self.shapes.items():
			x = value[0]
			y = value[1]
			self.create_oval(x-self.mark_size,y-self.mark_size,x+self.mark_size,y+self.mark_size,width=1,outline="black",fill="SkyBlue2")
	
	# Convert from pixel space to label space
	def convertToLabel(self,axis, value):
		
		# Defaultly use X-axis info
		label0  = self.xlabels[0]
		label1  = self.xlabels[1]
		spacing = self.spacingx
		min     = self.xmin
		
		# Set info for Y-axis use
		if axis == "Y":
			label0    = self.ylabels[0]
			label1    = self.ylabels[1]
			spacing   = self.spacingy
			min       = self.ymin	
		
		pixel = value - min
		label = pixel / spacing
		label = label0 + label * abs(label1 - label0)
		
		if axis == "Y":
			label = - label
		
		return label
	
	# Converts value from 'label' space to 'pixel' space
	def convertToPixel(self,axis, value):
		
		# Defaultly use X-axis info
		label0  = self.xlabels[0]
		label1  = self.xlabels[1]
		spacing = self.spacingx
		min     = self.xmin
		
		# Set info for Y-axis use
		if axis == "Y":
			label0    = self.ylabels[0]
			label1    = self.ylabels[1]
			spacing   = self.spacingy
			min       = self.ymin	
		
		
		# Get axis increment in 'label' space
		inc = abs(label1 - label0)
		
		# 'Label' difference from value and smallest label (label0)
		diff = float(value - label0)
		
		# Get whole number in 'label' space
		whole = int(diff / inc)
		
		# Get fraction number in 'label' space
		part = float(float(diff/inc) - whole)
		
		# Return 'pixel' position value
		pixel = whole * spacing + part * spacing
		
		#		print "Pixel: %f * %f + %f * %f = %f" % (whole, spacing, part, spacing,pixel)
		
		# Reverse number by subtracting total number of pixels - value pixels
		if axis == "Y":
			tot_label_diff = float(self.ylabels[len(self.ylabels)- 1] - label0)
			tot_label_whole = int(tot_label_diff / inc)
			tot_label_part = float(float(tot_label_diff / inc) - tot_label_whole)
			tot_label_pix  = tot_label_whole * spacing + tot_label_part *spacing
			
			pixel = tot_label_pix - pixel
		
		# Add min edge pixels
		pixel = pixel + min
		
		return pixel
	
	
	# Print out which data point you just clicked on..
	def pickWhich(self,event):
		
		# Find closest data point		    
		x = event.widget.canvasx(event.x)
		y = event.widget.canvasx(event.y)
		spot = event.widget.find_closest(x,y)
		
		# Print the shape's meta information corresponding with the shape that was picked
		if self.shapes.has_key(spot[0]):
			print "Residue(Ca): %s\n" % str(self.shapes[spot[0]][5][2])
	
	
	# Mouse Down Event
	def down(self,event):
		
		# Store x,y position
		self.lastx = event.x
		self.lasty = event.y
		
		# Find the currently selected item
		x = event.widget.canvasx(event.x)
		y = event.widget.canvasx(event.y)
		self.item = event.widget.find_closest(x,y)
		
		# Identify that the mouse is down
		self.down  = 1
	
	# Mouse Up Event
	def up(self,event):
		
		# Get label space version of x,y
		labelx = self.convertToLabel("X",event.x)
		labely = self.convertToLabel("Y",event.y)
		
		# Convert new position into label space..
		if self.shapes.has_key(self.item[0]):
			self.shapes[self.item[0]][0] = event.x
			self.shapes[self.item[0]][1] = event.y
			self.shapes[self.item[0]][2] =  1
			self.shapes[self.item[0]][3] = labelx
			self.shapes[self.item[0]][4] = labely
		
		# Reset Flags
		self.item = (0,)
		self.down = 0
	
	
	# Mouse Drag(Move) Event
	def drag(self,event):
		
		# Check that mouse is down and item clicked is a valid data point
		if self.down and self.shapes.has_key(self.item[0]):
			
			self.move(self.item, event.x - self.lastx, event.y - self.lasty)
			
			self.lastx = event.x
			self.lasty = event.y


def __init__(self):
	
	self.menuBar.addcascademenu('Plugin', 'PlotTools', 'Plot Tools',
	label='Plot Tools')
	self.menuBar.addmenuitem('PlotTools', 'command',
	'Launch Rama Plot',
	label='Rama Plot',
	command = lambda s=self: ramaplot())


def ramaplot(x=0,y=0,meta=[],clear=0):
	global canvas
	global rootframe
	global init
	
