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===DESCRIPTION===
{{Infobox script-repo
|type      = plugin
|filename  = plugins/dynoplot.py
|author    = [[User:Tmwsiy|Dan Kulp]]
|license  = -
}}
== Introduction ==
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 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.


Line 5: Line 11:


===IMAGES===
===IMAGES===
[[Image:RamaPlotInitComposite.png|thumb|left|Initial Ramachandran plot of 1ENV]]
<gallery>
[[Image:RamaPlotBentComposite.png|thumb|left|Modified pose and plot of 1ENV]]
Image:RamaPlotInitComposite.png|Initial Ramachandran plot of 1ENV
 
Image:RamaPlotBentComposite.png|Modified pose and plot of 1ENV
 
</gallery>
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


===SETUP===
===SETUP===
place the DynoPlot.py script into the appropriate startup directory then restart PyMol
Install from the plugins menu with ''Plugin > Manage Plugins > Install ...'' or just [[run]] the script.
 
==== 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===
===NOTES / STATUS===
*Tested on Windows, PyMol version 0.97
*Tested on Linux, PyMol version 1.4
*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
*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
*Post comments/questions or send them to: dwkulp@mail.med.upenn.edu


===USAGE===
===USAGE===
rama SELECTION
 
rama [ sel [, name [, symbols [, filename ]]]]


===EXAMPLES===     
===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===
<source lang="python">
fetch 1ENV, async=0 # (download it or use the PDB loader plugin)
select sel01, resi 129-136
rama sel01
rock  # the object needs to be moving in order for the angles to be updated.
</source>


===SCRIPTS (DynoPlot.py)===
Don't create callback object, use symbols by secondary structure and dump canvas as postscript file:
DynoPlot.py
<source lang="python">
#!/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 = 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 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 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)


<source lang="python">
fetch 2x19, async=0
color yellow, chain A
color forest, chain B
rama polymer, none, ss, /tmp/canvasdump.ps
rama ss H,    none, aa, /tmp/canvasdump_helix.ps
rama ss S,    none, aa, /tmp/canvasdump_sheet.ps
</source>
</source>
===ADDITIONAL RESOURCES===


[[Category:Script_Library|DynoPlot]]
[[Category:Script_Library|DynoPlot]]
[[Category:Structural_Biology_Scripts|DynoPlot]]
[[Category:Structural_Biology_Scripts|DynoPlot]]
[[Category:Pymol-script-repo]]

Latest revision as of 11:13, 15 January 2012

Type PyMOL Plugin
Download plugins/dynoplot.py
Author(s) Dan Kulp
License -
This code has been put under version control in the project Pymol-script-repo

Introduction

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

  • Initial Ramachandran plot of 1ENV

    Initial Ramachandran plot of 1ENV

  • Modified pose and plot of 1ENV

    Modified pose and plot of 1ENV

SETUP

Install from the plugins menu with Plugin > Manage Plugins > Install ... or just run the script.

NOTES / STATUS

  • Tested on Linux, PyMol version 1.4
  • 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 [ sel [, name [, symbols [, filename ]]]]

EXAMPLES

fetch 1ENV, async=0 # (download it or use the PDB loader plugin)
select sel01, resi 129-136
rama sel01
rock   # the object needs to be moving in order for the angles to be updated.

Don't create callback object, use symbols by secondary structure and dump canvas as postscript file: 

fetch 2x19, async=0
color yellow, chain A
color forest, chain B
rama polymer, none, ss, /tmp/canvasdump.ps
rama ss H,    none, aa, /tmp/canvasdump_helix.ps
rama ss S,    none, aa, /tmp/canvasdump_sheet.ps
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