Difference between revisions of "DynoPlot"

From PyMOLWiki
Jump to: navigation, search
(color support)
(postscript dump)
Line 18: Line 18:
  
 
===USAGE===
 
===USAGE===
rama SELECTION
+
 
 +
rama [ sel [, name [, symbols [, filename ]]]]
  
 
===EXAMPLES===     
 
===EXAMPLES===     
*load pdb file 1ENV (download it or use the PDB loader plugin)
+
 
*select sel01, resi 129-136
+
<source lang="python">
*rama sel01
+
fetch 1ENV, async=0 # (download it or use the PDB loader plugin)
*rock  # the object needs to be moving in order for the angles to be updated.
+
select sel01, resi 129-136
 +
rama sel01
 +
rock  # the object needs to be moving in order for the angles to be updated.
 +
</source>
 +
 
 +
Don't create callback object, use symbols by secondary structure and dump canvas as postscript file:
 +
 
 +
<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>
  
 
===SCRIPTS (DynoPlot.py)===
 
===SCRIPTS (DynoPlot.py)===
Line 70: Line 85:
 
         self.shapes = {}    # store plot data, x,y etc..
 
         self.shapes = {}    # store plot data, x,y etc..
 
         self.idx2resn = {}  # residue name mapping
 
         self.idx2resn = {}  # residue name mapping
 +
        self.symbols = 0    # 0: amino acids, 1: secondary structure
  
 
     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=[]):
Line 115: Line 131:
 
         resn, color, ss = self.idx2resn.get(meta)
 
         resn, color, ss = self.idx2resn.get(meta)
  
         if True:
+
         if self.symbols == 0:
 
             # symbols by amino acid (G/P/other)
 
             # symbols by amino acid (G/P/other)
 
             mark = {'GLY': 'Tri', 'PRO': 'Rect'}.get(resn, 'Oval')
 
             mark = {'GLY': 'Tri', 'PRO': 'Rect'}.get(resn, 'Oval')
Line 293: Line 309:
 
# New Callback object, so that we can update the structure when phi,psi points are moved.
 
# New Callback object, so that we can update the structure when phi,psi points are moved.
 
class DynoRamaObject:
 
class DynoRamaObject:
     def __init__(self, selection=None, name=None):
+
     def __init__(self, selection=None, name=None, symbols=''):
 
         from pymol import _ext_gui as pmgapp
 
         from pymol import _ext_gui as pmgapp
 
         if pmgapp is not None:
 
         if pmgapp is not None:
Line 314: Line 330:
 
                 ylabels=[-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()
 
         canvas.update()
 +
 +
        if symbols == 'ss':
 +
            canvas.symbols = 1
  
 
         if name is None:
 
         if name is None:
Line 357: Line 376:
 
         if self.lock:
 
         if self.lock:
 
             return
 
             return
 +
 
         # Loop through each item on plot to see if updated
 
         # Loop through each item on plot to see if updated
 
         for value in self.canvas.shapes.itervalues():
 
         for value in self.canvas.shapes.itervalues():
Line 367: Line 387:
 
                 value[2] = 0
 
                 value[2] = 0
  
def rama(sel='(all)', name=None):
+
def rama(sel='(all)', name=None, symbols='aa', filename=None):
 
     '''
 
     '''
 
DESCRIPTION
 
DESCRIPTION
Line 381: Line 401:
 
     angles when canvas points are dragged, or 'none' to not create a callback
 
     angles when canvas points are dragged, or 'none' to not create a callback
 
     object {default: DynoRamaObject}
 
     object {default: DynoRamaObject}
 +
 +
    symbols = string: aa for amino acid or ss for secondary structure {default: aa}
 +
 +
    filename = string: filename for postscript dump of canvas {default: None}
 
     '''
 
     '''
     DynoRamaObject(sel, name)
+
     dyno = DynoRamaObject(sel, name, symbols)
 +
    if filename is not None:
 +
        dyno.canvas.postscript(file=filename)
  
