Colorama

COLORAMA

COLORAMA is a PyMOL plugin which allows to color objects using adjustable scale bars.

Program features

In RGB mode, each color R, G, B is represented by one scale bar which can be manually adjusted while the selected object is colored in real time. For convenience, it is as well possible to switch to the HSV color system.

Additionally, a color gradient with user-defined start- and end-colors can be created for the selected molecule.

Screenshot

Usage

Install the program by copying the code below into an empty text file (e.g. "colorama.py") located in the \Pymol\modules\pmg_tk\startup directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. COLORAMA has not been tested with PyMOL versions older than 1.0.

Single color

1. Type the name of a PyMOL object to be colored into the COLORAMA entry field.
2. Push the "Set" button.
3. The scales are adjusted to the current color which is additionally visualized in a field left to the scales.
4. If one of the scales is moved, the color of the selected object will change in real-time.
5. Pushing the RGB or HSV buttons on the left allows to switch between both color systems.

Color gradients

1. After an object has been selected, push the "G" button (gradient).
2. Select the start color by pushing "C1" and adjusting it using the scales.
3. Select the end color "C2" in the same way.
4. To create the gradient, push "Set gradient".

A new object will be created which is called "dummy-OLD_OBJECT". The B-factor column of this object is overwritten and now contains the number of each residue. The original object is left unchanged. The gradient mode can be left by pushing "M" (monochrome). This part of the program uses a modified version of the color_b script by Robert L. Campbell & James Stroud.

Contact

Gregor Hagelueken, gh50@st-andrews.ac.uk

Code

"""
--- COLORAMA: Coloring Widget for PyMOL --- 
Author  : Gregor Hagelueken
Program : Color_select
Date    : Oct 2007
Version : 0.1.1
Mail    : gha@helmholtz-hzi.de



COLORAMA is a plugin for the PyMOL Molecular Graphics System. 
It allows to color molecules using RGB or HSV colors which can be manually adjusted. 
Alternatively, a user defined color gradient can be applied to the molecule.
The program works properly with PyMOL versions >=1.0.


The program uses a modified version of the color_b program by Robert L. Campbell & James Stroud
for the gradient calculation and the RGBToHTMLColor function by Paul Winkler.

Literature:
 DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org

----------------------------------------------------------------------
----------------------------------------------------------------------

"""

import colorsys,sys
from pymol import cmd,stored
from Tkinter import *
class Colorama:
    def __init__ (self,master):
        #create frames
        self.F1 = Frame(roota, padx=5, pady=5, bg='red')
        self.F2 = Frame(roota, padx=5, pady=5, bg='green')
        self.F3 = Frame(roota, padx=5, pady=5, bg='blue')
        self.F4 = Frame(self.F1, padx=5, pady=5, bg='yellow')
        self.F5 = Frame(self.F1, padx=5, pady=5, bg='white')
        self.F6 = Frame(self.F1, padx=5, pady=5, bg='pink')
        
        #color system radiobuttons
        self.Radiocolorsystem = IntVar()
        self.RGB = Radiobutton (self.F3, text='RGB', indicatoron=0, variable=self.Radiocolorsystem, value=1, command=self.Scalergb)
        self.HSV = Radiobutton (self.F3, text='HSV', indicatoron=0, variable=self.Radiocolorsystem, value=2, command=self.Scalehsv)
        
        #mono/gradient and Farbe1/Farbe2 radiobuttons
        self.RadioMonoGradient = IntVar()
        self.RadioFarbe12 = IntVar()
        self.Monobutton = Radiobutton (self.F3, text='M', indicatoron=0, variable=self.RadioMonoGradient, value=1, command=self.Mono)
        self.Gradbutton = Radiobutton (self.F3, text='G', indicatoron=0, variable=self.RadioMonoGradient, value=2, command=self.Grad)
        self.Farbe1button = Radiobutton (self.F3, text='C1', indicatoron=0, variable=self.RadioFarbe12, value=1, command=self.Farbe1) 
        self.Farbe2button = Radiobutton (self.F3, text='C2', indicatoron=0, variable=self.RadioFarbe12, value=2, command=self.Farbe2) 
        