	# If no window is open
	if init == 0:
		rootframe=Tk()
		rootframe.title(' Dynamic Angle Plotting ')
		rootframe.protocol("WM_DELETE_WINDOW", close_callback)
		
		canvas = SimplePlot(rootframe,width=320,height=320)
		canvas.bind("<Button-2>",canvas.pickWhich)
		canvas.bind("<Button-3>",canvas.pickWhich)
		canvas.bind("<ButtonPress-1>",canvas.down)
		canvas.bind("<ButtonRelease-1>",canvas.up)
		canvas.bind("<Motion>",canvas.drag)
		canvas.pack(side=Tkinter.LEFT,fill="both",expand=1)
		canvas.axis(xint=150,xlabels=range(-180,181,30),ylabels=range(-180,181, 30))
		canvas.update()
		init = 1
	else:
		canvas.plot(int(x), int(y),meta)

def close_callback():
	global init
	global rootframe
	init=0
	rootframe.destroy()



# New Callback object, so that we can update the structure when phi,psi points are moved.
class DynoRamaObject:
	global canvas
	
	def start(self,sel):
		
		# Get selection model
		model = cmd.get_model(sel)
		residues = ['dummy']
		resnames = ['dummy']
		phi = []
		psi = []
		dummy = []
		i = 0
		
		# Loop through each atom
		for at in model.atom:
			
			# Only plot once per residue
			if not at.chain+":"+at.resn+":"+at.resi in residues:
				residues.append(at.chain+":"+at.resn+":"+at.resi)
				resnames.append(at.resn+at.resi)
				dummy.append(i)
				i += 1
				
				# Check for a null chain id (some PDBs contain this) 
				unit_select = ""
				if not at.chain == "":
					unit_select = "chain "+str(at.chain)+" and "
				
				# Define selections for residue i-1, i and i+1    
				residue_def = unit_select+'resi '+str(at.resi)
				residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
				residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
				
				try:
					# Store phi,psi residue definitions to pass on to plot routine
					phi_psi = [
					# Phi angles
					residue_def_prev+' and name C',
					residue_def+' and name N',
					residue_def+' and name CA',
					residue_def+' and name C',
					# Psi angles
					residue_def+' and name N',
					residue_def+' and name CA',
					residue_def+' and name C',
					residue_def_next+' and name N']
					
					# Compute phi/psi angle
					phi = cmd.get_dihedral(phi_psi[0],phi_psi[1],phi_psi[2],phi_psi[3])
					psi = cmd.get_dihedral(phi_psi[4],phi_psi[5],phi_psi[6],phi_psi[7])
					
					print "Plotting Phi,Psi: "+str(phi)+","+str(psi)    
					ramaplot(phi,psi,meta=phi_psi)
				except:
					continue
	
	
	def __call__(self):
		
		# Loop through each item on plot to see if updated
		for key,value in canvas.shapes.items():
			dihedrals = value[5]
			
			# Look for update flag...
			if value[2]:
				
				# Set residue's phi,psi to new values
				print "Re-setting Phi,Psi: "+str(value[3])+","+str(value[4])    
				cmd.set_dihedral(dihedrals[0],dihedrals[1],dihedrals[2],dihedrals[3],value[3])		    	
				cmd.set_dihedral(dihedrals[4],dihedrals[5],dihedrals[6],dihedrals[7],value[4])		    	
				
				value[2] = 0



# The wrapper function, used to create the Ploting window and the PyMol callback object	    		
def rama(sel):
	rama = DynoRamaObject()
	rama.start(sel)
	cmd.load_callback(rama, "DynoRamaObject")
	cmd.zoom("all")


# Extend these commands
cmd.extend('rama',rama)		    			
cmd.extend('ramaplot',ramaplot)

ADDITIONAL RESOURCES