 
# Extend these commands
 
# Extend these commands

Revision as of 04:38, 18 November 2011

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

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

SCRIPTS (DynoPlot.py)

DynoPlot.py

###############################################
#  File:          DynoPlot.py
#  Author:        Dan Kulp
#  Creation Date: 8/29/05
#
#  Modified 2011-11-17 by Thomas Holder
#
#  Notes:
#  Draw plots that display interactive data.
#   Phi,Psi plot shown.
###############################################


from __future__ import division
from __future__ import generators

import Tkinter
from pymol import cmd

# workaround: Set to True if nothing gets drawn on canvas, for example on linux with "pymol -x"
with_mainloop = False

class SimplePlot(Tkinter.Canvas):

    # Class variables
    mark_size = 4

    def __init__(self, *args, **kwargs):
        Tkinter.Canvas.__init__(self, *args, **kwargs)
        self.xlabels = []   # axis labels
        self.ylabels = []
        self.spacingx = 0   # spacing in x direction
        self.spacingy = 0
        self.xmin = 0       # min value from each axis
        self.ymin = 0
        self.lastx = 0      # previous x,y pos of mouse
        self.lasty = 0
        self.isdown  = 0    # flag for mouse pressed
        self.item = (0,)    # items array used for clickable events
        self.shapes = {}    # store plot data, x,y etc..
        self.idx2resn = {}  # residue name mapping
        self.symbols = 0    # 0: amino acids, 1: secondary structure

    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)

        resn, color, ss = self.idx2resn.get(meta)

        if self.symbols == 0:
            # symbols by amino acid (G/P/other)
            mark = {'GLY': 'Tri', 'PRO': 'Rect'}.get(resn, 'Oval')
        else:
            # symbols by secondary structure
            mark = {'H': 'Oval', 'S': 'Rect'}.get(ss, 'Tri')

        if mark == 'Oval':
            create_shape = self.create_oval
            coords = [x-self.mark_size, y-self.mark_size,
                    x+self.mark_size, y+self.mark_size]
        elif mark == 'Tri':
            create_shape = self.create_polygon
            coords = [x, y-self.mark_size,
                    x+self.mark_size, y+self.mark_size,
                    x-self.mark_size, y+self.mark_size]
        else:
            create_shape = self.create_rectangle
            coords = [x-self.mark_size, y-self.mark_size,
                    x+self.mark_size, y+self.mark_size]

        if color >= 0x40000000:
            color = '#%06x' % (color & 0xffffff)
        else:
            color = '#%02x%02x%02x' % tuple([255*i
                for i in cmd.get_color_tuple(color)])

        oval = create_shape(*coords,
                width=1, outline="black", fill=color)
        self.shapes[oval] = [x,y,0,xp,yp,meta]

    # 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

        # 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:
            cmd.select('sele', '(%s`%d)' % self.shapes[spot[0]][5])
            cmd.iterate('sele', 'print " You clicked /%s/%s/%s/%s`%s/%s (DynoPlot)" %' + \
                    ' (model, segi, chain, resn, resi, name)')
            cmd.center('byres sele', animate=1)

    # 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.isdown  = 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.isdown = 0

    # Mouse Drag(Move) Event
    def drag(self,event):

        # Check that mouse is down and item clicked is a valid data point
        if self.isdown 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 set_phipsi(model, index, phi, psi):
    atsele = [
        'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
        'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
        '(%s`%d)' % (model, index),                             # this CA
        'last ((%s`%d) extend 1 and name C)' % (model, index),  # this C
        'last ((%s`%d) extend 2 and name N)' % (model, index),  # next N
    ]
    try:
        cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3], phi)
        cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4], psi)
    except:
        print ' DynoPlot Error: cmd.set_dihedral failed'