        #preselect RGB and mono
        self.RGB.select()
        self.Monobutton.select()
        self.Farbe1button.select()
        self.monograd='mono'
        self.colorsystem='rgb'
        self.farbe12='farbe1'
        
        #initialize the scales
        self.Scales()
        
        #other GUI elements
        self.selectionentry = Entry(master=self.F5, font=('Arial', 10))
        self.selectionentry.insert(0,"")
        self.selectionbutton = Button(master=self.F5, text='Set', command=self.setselection)
        self.setgradientbutton = Button(master=self.F5, text='Set Gradient', command=self.setgradient)
        self.label = Label(master=self.F4, text="None", font=('Arial', 10))
        self.selectionlabel = Label(master=self.F4, text="Active:", font=('Arial', 10))
        self.inputlabel = Label (master=self.F5, text="Object:", font=('Arial', 10))
        self.colorfield1 = Label(master=self.F3,width=3, height=10)
        self.colorfield2 = Label(master=self.F3,width=3, height=10)
        
        self.selection=""
        self.setselection()
        
        #start layout procedure
        self.layout()
    
    def layout(self):
        self.F1.pack(side=TOP, anchor=NW)
        self.F4.pack(side=BOTTOM, fill=X, anchor=W)
        self.F5.pack(side=TOP)
        self.F2.pack(side=RIGHT, fill=Y)
        self.F3.pack(side=LEFT, fill=X)
        
        #entry and buttons
        self.setgradientbutton.pack(side=RIGHT,fill=X, anchor=NE)
        self.selectionbutton.pack(side=RIGHT, anchor=N)
        self.selectionentry.pack(side=RIGHT,fill=X, anchor=NE)
        
        #labels
        self.inputlabel.pack(side=TOP, anchor=NW)
        self.selectionlabel.pack(side=LEFT, anchor=W)
        self.label.pack(side=LEFT)
        
        #colorfields
        self.colorfield2.pack(side=RIGHT)
        self.colorfield1.pack(side=RIGHT)
        
        #scales
        self.ScaleRed.pack(side=RIGHT, fill=Y)
        self.ScaleGreen.pack(side=RIGHT, fill=Y)
        self.ScaleBlue.pack(side=RIGHT, fill=Y)
        
        #radiobuttons
        self.RGB.pack(side=TOP, fill=X)
        self.HSV.pack(side=TOP, fill=X)
        self.Monobutton.pack(side=TOP, fill=X)
        self.Gradbutton.pack(side=TOP, fill=X)
        self.Farbe1button.pack(side=TOP, fill=X)
        self.Farbe2button.pack(side=TOP, fill=X)
    
    def Scales(self):
            self.ScaleRed = Scale(master=self.F2, label='R', length='3c',
                              from_=0, to=255,
                              #set(startred),
                              command=self.setzeFarbe)
            self.ScaleGreen = Scale(master=self.F2, label='G', length='3c',
                              from_=0, to=255,
                              #set(startgreen),
                              command=self.setzeFarbe)
            self.ScaleBlue = Scale(master=self.F2, label='B', length='3c',
                              from_=0, to=255,
                              #set(startblue),
                              command=self.setzeFarbe)
                              
    def Scalergb(self):
        if self.colorsystem=='hsv':
            h=float(self.ScaleRed.get())
            s=float(self.ScaleGreen.get())
            v=float(self.ScaleBlue.get())
            rgbcolor = colorsys.hsv_to_rgb(h,s,v)
            r=255*rgbcolor[0]
            g=255*rgbcolor[1]
            b=255*rgbcolor[2]
            self.ScaleRed.config(label='R', from_=0, to=255, resolution=1)
            self.ScaleGreen.config(label='G', from_=0, to=255, resolution=1)
            self.ScaleBlue.config(label='B', from_=0, to=255, resolution=1)
            self.ScaleRed.set(r)
            self.ScaleGreen.set(g)
            self.ScaleBlue.set(b)
            self.colorsystem='rgb'
            
