Colorblindfriendly - Revision history

Cchem: 1 revision

2017-12-11T04:50:13Z

1 revision

Jaredsampson: /* Download the script and run locally */ Add a "run from Github" example.

2017-11-15T19:21:03Z

Download the script and run locally: Add a "run from Github" example.

Cchem: 7 revisions

2017-11-13T03:27:07Z

7 revisions

Jaredsampson: /* Usage */ Add instructions for running as dowloaded script.

2017-10-26T20:08:59Z

Usage: Add instructions for running as dowloaded script.

Jaredsampson: /* Usage */ update code samples and use `instead of tags.`


2017-10-26T19:50:19Z
Usage:   update code samples and use <code> instead of <tt> tags.

				
				
				
				
				
				← Older revision
				Revision as of 19:50, 26 October 2017
				
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  == Usage ==   == Usage ==
    
− [[File:colorblindfriendly_menu.png|thumb|Screenshot of the <tt>cb_colors</tt> color menu in the OpenGL GUI in PyMOL 2.0.]] + [[File:colorblindfriendly_menu.png|thumb|Screenshot of the <code>cb_colors</code> color menu in the OpenGL GUI in PyMOL 2.0.]]
    
− After importing the module, + After importing the module, call the <code>set_colors()</code> function to add the colors to PyMOL's color palette.  Then, use these color names just like any other named color, using the <code>[[color]]</code> command.
    
  <syntaxhighlight lang="python">   <syntaxhighlight lang="python">
  import colorblindfriendly as cbf   import colorblindfriendly as cbf
− </syntaxhighlight>  
    
− call the <tt>set_colors()</tt> function to add the colors to PyMOL's color palette.  Then, use these color names just like any other named color, using the <code>[[color]]</code> command.  
−  
− <syntaxhighlight lang="python">  
  # Add the new colors   # Add the new colors
  cbf.set_colors()   cbf.set_colors()
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  </syntaxhighlight>   </syntaxhighlight>
    
− The colors can also be made to replace the built-in colors (i.e. they are created both with and without the "<tt>cb_</tt>" prefix.). Do this by passing the <tt>replace</tt> keyword argument. + The colors can also be made to replace the built-in colors (i.e. they are created both with and without the "<code>cb_</code>" prefix.). Do this by passing the <code>replace</code> keyword argument.
    
  <syntaxhighlight lang="python">   <syntaxhighlight lang="python">
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  </syntaxhighlight>   </syntaxhighlight>
    
− One can also add an entry to the color menu in the right-side OpenGL GUI.  So clicking on [C], there will now be a <tt>cb_colors</tt> menu item, which expands to give all the color blind-friendly colors, except black, which is available in the <tt>grays</tt> menu. + One can also add an entry to the color menu in the right-side OpenGL GUI.  So clicking on [C], there will now be a <code>cb_colors</code> menu item, which expands to give all the color blind-friendly colors, except black, which is available in the <code>grays</code> menu.
    
  <syntaxhighlight lang="python">   <syntaxhighlight lang="python">
− # Add a cb_colors menu item to the OpenGL GUI ([C] menu in the right panel) + # Add a `cb_colors` menu to the OpenGL GUI (see screenshot)
− # this also adds the colors + # This will also add the colors if `set_colors()` hasn't yet been run.
  cbf.add_menu()   cbf.add_menu()
  </syntaxhighlight>   </syntaxhighlight>



Speleo3: color command argument order
2017-10-26T13:54:56Z
color command argument order

				
				
				
				
				
				← Older revision
				Revision as of 13:54, 26 October 2017
				
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  # Add the new colors   # Add the new colors
  cbf.set_colors()   cbf.set_colors()
− color myObject, cb_red + color cb_red, myObject
  </syntaxhighlight>   </syntaxhighlight>
    
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  # Replace built-in colors with cbf ones   # Replace built-in colors with cbf ones
  cbf.set_colors(replace=True)   cbf.set_colors(replace=True)
− color myOtherObject, yellow   # actually cb_yellow + color yellow, myOtherObject   # actually cb_yellow
  </syntaxhighlight>   </syntaxhighlight>
    



Jaredsampson: /* Requirements */ update to reflect support for older PyMOLs
2017-10-26T13:51:08Z
Requirements:  update to reflect support for older PyMOLs

				
				
				
				
				
				← Older revision
				Revision as of 13:51, 26 October 2017
				
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  == Requirements ==   == Requirements ==
− The <tt>add_menu()</tt> function and OpenGL <tt>cb_colors</tt> menu currently only works with PyMOL 2.0 and later. + The <tt>cb_colors</tt> GUI menu (generated by the <tt>add_menu()</tt> function) requires PyMOL 1.6.0 and later.
    
