DynoPlot

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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 += (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[-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 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=[-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)

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 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