packmol-memgen-minimal 1.1.16__py3-none-any.whl

packmol_memgen/lib/pdbremix/data/color_b.py

@@ -0,0 +1,682 @@
+# rlc color_b.py version 8.0
+# Copyright (c) 2004 Robert L. Campbell
+# added user defined colors for 3 color ramp- Mark A. Wall
+
+import colorsys,sys,re
+from pymol import cmd
+
+# main function called from within PyMOL
+def color_b(selection='all',item='b',mode='hist',gradient='bgr',nbins=11,sat=1.,value=1.,minimum='',maximum='',user_rgb=''):
+  """
+    
+  AUTHOR 
+
+    Robert L. Campbell with enhancements from James Stroud
+
+  USAGE
+
+    color_b selection='sel',item='b', 'q', 'partial_charge' or 'formal_charge'
+      gradient='bgr' or 'rgb' or 'bwr' or 'rwb' or 'bmr' or 'rmb' or
+      'rw' or 'wr' or 'gw' or 'wg' or 'bw' or wb' or 'gy' or 'yg' or 
+      'gray' or 'reversegray' or 'user'
+
+      mode='hist' or 'ramp' (default is 'hist')
+
+      [minimum=''],[maximum=20.],
+
+      nbins=11, sat=1.0, value=1.0, 
+      
+      user_rgb = '(r1,g1,b1,r2,g2,b2,r3,g3,b3') [for use with gradient=user]
+
+      The "item" argument allows specifying 'b', 'q', 'partial_charge'
+      or 'formal_charge'as the item to color on.  The "color_q" function
+      is really just the same as "color_b item=q".
+
+      This function allows coloring of a selection as a function of
+      B-value or occupancy, following a gradient of colours.  The
+      gradients can be:
+
+      'bgr': blue -> green   -> red
+      'rgb': red  -> green   -> blue
+      'bwr': blue -> white   -> red
+      'rwb': red  -> white   -> blue
+      'bmr': blue -> magenta -> red
+      'rmb': red  -> magenta -> blue
+      'rw' : red -> white
+      'wr' : white -> red
+      'gw' : green -> white
+      'wg' : white -> green
+      'bw' : blue -> white
+      'wb' : white -> blue
+      'gy' : green -> yellow
+      'yg' : yellow -> green
+      'gray' : black -> white
+      'reversegray' : white -> black
+      'user' : user defined in this script
+
+      ('rainbow' and 'reverserainbow' can be used as synonyms for 
+      'bgr' and 'rgb' respectively and 'grey' can be used as a synonym for 'gray').
+
+      User-defined gradients are entered on the command line in
+      parentheses as either integers between 0 and 255 or floats between
+      0 and 1.  If any one value is larger than 1, then it is assumed
+      that all are being entered as integers between 0 and 255.  Hence one can type:
+
+      color_b selection, gradient=user, user_rgb=(0,0,1, 0,.5,1., 1.,.5,0.)
+
+        or
+
+      color_b selection, gradient=user, user_rgb=(0,0,255, 0,128,255, 255,128,0.)
+
+      The division of B-value ranges can in either of two modes: 'hist' or
+      'ramp'. 'hist' is like a histogram (equal-sized B-value increments
+      leading to unequal numbers of atoms in each bin). 'ramp' as a ramp
+      of B-value ranges with the ranges chosen to provide an equal number
+      of atoms in each group.
+
+      You can also specify the lower or upper limits of the data used to determine
+      the color bins (minimum,maximum). e.g. color_b my_molecule, minimum=15., maximum=25.
+
+      You can also specify the saturation and value (i.e. the "s" and "v"
+      in the "HSV" color scheme) to be used for the gradient. The defaults
+      are 1.0 for both "sat" and "value".
+
+      In the case of the gray scale gradients, "sat" sets the minimum intensity 
+      (normally black) and "value" sets the maximum (normally white)
+
+    usage:
+      from within PyMOL do "run color_b.py" to load the function definition.  
+      Then you can use for example:
+
+          color_b (c. a | c. b),mode=ramp,gradient=bwr,nbins=30,sat=.5, value=1.
+
+      to color chains A and B with the Blue-White-Red gradient in 30 colors of equal 
+      numbers of atoms in each color.