    



Jaredsampson: /* Usage */ fix object name for consistency
2017-10-26T04:42:54Z
Usage:  fix object name for consistency

				
				
				
				
				
				← Older revision
				Revision as of 04:42, 26 October 2017
				
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  # Replace built-in colors with cbf ones   # Replace built-in colors with cbf ones
  cbf.set_colors(replace=True)   cbf.set_colors(replace=True)
− color my_other_object, yellow   # actually cb_yellow + color myOtherObject, yellow   # actually cb_yellow
  </syntaxhighlight>   </syntaxhighlight>
    



Jaredsampson: /* Usage */ Update usage for version 0.2; Add requirements section.
2017-10-26T04:41:20Z
Usage:  Update usage for version 0.2; Add requirements section.

				
				
				
				
				
				← Older revision
				Revision as of 04:41, 26 October 2017
				
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  == Usage ==   == Usage ==
− Use these color names just like any other named color, using the <code>[[color]]</code> command: +  
  + [[File:colorblindfriendly_menu.png|thumb|Screenshot of the <tt>cb_colors</tt> color menu in the OpenGL GUI in PyMOL 2.0.]]
  +  
  + After importing the module,
  +  
  + <syntaxhighlight lang="python">
  + import colorblindfriendly as cbf
  + </syntaxhighlight>
  +  
  + call the <tt>set_colors()</tt> function to add the colors to PyMOL's color palette.  Then, use these color names just like any other named color, using the <code>[[color]]</code> command.
  +  
  + <syntaxhighlight lang="python">
  + # Add the new colors
  + cbf.set_colors()
  + color myObject, cb_red
  + </syntaxhighlight>
  +  
  + The colors can also be made to replace the built-in colors (i.e. they are created both with and without the "<tt>cb_</tt>" prefix.). Do this by passing the <tt>replace</tt> keyword argument.
  +  
  + <syntaxhighlight lang="python">
  + # Replace built-in colors with cbf ones
  + cbf.set_colors(replace=True)
  + color my_other_object, yellow   # actually cb_yellow
  + </syntaxhighlight>
  +  
  + One can also add an entry to the color menu in the right-side OpenGL GUI.  So clicking on [C], there will now be a <tt>cb_colors</tt> menu item, which expands to give all the color blind-friendly colors, except black, which is available in the <tt>grays</tt> menu.
  +  
  <syntaxhighlight lang="python">   <syntaxhighlight lang="python">
− import colorblindfriendly + # Add a cb_colors menu item to the OpenGL GUI ([C] menu in the right panel)
− color cb_skyblue, all + # this also adds the colors
  + cbf.add_menu()
  </syntaxhighlight>   </syntaxhighlight>
    
  + == Requirements ==
  + The <tt>add_menu()</tt> function and OpenGL <tt>cb_colors</tt> menu currently only works with PyMOL 2.0 and later.
    
    



Jaredsampson: /* Colors */ show 0-255 values instead.
2017-10-26T04:04:34Z
Colors:  show 0-255 values instead.

