Difference between revisions of "DynoPlot"

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Line 116: Line 116:
 
nextspot = xmax
 
nextspot = xmax
 
    else:
 
    else:
        nextspot = nextspot + (xmax - xmin)/ (len(xlabels) - 1)
+
        nextspot += (xmax - xmin)/ (len(xlabels) - 1)
  
  
Line 126: Line 126:
 
nextspot = ymin
 
nextspot = ymin
 
    else:
 
    else:
        nextspot = nextspot - (ymax - ymin)/ (len(ylabels) - 1)
+
        nextspot -= (ymax - ymin)/ (len(ylabels) - 1)
  
  
Line 144: Line 144:
 
# Repaint all points
 
# Repaint all points
 
def repaint(self):
 
def repaint(self):
for key,value in self.shapes.items():
+
for value in self.shapes.values():
 
x = value[0]
 
x = value[0]
 
y = value[1]
 
y = value[1]
Line 232: Line 232:
  
 
    # 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 self.shapes.has_key(spot[0]):
+
    if spot[0] in self.shapes:
print "Residue(Ca): %s\n" % str(self.shapes[spot[0]][5][2])
+
print "Residue(Ca): %s\n" % self.shapes[spot[0]][5][2]
  
  
Line 259: Line 259:
  
 
    # Convert new position into label space..
 
    # Convert new position into label space..
    if self.shapes.has_key(self.item[0]):
+
    if self.item[0] in self.shapes:
 
        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
Line 275: Line 275:
 
 
 
# 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.shapes.has_key(self.item[0]):
+
if self.down and self.item[0] in self.shapes:
 
 
 
    self.move(self.item, event.x - self.lastx, event.y - self.lasty)
 
    self.move(self.item, event.x - self.lastx, event.y - self.lasty)
Line 335: Line 335:
  
 
# Only plot once per residue
 
# Only plot once per residue
     if not at.chain+":"+at.resn+":"+at.resi in residues:
+
     if at.chain+":"+at.resn+":"+at.resi not in residues:
 
        residues.append(at.chain+":"+at.resn+":"+at.resi)
 
        residues.append(at.chain+":"+at.resn+":"+at.resi)
 
        resnames.append(at.resn+at.resi)
 
        resnames.append(at.resn+at.resi)
Line 343: Line 343:
 
             # Check for a null chain id (some PDBs contain this)  
 
             # Check for a null chain id (some PDBs contain this)  
 
        unit_select = ""
 
        unit_select = ""
        if not at.chain == "":
+
        if at.chain != "":
 
    unit_select = "chain "+str(at.chain)+" and "
 
    unit_select = "chain "+str(at.chain)+" and "
  
Line 385: Line 385:
  
 
    # Set residue's phi,psi to new values
 
    # Set residue's phi,psi to new values
    print "Re-setting Phi,Psi: "+str(value[3])+","+str(value[4])     
+
    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[0],dihedrals[1],dihedrals[2],dihedrals[3],value[3])    
 
    cmd.set_dihedral(dihedrals[4],dihedrals[5],dihedrals[6],dihedrals[7],value[4])    
 
    cmd.set_dihedral(dihedrals[4],dihedrals[5],dihedrals[6],dihedrals[7],value[4])    

Revision as of 15:21, 17 December 2009

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
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 += (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 -= (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 value in self.shapes.values():
			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 spot[0] in self.shapes:
		print "Residue(Ca): %s\n" % 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.item[0] in self.shapes:
	        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.item[0] in self.shapes:
			
		    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 init

    # If no window is open
    if init == 0:
        rootframe=Tk()
        rootframe.title(' Dynamic Angle Plotting ')

        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)


# 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 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)    
		        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: %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	    		
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