+  """
+
+  nbins=int(nbins)
+  sat=float(sat)
+  value=float(value)
+# 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)
+  if gradient == 'user' and user_rgb == '':
+    user_rgb = '50,50,195, 245,245,20, 255,20,20'
+
+# 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
+  elif gradient not in ('bgr','rgb','rainbow','reverserainbow','bwr','rwb','user',
+                        'bmr','rmb','rw','wr','gw','wg','bw','wb','gy','yg','gray','grey','reversegray','reversegrey','user'):
+    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)):
+        b_list.append(m.atom[i].b)
+    elif item == 'q':
+      for i in range(len(m.atom)):
+        b_list.append(m.atom[i].q)
+
+    elif item == 'partial_charge':
+      for i in range(len(m.atom)):
+        b_list.append(m.atom[i].partial_charge)
+
+    elif item == 'formal_charge':
+      for i in range(len(m.atom)):
+        b_list.append(m.atom[i].formal_charge)
+
+    else:
+      print("Not configured to work on item %s" % item)
+      return
+
+    max_b = max(b_list)
+    min_b = min(b_list)
+    print("Minimum and Maximum B-values: ", min_b, max_b)
+
+    if mode == 'ramp':
+      # color in bins of equal numbers of atoms
+      b_list.sort()
+
+      # subtract 0.1 from the lowest B in order to ensure that the single
+      # atom with the lowest B value doesn't get omitted
+#      b_list[0] = b_list[0] - 0.1
+
+      bin_num = int(len(b_list)/nbins)
+#      sel.append(selection + " and (b < " + str(b_list[bin_num]) + " or b = " + str(b_list[bin_num]) + ")")
+      sel.append(selection + " and (%s < %4.4g" % (item,b_list[bin_num]) + " or %s = %4.4g" % (item,b_list[bin_num]) + ")")
+      for j in range(1,nbins):
+#        sel.append(selection + " and b > " + str(b_list[j*bin_num]))
+        sel.append(selection + " and %s > %4.4g" % (item,b_list[j*bin_num]))
+        #print "Color select: ",sel[j]
+
+    elif mode == 'hist':
+
+# check if minimum or maximum was specified and use the entered values
+      if minimum != '':
+        min_b = float(minimum)
+      if maximum != '':
+        max_b = float(maximum)
+      # 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) + " or %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))
+        #print "Color select: ",sel[j]
+
+# call the function to create the gradient which returns a list of colours
+    colours = make_gradient(sel,gradient,nbins,sat,value, user_rgb)
+
+# do the colouring now
+    for j in range(nbins):
+      print("Color select: ",sel[j])
+      cmd.color(colours[j],sel[j])
+
+def color_q(selection="all",mode="hist",gradient="bgr",nbins=11,sat=1.,value=1.,minimum='',maximum=''):
+  """
+    
+  USAGE
+
+    color_q(selection,gradient,mode,nbins,sat,value) ='sel',
+      gradient='bgr' or 'rgb' or 'bwr' or 'rwb' or 'bmr' or 'rmb' 
+      'rw' or 'wr','gw' or 'wg' or 'bw' or 'wb' or 'gy' or 'yg' or 'gray' or 'reversegray' or 'user'
+      mode='hist' or 'ramp', q0=0.,q1=1.0,
+      nbins=11, sat=1.0, value=1.0)
+
+      This function allows coloring of a selection as a function of
+      occupancy.  See color_b for details.
+  """
+  item='q'
+  color_b(selection,item,mode,gradient,nbins,sat,value,minimum,maximum)
+
+# function for creating the gradient
+def make_gradient(sel,gradient,nbins,sat,value,user_rgb):
+  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('col' + 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 = (colorsys.TWO_THIRD - colorsys.TWO_THIRD * float(j) / (nbins-1), sat, value)
+      #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("col" + str(j),col[j])
+      # print "defined as ", str(sel[j])
+
+  elif gradient == 'user':
+    # --------------------------------------------
+    #  Modified color ramp by Mark Wall 2007.07.20
+    # --------------------------------------------
+    # assign 3-color ramp values (rgb 0-255)
+    # could easily assign RGB color values between 0.0 and 1.0 below
+    # !!! Black must be at least 1,0,0 or div by zero error !!!
