Color Objects - Revision history

Pyadmin: 7 revisions

2014-03-28T02:15:06Z

7 revisions

Speleo3: fix (imports, get_names)

2011-12-19T08:34:00Z

fix (imports, get_names)

Cowsandmilk at 12:56, 2 February 2010

2010-02-02T12:56:42Z

New page

<source lang="python">
#####################################################################
#
# Colour by object
#
#####################################################################

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

"""

# Process arguments
rainbow = int(rainbow)

# Get names of all PyMOL objects
obj_list = cmd.get_names('models')

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)

</source>

[[Category:Script_Library|Color Objects]]
[[Category:Coloring]]
[[Category:ObjSel_Scripts]]

Rlc: corrected web page reference for RLC's web site

2008-06-23T20:39:27Z

corrected web page reference for RLC's web site

New page

<source lang="python">
#####################################################################
#
# Colour by object
#
#####################################################################

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

"""

# Process arguments
rainbow = int(rainbow)

# Get names of all PyMOL objects
obj_list = cmd.get_names('models')

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)
</source>

[[Category:Script_Library|Color Objects]]

Krother at 15:21, 23 February 2005

2005-02-23T15:21:49Z

New page

<source lang="python">
#####################################################################
#
# Colour by object
#
#####################################################################

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

"""

# Process arguments
rainbow = int(rainbow)

# Get names of all PyMOL objects
obj_list = cmd.get_names('models')

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://biophysics.med.jhmi.edu/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)
</source>

[[Category:Scripting_Script_Library|Color Objects]]

← Older revision	Revision as of 02:15, 28 March 2014
(No difference)

@@ Line 1: / Line 1: @@
 <source lang="python">
 #####################################################################
@@ Line 6: / Line 11: @@
 #####################################################################
 def color_obj(rainbow=0):
@@ Line 23: / Line 30: @@
          gets the same colour as the first), or are the colours of the rainbow
          """
@@ Line 29: / Line 39: @@
          # Get names of all PyMOL objects
-         obj_list = cmd.get_names('models')
+         obj_list = cmd.get_names('objects')
          if rainbow: