Tcl line command interface to gOpenMol


The command line parser is implemented using the Tcl (Tool command language). The language is rich of commands and I strongly recommend you first to have a look the the Tcl commands (http://dev.scriptics.com/). For most commands it is enough just to use the four first characters to uniquely define the command. A clear exception is the 'contour' command where the first five characters are needed not to mix the command with the 'continue' statement. Through the help files I have used a dollar ($) sign to indicate there characters needed to define a command. You can also get a list of all available commands by typing the question (?) mark at the command prompt. Very many of the commands return a parameter (or several) which can be used as an input to a new command.

Please observe that when using the commands in scripts one needs to fill in the full command name!


Commands available:

atom               define various properties about atoms    
calc$ulate         calculate molecular properties
cent$er            center the system on the screen
conto$ur           display and define isosurface plots
defi$ne            define general properties
displ$ay           display the current picture
edit               edit molecule and molecule properties
expo$rt            export molecular structures
fill               fill time series vectors
find               find/calculate various things
gomError "text"    print the "text" through the ERROR module
gomPrint "text"    print the "text" through the Print module          
gscal$e            scale the current display
hard$copy          make a hardcopy of the currecnt display
help               help system
impo$rt            import molecular coordinates and other things
mani$pulate        manipulate time series
moni$tor           monitor molecular properties from a trajectory
mope$n             open old model file
msav$e             save model file
pause    Fvalue    pause for Fvalue seconds
plot               plot various things
plum$ber           plot a ribbon or tube through atoms
ptra$ce            trace atoms through the trajectory
quit               stop program and exit
rese$t             reset the system
rota$te            rotate the current display
run                run various programs
sele$ct            make a selection from the current atoms
show               show various things
traj$ectory        trajectory display and analysis control
tran$slate         translate the current display
wind$ow            window operations


You don't always need the graphics when you use gOpenMol. In fact in
some cases it's an advantage not to use the graphics. The command
line options when you start gOpenMol are:

    gopenmol -cInputCoord.Ext -h -t -ln -mModel.gom -pFile.Name  
                                                                 
    -mModel.gom start GopenMol with the model file Model.gom     
    -cInputCoord.Ext start gOpenMol with coordinate file         
    -pfile.name start gOpenMol with parameter file 'File.Name'  
    -t start gOpenMol without any graphics      
    -ln do not write a log file  (GOPENMOL.LOG) 
    -ly force the write of the log file (GOPENMOL.LOG) 
    -h print this help                                 

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LUL/1996
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