+    #
+    #r1, g1, b1 = 255, 255, 225   # low   white
+    #r1, g1, b1 = 170, 170, 170   # low   gray
+    user_rgb = re.compile('[\[\](){}]').sub('',user_rgb)
+    user_rgb_fract = 0
+    try:
+      r1,g1,b1, r2,g2,b2, r3,g3,b3 = list(map(int,user_rgb.split(',')))
+    except ValueError:
+      r1,g1,b1, r2,g2,b2, r3,g3,b3 = list(map(float,user_rgb.split(',')))
+      user_rgb_fract = 1
+      
+    print('user_rgb', r1,g1,b1, r2,g2,b2, r3,g3,b3)
+
+#    r1, g1, b1 = 50, 50, 195     # low   med blue
+#    r2, g2, b2 = 245, 245, 20    # mid   yellow
+#    r3, g3, b3 = 255, 20, 20     # high  red
+    #
+    #r1, g1, b1 = 255, 20, 20     # low   red
+    #r2, g2, b2 = 150, 150, 20    # mid   yellow
+    #r3, g3, b3 = 20, 20, 195     # high   med blue
+    #
+    #r1, g1, b1 = 1, 0, 0         # low   black
+    #r2, g2, b2 = 155, 155, 155   # mid  gray
+    #r3, g3, b3 = 255, 255, 255   # high  white
+    #
+    #r1, g1, b1 = 0, 50, 200      # low  blue
+    #r2, g2, b2 = 1, 0, 0         # mid   black
+    #r3, g3, b3 = 255, 255, 20    # high  yellow
+    #
+    #r1, g1, b1 = 0, 0, 1         # low   black
+    #r2, g2, b2 = 200, 0, 0       # mid  red
+    #r3, g3, b3 = 255, 255, 0     # high  yellow
+    #
+    #r1, g1, b1 = 180, 170, 170   # low   gray
+    #r2, g2, b2 = 250, 90, 40     # mid  orange
+    #r3, g3, b3 = 255, 255, 0     # high  yellow
+    #
+    #r1, g1, b1 = 235, 255, 255   # low   white
+    #r2, g2, b2 = 55, 255, 255    # mid   cyan
+    #r3, g3, b3 = 0, 0, 180       # high  blue
+    #
+    # change color values to fractions
+    # 
+    if max(r1,g1,b1,r2,g2,b2,r3,g3,b3) > 1:
+      r1, g1, b1 = float(r1)/255.0, float(g1)/255.0, float(b1)/255.0
+      r2, g2, b2 = float(r2)/255.0, float(g2)/255.0, float(b2)/255.0 
+      r3, g3, b3 = float(r3)/255.0, float(g3)/255.0, float(b3)/255.0
+
+    col=[]
+    coldesc=[]
+#    print "r1,g1,b1, r2,g2,b2, r3,g3,b3", r1,g1,b1, r2,g2,b2, r3,g3,b3
+    for j in range(nbins/2):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from low to mid 
+      rgb = [r1*((float(nbins)-float(j)*2.0)/float(nbins))+r2*(float(j)*2.0/float(nbins)), \
+             g1*((float(nbins)-float(j)*2.0)/float(nbins))+g2*(float(j)*2.0/float(nbins)), \
+             b1*((float(nbins)-float(j)*2.0)/float(nbins))+b2*(float(j)*2.0/float(nbins))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
+      print(j,"rgb: %4.3f %4.3f %4.3f"% rgb)
+
+      col.append(rgb)
+      # cmd.set_color("col" + str(sel[j]) + str(j),col[j])
+      cmd.set_color("col" + str(j),col[j])
+
+    for j in range(nbins/2,nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from mid to high
+      rgb = [r2*((float(nbins)-((float(j+1)-float(nbins)/2.0)*2.0))/float(nbins))+r3*(((float(j+1)-float(nbins)/2.0)*2.0)/float(nbins)), \
+             g2*((float(nbins)-((float(j+1)-float(nbins)/2.0)*2.0))/float(nbins))+g3*(((float(j+1)-float(nbins)/2.0)*2.0)/float(nbins)), \
+             b2*((float(nbins)-((float(j+1)-float(nbins)/2.0)*2.0))/float(nbins))+b3*(((float(j+1)-float(nbins)/2.0)*2.0)/float(nbins))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
+      print(j,"rgb: %4.3f %4.3f %4.3f"% rgb)
+
+      col.append(rgb)
+      # cmd.set_color("col" + str(sel[j]) + str(j),col[j])
+      cmd.set_color("col" + str(j),col[j])
+
+  elif gradient == 'rgb' or gradient == 'reverserainbow':
+    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('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+
+      # create colors using hsv scale (fractional) starting at red(.00000) 
+      # through blue(0.66667) 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 = (colorsys.TWO_THIRD * float(j) / (nbins-1), sat, value)
+      #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("col" + str(j),col[j])
+
+  elif gradient == 'bmr':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from blue through magenta to red
+      rgb = [min(1.0, float(j)*2/(nbins-1)), 0.0, min(1.0, float(nbins-j-1)*2/(nbins-1))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'rmb':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from red through magenta to blue
+      rgb = [min(1.0, float(nbins-j-1)*2/(nbins-1)), 0.0, min(1.0, float(j)*2/(nbins-1))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'rw':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from red through white