				
				
				
				
				
				← Older revision
				Revision as of 04:04, 26 October 2017
				
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  == Colors ==   == Colors ==
− The 0-255 RGB values from the J*FLY page have been used and converted to decimal notation (e.g. 230/255 = 0.902). + These are the 0-255 RGB values from the J*FLY page that are used in the script, with the defined color names and alternate names.
  {| cellpadding="1"   {| cellpadding="1"
  |- align="center"   |- align="center"
  ! width="20"|&nbsp;||bgcolor=#ddd width="100"|name||bgcolor=#ddd width="50"|R||bgcolor=#ddd width="50"|G||bgcolor=#ddd width="50"|B||bgcolor=#ddd|alternate names   ! width="20"|&nbsp;||bgcolor=#ddd width="100"|name||bgcolor=#ddd width="50"|R||bgcolor=#ddd width="50"|G||bgcolor=#ddd width="50"|B||bgcolor=#ddd|alternate names
  |- align="center"   |- align="center"
− |bgcolor=#000000|&nbsp;||cb_black||0.0||0.0||0.0|| + |bgcolor="#000000"|&nbsp;||cb_black||0||0||0||
  |- align="center"   |- align="center"
− |bgcolor=#e69f00|&nbsp;||cb_orange||0.902||0.624||0.0|| + |bgcolor="#e69f00"|&nbsp;||cb_orange||230||159||0||
  |- align="center"   |- align="center"
− |bgcolor=#56b4e9|&nbsp;||cb_sky_blue||0.337||0.706||0.914||cb_skyblue, cb_light_blue, cb_lightblue + |bgcolor="#56b4e9"|&nbsp;||cb_sky_blue||86||180||233||cb_skyblue, cb_light_blue, cb_lightblue
  |- align="center"   |- align="center"
− |bgcolor=#009e73|&nbsp;||cb_bluish_green||0.0||0.62||0.451||cb_bluishgreen, cb_green + |bgcolor="#009e73"|&nbsp;||cb_bluish_green||0||158||115||cb_bluishgreen, cb_green
  |- align="center"   |- align="center"
− |bgcolor=#f0e442|&nbsp;||cb_yellow||0.941||0.894||0.259|| + |bgcolor="#f0e442"|&nbsp;||cb_yellow||240||228||66||
  |- align="center"   |- align="center"
− |bgcolor=#0072b2|&nbsp;||cb_blue||0.0||0.447||0.698|| + |bgcolor="#0072b2"|&nbsp;||cb_blue||0||114||178||
  |- align="center"   |- align="center"
− |bgcolor=#d55e00|&nbsp;||cb_vermillion||0.835||0.369||0.0||cb_red, cb_red_orange, cb_redorange + |bgcolor="#d55e00"|&nbsp;||cb_vermillion||213||94||0||cb_red, cb_red_orange, cb_redorange
  |- align="center"   |- align="center"
− |bgcolor=#cc79a7|&nbsp;||cb_reddish_purple||0.8||0.475||0.655||cb_reddishpurple, cb_rose, cb_violet, cb_magenta + |bgcolor="#cc79a7"|&nbsp;||cb_reddish_purple||204||121||167||cb_rose, cb_violet, cb_magenta
  |}   |}
−  
    
  == Usage ==   == Usage ==

← Older revision	Revision as of 04:50, 11 December 2017
(No difference)

← Older revision	Revision as of 03:27, 13 November 2017
(No difference)

← Older revision		Revision as of 13:51, 26 October 2017
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	== Requirements ==		== Requirements ==
−	The <tt>~~add_menu()~~</tt> ~~function and OpenGL~~ <tt>~~cb_colors~~</tt> ~~menu currently only works with~~ PyMOL 2.0 and later.	+	The <tt>cb_colors</tt> GUI menu (generated by the <tt>add_menu()</tt> function) requires PyMOL 1.6.0 and later.

Colorblindfriendly - Revision history

Cchem: 1 revision

Jaredsampson: /* Download the script and run locally */ Add a "run from Github" example.

Cchem: 7 revisions

Jaredsampson: /* Usage */ Add instructions for running as dowloaded script.

Jaredsampson: /* Usage */ update code samples and use instead of tags.

Speleo3: color command argument order

Jaredsampson: /* Requirements */ update to reflect support for older PyMOLs

Jaredsampson: /* Usage */ fix object name for consistency

Jaredsampson: /* Usage */ Update usage for version 0.2; Add requirements section.

Jaredsampson: /* Colors */ show 0-255 values instead.

Jaredsampson: /* Usage */ update code samples and use `instead of tags.`