    def Scalehsv(self):
        if self.colorsystem=='rgb':
            r=float(self.ScaleRed.get())/255
            g=float(self.ScaleGreen.get())/255
            b=float(self.ScaleBlue.get())/255
            hsvcolor = colorsys.rgb_to_hsv(r,g,b)
            h=hsvcolor[0]
            s=hsvcolor[1]
            v=hsvcolor[2]
            self.ScaleRed.config(label='H', from_=0, to=1, resolution=0.01)
            self.ScaleGreen.config(label='S', from_=0, to=1, resolution=0.01)
            self.ScaleBlue.config(label='V', from_=0, to=1, resolution=0.01)
            self.ScaleRed.set(h)
            self.ScaleGreen.set(s)
            self.ScaleBlue.set(v)
            self.colorsystem='hsv'
    
    def Mono(self):
        self.monograd='mono'
    
    def Grad(self):
        self.monograd='grad'
        
    def Farbe1(self):
        #Let the scales know which color is to be changed
        self.farbe12='farbe1'
        #set scales to farbe1
        if self.monograd=='grad':
            if self.colorsystem=='rgb':
                startred=self.farbe1[0]
                startgreen=self.farbe1[1]
                startblue=self.farbe1[2]							  
                self.ScaleRed.set(startred)
                self.ScaleGreen.set(startgreen)
                self.ScaleBlue.set(startblue)
            elif self.colorsystem=='hsv':
                hsvcolor=colorsys.rgb_to_hsv(self.farbe1[0], self.farbe1[1], self.farbe1[2])
                h=hsvcolor[0]
                s=hsvcolor[1]
                v=hsvcolor[2]
                self.ScaleRed.set(h)
                self.ScaleGreen.set(s)
                self.ScaleBlue.set(v)
    
    def Farbe2(self):
        #Let the scales know which color is to be changed
        self.farbe12='farbe2'
        #set scales to farbe1
        if self.monograd=='grad':
            if self.colorsystem=='rgb':
                startred=self.farbe2[0]
                startgreen=self.farbe2[1]
                startblue=self.farbe2[2]							  
                self.ScaleRed.set(startred)
                self.ScaleGreen.set(startgreen)
                self.ScaleBlue.set(startblue)
            elif self.colorsystem=='hsv':
                hsvcolor=colorsys.rgb_to_hsv(self.farbe2[0], self.farbe2[1], self.farbe2[2])
                h=hsvcolor[0]
                s=hsvcolor[1]
                v=hsvcolor[2]
                self.ScaleRed.set(h)
                self.ScaleGreen.set(s)
                self.ScaleBlue.set(v)
        
    def setselection(self):
        if self.selectionentry.get() != "":
            self.selection=self.selectionentry.get()
            
            #Color of each residue is stored in  stored.colorlist to check if the molecule has a colorgradient
            stored.colorlist = []
            cmd.iterate (self.selection+" & name CA", "stored.colorlist.append(int(color))")
            
            if len(stored.colorlist)==0:
                #for other objects (e.g. density...)
                stored.colorlist.append(cmd.get_object_color_index(self.selection))
                stored.colorlist.append(cmd.get_object_color_index(self.selection))
            
            
            initialcolornterm=cmd.get_color_tuple(stored.colorlist[0])
            initialcolorcterm=cmd.get_color_tuple(stored.colorlist[len(stored.colorlist)-1])
            self.farbe1=initialcolornterm[0]*255, initialcolornterm[1]*255, initialcolornterm[2]*255
            self.farbe2=initialcolorcterm[0]*255, initialcolorcterm[1]*255, initialcolorcterm[2]*255
            
            #Set active object to label
            self.label.config(text=self.selection)
            