+      rgb = [1.0, float(j)/(nbins-1), float(j)/(nbins-1)]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'wr':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from white through red 
+      rgb = [1.0, float(nbins-j-1)/(nbins-1), float(nbins-j-1)/(nbins-1)]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'gw':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from green through white
+      rgb = [float(j)/(nbins-1), 1.0, float(j)/(nbins-1)]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'wg':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from white through green 
+      rgb = [float(nbins-j-1)/(nbins-1), 1.0, float(nbins-j-1)/(nbins-1)]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'bw':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from blue through white
+      rgb = [float(j)/(nbins-1), float(j)/(nbins-1), 1.0 ]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'wb':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from blue through white
+      rgb = [float(nbins-j-1)/(nbins-1), float(nbins-j-1)/(nbins-1), 1.0 ]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'wr':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from white through blue 
+      rgb = [float(nbins-j-1)/(nbins-1), float(nbins-j-1)/(nbins-1), 1.0]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'gy':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from green through yellow
+      rgb = [float(j)/(nbins-1), 1.0, 0.]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'yg':
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from green through yellow
+      rgb = [float(nbins-j-1)/(nbins-1), 1.0, 0.]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'bwr':
+    col=[]
+    coldesc=[]
+    for j in range(nbins/2):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from blue to white 
+      rgb = [min(1.0, float(j)*2/(nbins-1)), min(1.0,float(j)*2/(nbins-1)), min(1.0, float(nbins-j-1)*2/(nbins-1))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+    for j in range(nbins/2,nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from white to red
+      rgb = [min(1.0, float(j)*2/(nbins-1)), min(1.0,float(nbins-j-1)*2/(nbins-1)), min(1.0, float(nbins-j-1)*2/(nbins-1))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'rwb':
+    col=[]
+    coldesc=[]
+    for j in range(nbins/2):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient from red to white
+      rgb = [min(1.0, float(nbins-j-1)*2/(nbins-1)), min(1.0,float(j)*2/(nbins-1)), min(1.0, float(j)*2/(nbins-1))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+    for j in range(nbins/2,nbins):
+      coldesc.append('col' + str(j))
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      # create colors in a gradient from white to blue
+      rgb = [min(1.0, float(nbins-j-1)*2/(nbins-1)), min(1.0,float(nbins-j-1)*2/(nbins-1)), min(1.0, float(j)*2/(nbins-1))]
+
+      # convert rgb to hsv,  modify saturation and value and convert back to rgb
+      hsv = list(colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2]))
+      hsv[1] = hsv[1]*sat
+      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'gray' or gradient == 'grey':
+# if it is "gray" then sat must be 0!
+    sat = 0.0
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient of grays from "sat" to "value"
+
+      hsv = [0, 0, sat + (value-sat)*float(j)/(nbins-1)]
+#      hsv[1] = hsv[1]*sat
+#      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+  elif gradient == 'reversegray' or gradient == 'reversegrey':
+# if it is "gray" then sat must be 0!
+    sat = 0.0
+    col=[]
+    coldesc=[]
+    for j in range(nbins):
+      # coldesc.append('col' + str(sel[j]) + str(j))
+      coldesc.append('col' + str(j))
+      # create colors in a gradient of grays from "sat" to "value"
+
+      hsv = [0, 0, value - (value-sat)*float(j)/(nbins-1)]
+#      hsv[1] = hsv[1]*sat
+#      hsv[2] = hsv[2]*value
+      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("col" + str(j),col[j])
+
+
+# return the gradient as a list of colors named by their index (i.e. col0,col1,col2,col3,...)
+  return coldesc
+
+# allow calling without parentheses: color_hist_b [selection=], [mode= ],[gradient= ],[nbins= ]
+cmd.extend("color_b",color_b)
+cmd.extend("color_q",color_q)
+