 |  |  |  |
 |  |  |  |
 |
 |
 |
 |
|
 |
|
 |
|
 |
|
° |
Commands | - | Tell YASARA what to do |
When you use the graphical user interface, the options you select are translated to a YASARA command which is sent to the console. You can look at these commands by activating the console with
<SPACE>. The big advantage of this approach is that your input can be recorded as a macro or logged to a file
. You can of course type commands directly in the console, and write or modify macros with your favorite text editor.
YASARA command names follow the syntax of the early text adventures that were popular in the
1980's:
<Verb><Object> <Argument 1>,<Argument 2>...
Example:
DelAtom CA | Delete all Calpha atoms |
ColorRes Lys,yellow | Color all lysine residues yellow |
Sometimes the object is split in two parts:
ShowSecStrMol B,Ribbon | Show secondary structure for molecule B using a ribbon |
If the verb is 'Get' or
'Set', it is omitted. You choose the 'Set' version if you supply arguments, and the
'Get' version if you do not or assign the return value to a variable:
Time 250 | Set simulation time to 250 femtoseconds |
Time | Get current simulation time and print it to the console |
MyVar=Time | Get current simulation time, print it and assign it to variable MyVar |
For every YASARA command,
you will find a description with examples and often screenshots in the following sections. All command arguments are listed with their datatypes,
which are summarized in the following table.
| Selection | A selection using the syntax described in detail separately |
| Integer | An integer number without a decimal point, e.g. 1, 5, -6, 0 |
| Float | A floating point number, e.g. 1.0, 534.789, 1.23e-4, -56e3, 0 |
| Char | A single character, e.g. A, B, 1 |
| String | A text string, without any quotes. Use quotes only if the string contains a comma |
| RGBColor | An RGB color specified by name or in HTML format, e.g. Red, ff0000, Green, 1456af |
| BowColor | A rainbow color specified by name or by number in the rainbow circle (where 0 is blue, 120 is red, 240 is green and 360 is blue again). |
Note that YASARA commands are not case sensitive except for filenames and some rare
selection cases.
When looking at a macro or plugin,
you might run into a command you do not know yet. The quickest way to find the command description is by clicking twice on the section header
'Command - Tell YASARA what to do'. You get a list of all commands and can use your Browser's find option to locate your command
(omitting the command extension).
