Colorama
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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 does not properly work with PyMOL versions older than 1.0.
Single color
- Type the name of a PyMOL object to be colored into the COLORAMA entry field.
- Push the "Set" button.
- The scales are adjusted to the current color which is additionally visualized in a field left to the scales.
- If one of the scales is moved, the color of the selected object will change in real-time.
- Pushing the RGB or HSV buttons on the left allows to switch between both color systems.
Color gradients
- After an object has been selected, push the "G" button (gradient).
- Select the start color by pushing "C1" and adjusting it using the scales.
- Select the end color "C2" in the same way.
- 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