# New Callback object, so that we can update the structure when phi,psi points are moved.
class DynoRamaObject:
    def __init__(self, selection=None, name=None, symbols=''):
        from pymol import _ext_gui as pmgapp
        if pmgapp is not None:
            import Pmw
            rootframe = Pmw.MegaToplevel(pmgapp.root)
            parent = rootframe.interior()
        else:
            rootframe = Tkinter.Tk()
            parent = rootframe

        rootframe.title(' Dynamic Angle Plotting ')
        rootframe.protocol("WM_DELETE_WINDOW", self.close_callback)

        canvas = SimplePlot(parent,width=320,height=320)
        canvas.bind("<Button-2>",canvas.pickWhich)
        canvas.bind("<Button-3>",canvas.pickWhich)
        canvas.pack(side=Tkinter.LEFT,fill="both",expand=1)
        canvas.axis(xint=150,
                xlabels=[-180,-120,-60,0,60,120,180],
                ylabels=[-180,-150,-120,-90,-60,-30,0,30,60,90,120,150,180])
        canvas.update()

        if symbols == 'ss':
            canvas.symbols = 1

        if name is None:
            try:
                name = cmd.get_unused_name('DynoRama')
            except AttributeError:
                name = 'DynoRamaObject'

        self.rootframe = rootframe
        self.canvas = canvas
        self.name = name
        self.lock = 0

        if name != 'none':
            auto_zoom = cmd.get('auto_zoom')
            cmd.set('auto_zoom', 0)
            cmd.load_callback(self, name)
            cmd.set('auto_zoom', auto_zoom)
            canvas.bind("<ButtonPress-1>",canvas.down)
            canvas.bind("<ButtonRelease-1>",canvas.up)
            canvas.bind("<Motion>",canvas.drag)

        if selection is not None:
            self.start(selection)

        if with_mainloop and pmgapp is None:
            rootframe.mainloop()

    def close_callback(self):
        cmd.delete(self.name)
        self.rootframe.destroy()

    def start(self,sel):
        self.lock = 1
        cmd.iterate('(%s) and name CA' % sel,'idx2resn[model,index] = (resn, color, ss)',
                space={'idx2resn': self.canvas.idx2resn})
        for model_index, (phi,psi) in cmd.get_phipsi(sel).iteritems():
            print " Plotting Phi,Psi: %8.2f,%8.2f" % (phi, psi)
            self.canvas.plot(phi, psi, model_index)
        self.lock = 0

    def __call__(self):
        if self.lock:
            return

        # Loop through each item on plot to see if updated
        for value in self.canvas.shapes.itervalues():
            # Look for update flag...
            if value[2]:
                # Set residue's phi,psi to new values
                model, index = value[5]
                print " Re-setting Phi,Psi: %8.2f,%8.2f" % (value[3],value[4])
                set_phipsi(model, index, value[3], value[4])
                value[2] = 0

def rama(sel='(all)', name=None, symbols='aa', filename=None):
    '''
DESCRIPTION

    Ramachandran Plot
    http://pymolwiki.org/index.php/DynoPlot

ARGUMENTS

    sel = string: atom selection {default: all}

    name = string: name of callback object which is responsible for setting
    angles when canvas points are dragged, or 'none' to not create a callback
    object {default: DynoRamaObject}

    symbols = string: aa for amino acid or ss for secondary structure {default: aa}

    filename = string: filename for postscript dump of canvas {default: None}
    '''
    dyno = DynoRamaObject(sel, name, symbols)
    if filename is not None:
        dyno.canvas.postscript(file=filename)

# Extend these commands
cmd.extend('ramachandran', rama)
cmd.auto_arg[0]['ramachandran'] = cmd.auto_arg[0]['zoom']

# Add to plugin menu
def __init_plugin__(self):
    self.menuBar.addcascademenu('Plugin', 'PlotTools', 'Plot Tools', label='Plot Tools')
    self.menuBar.addmenuitem('PlotTools', 'command', 'Launch Rama Plot', label='Rama Plot',
            command = lambda: DynoRamaObject('(enabled)'))

# vi:expandtab:smarttab

ADDITIONAL RESOURCES