            #check if there is a gradient and adjust Mono/Gradbutton
            if initialcolornterm==initialcolorcterm:
                self.Monobutton.select()
                self.Mono()
                
            elif initialcolornterm!=initialcolorcterm:
                self.Gradbutton.select()
                self.Grad()
            
            #adjust colorfields
            self.colorfield1.config(bg=self.RGBToHTMLColor(self.farbe1))
            self.colorfield2.config(bg=self.RGBToHTMLColor(self.farbe2))
            self.Farbe1button.select()
            self.Farbe1()
            
            #Set scales to initialcolor of the new object    
            if self.colorsystem=='rgb':
                startred=255*initialcolornterm[0]
                startgreen=255*initialcolornterm[1]
                startblue=255*initialcolornterm[2]							  
                self.ScaleRed.set(startred)
                self.ScaleGreen.set(startgreen)
                self.ScaleBlue.set(startblue)
            elif self.colorsystem=='hsv':
                hsvcolor=colorsys.rgb_to_hsv(initialcolornterm[0], initialcolornterm[1], initialcolornterm[2])
                h=hsvcolor[0]
                s=hsvcolor[1]
                v=hsvcolor[2]
                self.ScaleRed.set(h)
                self.ScaleGreen.set(s)
                self.ScaleBlue.set(v)
             
    def setzeFarbe(self, event):
        if self.selection != "" && self.monograd == 'mono':
            if self.colorsystem=='rgb':
                col=[]
                #read RGB values from scales
                r=int(self.ScaleRed.get())
                g=int(self.ScaleGreen.get())
                b=int(self.ScaleBlue.get())
                rgbcolor=r,g,b
                #Prepare a rgb tupel
                col.append(rgbcolor)
                #hexcolor for colorfields
                hexcolor=self.RGBToHTMLColor(rgbcolor)
                self.colorfield1.config(bg=hexcolor)
                self.colorfield2.config(bg=hexcolor)
                cmd.delete(self.selection+"_color")
                cmd.set_color(self.selection+"_color", col[0])
                cmd.color(self.selection+"_color", self.selection)
                del col[0]
            elif self.colorsystem=='hsv':
                col=[]
                #read HSV values from scales
                h=float(self.ScaleRed.get())
                s=float(self.ScaleGreen.get())
                v=float(self.ScaleBlue.get())
                
                #HSV to RGB and change from 1.0, 1.0, 1.0 format to 255,255,255 format
                rgbcolor = colorsys.hsv_to_rgb(h,s,v)
                r = 255*rgbcolor[0]
                g = 255*rgbcolor[1]
                b = 255*rgbcolor[2]
                #as above
                rgbcolor = r,g,b
                col.append(rgbcolor)
                #hexcolor for colorfields
                hexcolor=self.RGBToHTMLColor(rgbcolor)
                self.colorfield1.config(bg=hexcolor)
                self.colorfield2.config(bg=hexcolor)
                cmd.delete(self.selection+"_color")
                cmd.set_color(self.selection+"_color", col[0])
                cmd.color(self.selection+"_color", self.selection)
                del col[0]
        elif self.selection !="" && self.monograd == 'grad':
            
            if self.colorsystem=='rgb':
                col=[]
                #read RGB values from scales
                r=int(self.ScaleRed.get())
                g=int(self.ScaleGreen.get())
                b=int(self.ScaleBlue.get())
                rgbcolor=r,g,b
                #Prepare a rgb tupel
                col.append(rgbcolor)
                #hexcolor for colorfields
                hexcolor=self.RGBToHTMLColor(rgbcolor)
                if self.farbe12=='farbe1':
                    self.colorfield1.config(bg=hexcolor)
                    self.farbe1=rgbcolor
                elif self.farbe12=='farbe2':
                    self.colorfield2.config(bg=hexcolor)
                    self.farbe2=rgbcolor

            elif self.colorsystem=='hsv':
                col=[]
                #read HSV values from scales
                h=float(self.ScaleRed.get())
                s=float(self.ScaleGreen.get())
                v=float(self.ScaleBlue.get())
                
