Color Objects

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Type Python Script
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Author(s) Gareth Stockwell
License
#####################################################################
#
# Colour by object
#
#####################################################################
 
from pymol import cmd

def color_obj(rainbow=0):
 
        """
 
AUTHOR 
 
        Gareth Stockwell
 
USAGE
 
        color_obj(rainbow=0)
 
        This function colours each object currently in the PyMOL heirarchy
        with a different colour.  Colours used are either the 22 named
        colours used by PyMOL (in which case the 23rd object, if it exists,
        gets the same colour as the first), or are the colours of the rainbow
 
SEE ALSO

        util.color_objs()
        """
 
        # Process arguments
        rainbow = int(rainbow)
 
        # Get names of all PyMOL objects
        obj_list = cmd.get_names('objects')
 
        if rainbow:
 
           print "\nColouring objects as rainbow\n"
 
           nobj = len(obj_list)
 
           # Create colours starting at blue(240) to red(0), using intervals
           # of 240/(nobj-1)
           for j in range(nobj):
              hsv = (240-j*240/(nobj-1), 1, 1)
              # Convert to RGB
              rgb = hsv_to_rgb(hsv)
              # Define the new colour
              cmd.set_color("col" + str(j), rgb)
              print obj_list[j], rgb
              # Colour the object
              cmd.color("col" + str(j), obj_list[j])
 
        else:
 
           print "\nColouring objects using PyMOL defined colours\n"
 
           # List of available colours
           colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan',    \
           'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \
           'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate',    \
           'wheat', 'white', 'grey' ]
           ncolours = len(colours)
 
           # Loop over objects
           i = 0
           for obj in obj_list:
              print "  ", obj, colours[i]
              cmd.color(colours[i], obj)
              i = i+1
              if(i == ncolours):
                 i = 0
 
 
# HSV to RGB routine taken from Robert L. Campbell's color_b.py script
#   See http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
# Original algorithm from: http://www.cs.rit.edu/~ncs/color/t_convert.html
def hsv_to_rgb(hsv):
 
        h = float(hsv[0])
        s = float(hsv[1])
        v = float(hsv[2])
 
        if( s == 0 ) :
                #achromatic (grey)
                r = g = b = v
 
        else:
                # sector 0 to 5
                h = h/60.            
                i = int(h)
                f = h - i                       # factorial part of h
                #print h,i,f
                p = v * ( 1 - s )
                q = v * ( 1 - s * f )
                t = v * ( 1 - s * ( 1 - f ) )
 
                if i == 0:
                        (r,g,b) = (v,t,p)
                elif i == 1:
                        (r,g,b) = (q,v,p)
                elif i == 2:
                        (r,g,b) = (p,v,t)
                elif i == 3:
                        (r,g,b) = (p,q,v)
                elif i == 4:
                        (r,g,b) = (t,p,v)
                elif i == 5:
                        (r,g,b) = (v,p,q)
                else:
                        (r,g,b) = (v,v,v)
                        print "error, i not equal 1-5"
 
        return [r,g,b]
 
 
 
# Add color_obj to the PyMOL command list 
cmd.extend("color_obj",color_obj)