[chimerax-users] using variables in command files

[Tom Goddard]

Hi Pranav,

  I improved the ChimeraX runscript command so it can pass arguments to a ChimeraX command file (.cxc suffix) replacing $1, $2, $3 ... in the commands with the given arguments.  This will be in tomorrow's daily builds.  For example,

	run radcolor.cxc mymap.mrc mymap.png

where the radcolor.cxc text file contains

# Color map radially and save an image
open $1
color radial palette rainbow
save $2 height 512 width 512 transparentBackground true

Thanks suggesting the idea.

	Tom


> On Jun 24, 2022, at 12:09 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Pranav,
> 
>  Currently ChimeraX does not have a way to substitute argument values into a *.cxc file except for the open command "foreach" option which allows substituting the file name in for $file.  For simple series of commands you could define an alias, for example,
> 
> 	alias radcolor open $1 ; color radial palette rainbow ; save $2 height 512 width 512 transparentBackground true
> 
> This defines the radcolor command that you can use like
> 
> 	radcolor mymap.mrc image.png
> 
> Here's the documentation for the "alias" command
> 
> 	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/alias.html
> 
> The other mechanism for handing arguments to a script is the "runscript" command which passes arguments to Python scripts only.  I could imagine runscript being enhanced so that it works with a *.cxc command script and substitutes arguments in for $1, $2, $3, ... occurring in the script.
> 
> 	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/runscript.html
> 
>  Tom
> 
> 
> 
> 
>> On Jun 24, 2022, at 5:57 AM, Pranav Shah via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi Team,
>> Is it possible for one to declare a variable in a command file that
>> can then be passed to via the chimeraX command line interface. A
>> minimal example of something I would like to do is -
>> command.cxc
>> open $file
>> color radial palette rainbow
>> save $outfile.png height 512 width 512 transparentBackground True
>> 
>> In the chimeraX command line window I would then like to run
>> open command.cxc infile.mrc outfile.png
>> Best,
>> Pranav
>> --
>> Pranav Shah
>> Postdoctoral Research Fellow.
>> 
>> Division of Structural Biology,
>> Wellcome Trust Centre for Human Genetics,
>> University of Oxford,
>> Roosevelt Drive, Oxford OX3 7BN,
>> UK
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> 
> 
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