                #HSV to RGB and change from 1.0, 1.0, 1.0 format to 255,255,255 format
                rgbcolor = colorsys.hsv_to_rgb(h,s,v)
                r = 255*rgbcolor[0]
                g = 255*rgbcolor[1]
                b = 255*rgbcolor[2]
                #as above
                rgbcolor = r,g,b
                col.append(rgbcolor)
                #hexcolor for colorfields
                hexcolor=self.RGBToHTMLColor(rgbcolor)
                
                if self.farbe12=='farbe1':
                    self.colorfield1.config(bg=hexcolor)
                    self.farbe1=rgbcolor
                elif self.farbe12=='farbe2':
                    self.colorfield2.config(bg=hexcolor)
                    self.farbe2=rgbcolor
    
    def setgradient(self):
        
        stored.residuelist = []
        cmd.iterate (self.selection, "stored.residuelist.append(int(resi))")
        firstresidue=min(stored.residuelist)
        lastresidue=max(stored.residuelist)
        rs=float(self.farbe1[0])/float(255)
        gs=float(self.farbe1[1])/float(255)
        bs=float(self.farbe1[2])/float(255)
        re=float(self.farbe2[0])/float(255)
        ge=float(self.farbe2[1])/float(255)
        be=float(self.farbe2[2])/float(255)
        hsvcolorstart = colorsys.rgb_to_hsv(rs, gs, bs)
        hs=hsvcolorstart[0]
        ss=hsvcolorstart[1]
        vs=hsvcolorstart[2]
        hsvcolorend = colorsys.rgb_to_hsv(re, ge, be)
        he=hsvcolorend[0]
        se=hsvcolorend[1]
        ve=hsvcolorend[2]
        color_grad(selection=self.selection, minimum=firstresidue, maximum=lastresidue, hs=hs, he=he,ss=ss,se=se,vs=vs,ve=ve)
        

    def RGBToHTMLColor(self, rgb_tuple):
	    #by Paul Winkler
        """ convert an (R, G, B) tuple to #RRGGBB """
        hexcolor = '#%02x%02x%02x' % rgb_tuple
        # that's it! '%02x' means zero-padded, 2-digit hex values
        return hexcolor

def __init__(self):
    self.menuBar.addmenuitem('Plugin', 'command',
                             'Colorama',
                             label = 'Colorama',
                             command = lambda s=self : open_Colorama())
	
def open_Colorama():
    #initialize window (roota)
    global roota
    roota = Tk()
    roota.title(' COLORAMA by gha')
    global colorama
    colorama = Colorama(roota)

def color_grad(selection='',item='b',mode='hist',gradient='bgr',nbins=11,sat=1,value=1,minimum='1',maximum='1',dummy='dummy_all', hs=1, he=1, ss=1,se=1,vs=1,ve=1, colorname='init'):
  """
    --- color_grad: color gradient tool for PyMOL --- 
    Author  : Gregor Hagelueken
    Program : Color_grad
    Date    : Oct 2007
    Version : 0.1.0
    Mail    : gha@helmholtz-hzi.de

    


    This is a modified version of the color_b program by Robert L. Campbell & James Stroud

    Literature:
    DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org

    ----------------------------------------------------------------------
    ----------------------------------------------------------------------
  """

  nbins=int(nbins)
  sat=float(sat)
  value=float(value)
  hs=float(hs)
  he=float(he)
  ss=float(ss)
  se=float(se)
  vs=float(vs)
  ve=float(ve)
  colorname='color_'+selection
  
  nbins=int(maximum)-int(minimum)+2
  dummy="dummy-"+selection
  colname="col"+selection
  

# make sure sat and value are in the range 0-1.0
  sat = min(sat, 1.0)
  sat = max(sat, 0.0)
  value = min(value, 1.0)
  value = max(value, 0.0)

# make sure lowercase
  gradient.lower()
  mode.lower()

# Sanity checking
  if nbins == 1:
    print "\n     WARNING: You specified nbins=1, which doesn't make sense...resetting nbins=11\n"
    nbins=11

  if mode not in ('hist','ramp'):
    print "\n     WARNING: Unknown mode ",mode, "    ----->   Nothing done.\n"
    return
  if selection == '':
	print "\n USAGE: color_grad dimB, minimum=380, maximum=531, hs=0.3, he=0.25,ss=0.7,se=0.2,vs=1,ve=0.5\n"
	return
  elif gradient not in ('bgr','rgb','rainbow','reverserainbow','bwr','rwb',
                        'bmr','rmb','rw','wr','gw','wg','bw','wb','gy','yg','gray','grey','reversegray','reversegrey'):
    print "\n     WARNING: Unknown gradient: ",gradient, "    ----->   Nothing done.\n"
    return

  print "MODE, GRADIENT, NBINS:", mode,gradient, nbins

# get list of B-factors from selection
  m = cmd.get_model(selection)
  sel = []
  b_list = []

  if len(m.atom) == 0:
    print "Sorry, no atoms selected"

  else:
    if item == 'b':
      for i in range(len(m.atom)):
        m.atom[i].b=m.atom[i].resi
        b_list.append(m.atom[i].b) 
        
    elif item == 'q':
      for i in range(len(m.atom)):
        b_list.append(m.atom[i].q)

    else:
      print "Not configured to work on item %s" % item
      return
    
    cmd.load_model(m, dummy)
    
    print selection
    max_b = maximum
    min_b = minimum
    print "Minimum and Maximum B-values: ", min_b, max_b
    #nbins = (max_b - min_b)
    

    if mode == 'hist':

# check if minimum or maximum was specified and use the entered values
      if minimum != '':
        min_b = int(minimum)-1
      if maximum != '':
        max_b = int(maximum)+1
      # histogram:
      # color in bins of equal B-value ranges
      # subtract 0.1 from the lowest B in order to ensure that the single
      # atom with the lowest B value doesn't get omitted
      bin_width = (max_b - min_b)/nbins
      sel.append(selection + " and (%s = %4.4g" % (item,min_b + bin_width) + ")")
      for j in range(1,nbins):
        #sel.append(selection + " and %s > %4.4g" % (item,min_b + j*bin_width))
        sel.append(dummy + " and %s = %4.4g" % (item,min_b + j*bin_width))
        

# call the function to create the gradient which returns a list of colours
    colours = make_gradient(sel,gradient,nbins,sat,value,hs,he,ss,se,vs,ve,colorname)

# do the colouring now
    for j in range(nbins):
      print "Color select: ",sel[j]
      cmd.color(colours[j],sel[j])
  sel = []
  colours = []
# function for creating the gradient
def make_gradient(sel,gradient,nbins,sat,value,hs,he,ss,se,vs,ve,colorname):
  if gradient == 'bgr' or gradient == 'rainbow':
    col=[]
    coldesc=[]
    for j in range(nbins):
      # must append the str(sel[j]) to the color name so that it is unique 
      # for the selection
      coldesc.append(colorname + str(j))
      # coldesc.append('col' + str(sel[j]) + str(j))

      # create colors using hsv scale (fractional) starting at blue(.6666667) 
      # through red(0.00000) in intervals of .6666667/(nbins -1) (the "nbins-1" 
      # ensures that the last color is, in fact, red (0)
      # rewrote this to use the colorsys module to convert hsv to rgb
      hsv = (hs - (hs-he) * float(j) / (nbins-1), ss-(ss-se)*float(j)/(nbins-1), vs-(vs-ve)*float(j)/(nbins-1) )
      #convert to rgb and append to color list
      rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])

      col.append(rgb)
      # cmd.set_color("col" + str(sel[j]) + str(j),col[j])
      cmd.set_color(colorname + str(j),col[j])
      
      #cmd.color(,resi[j])

  # return the gradient as a list of colors named by their index (i.e. col0,col1,col2,col3,...)
  return coldesc

Download

colorama-0.1.1.tar.bz2