11.1 Introduction to extended commands
VEGA can interpret commands with extended syntax that can be send trough the console window, the windows class port and the TCP/IP (PowerNet plugin). The syntax of these commands is:
COMMAND_NAME ARG1 ARG2 ...
The command name is case insensitive and the number of arguments is typical for each command. The arguments must be separated with one or more spaces. Like showed in the following table, an argument can be:
Type | Description |
BOOL | Boolean value (0 = false, 1 = true). |
CHAR | Character string. If it contains one or more spaces, you must use the double quotes " at the beginning and at the end of the string (e.g. "Hello World"). |
MCHAR | Multiple selection string. The MCHAR argument must be a specific keyword (string). |
FLOAT | Floating point number with standard C syntax (the decimal separator must be a dot . and not a comma ,). |
UFLOAT | Unsigned float number. |
INT | Integer number. |
UINT | Unsigned integer number. |
In order to interpret much easier the syntax of the commands present in this guide, for each argument is highlighted its type (BOOL, CHAR, INT, etc).
Command | Type | Description | ||
ADDHYDROG | Std | Add hydrogens. | ||
ADDIONS | Std | Add ions. | ||
ANGLE | Ogl | Measure the bond angle between three atoms. | ||
ANTIALIAS | Ogl | Enable/disable the anti-aliased visualization. | ||
BIODOCK | Ogl | Start a BioDock background calculation. | ||
CHARGE | Std | Assign the atomic partial charges. | ||
CHDIR | Std | Change the current directory. | ||
COLOR | Ogl | Change the color of the current selection. | ||
COLORIDDLG | Gen | Show the predefined color dialog box. | ||
COLORRGBDLG | Gen | Show the RGB color table. | ||
CONCLRHIST | Ogl | Clear the console command history buffer. | ||
CONCLS | Ogl | Clear the console line buffer. | ||
CONSAVE | Ogl | Save the console output. | ||
CONSET | Ogl | Set the console line buffer size and the command history size. | ||
CONWIN | Ogl | Change the position and the size of the console window. | ||
COPY | Ogl | Copy the molecule into the clipboard. | ||
CPKPROP | Ogl | Change the CPK visualization properties. | ||
CPUFINDFILE | Std |
Check if an executable is present and choose the best available for the installed CPU. |
||
DBCLOSE | Dbase | Close a database. | ||
DBCREATE | Dbase | Create a new empty database. | ||
DBGET | Dbase | Extract a molecule from the database specifying its name. | ||
DBGETID | Dbase | Extract a molecule from the database specifying its identification number (ID). | ||
DBINFO | Dbase | Obtain the value of a database variable | ||
DBOPEN | Dbase | Open an existing database. | ||
DEPTHCUE | Ogl | Enable/disable the depth cueing. | ||
DIRDLG | Gen | Show the directory dialog box. | ||
DISTANCE | Ogl | Measure the distance between two atoms | ||
ERRMSG | Std | Return the error description. | ||
FORCEFIELD | Std | Assigns the atom types. | ||
GET | Std | Get the value of a specific internal variable. | ||
GRAPHADD | Ogl | Add a point value in the chart. | ||
GRAPHCALC | Ogl | Calculate a statistical value. | ||
GRAPHCLOSE | Ogl | Close the Graph Editor window. | ||
GRAPHDELETE | Ogl | Delete a point. | ||
GRAPHGET | Ogl | Get the point values. | ||
GRAPHLABELX | Ogl | Set the X axis label. | ||
GRAPHLABELY | Ogl | Set the Y axis label. | ||
GRAPHLOAD | Ogl | Load the graph data file. | ||
GRAPHNEW | Ogl | Clear all data in the chart. | ||
GRAPHOPEN | Ogl | Open the Graph Editor window. | ||
GRAPHSAVE | Ogl | Save the graph data into a file. | ||
GRAPHSET | Ogl | Set the point values. | ||
GRAPHSETCUR | Ogl | Set the current Graph Editor window. | ||
GRAPHTITLE | Ogl | Set the chart title. | ||
GRAPHWIN | Ogl | Change the position and the size of the Graph Editor window. | ||
LIQPROP | Ogl | Change the liquorice visualization properties. | ||
MAINWIN | Ogl | Change the position and the size of the main window. | ||
MESSAGEBOX | Gen | Show a message box. | ||
MERGE | Std | Merge the loaded molecule with one or more parts of another molecule. | ||
MINIED | Gen | Open the mini text editor. | ||
MONITORPOWER | Gen | Change the monitor power status (CRT, Windows 9x only). | ||
MOPAC | Ogl | Start a Mopac background calculation. | ||
MSGERRMODE | Std | Set the mode used to show an error message. | ||
MULTISELDLG | Gen | Show the multiselection dialog box. | ||
NEW | Std | Clean all objects. | ||
OPEN | Std | Open molecules/surface/ trajectory files. | ||
OPENDLG | Gen | Show the requester to open a file. | ||
PLANEANG | Ogl | Angle between two planes. | ||
PLUGINABOUT | Ogl | Show the plugin about information. | ||
PLUGINCALL | Ogl | Call a plugin user function. | ||
PLUGINCONFIG | Ogl | Open the plugin configuration dialog. | ||
PLUGINGET | Ogl | Get the value of a specific internal variable. | ||
PLUGINHELP | Ogl | Show the plugin help. | ||
REFRESH | Ogl | Force the main window refresh. | ||
REMATOMS | Std | Remove one or more atoms using the pattern matching. | ||
ROTATE | Ogl | Rotate the active object. | ||
SAVE | Std | Save the molecule. | ||
SAVEDLG | Gen | Show the requester to save a file. | ||
SAVEIMG | Ogl | Save the current view as bitmap. | ||
SELECT | Ogl | Show the atoms using the pattern matching. | ||
SELRANGE | Ogl | Show an atom or a residue range. | ||
SMARTMOVE | Ogl | Enable/disable the SmartMove operation. | ||
SMARTMOVEATM | Ogl | Change the atom threshold to auto enable the SmartMove. | ||
SONGPLAY | Fmod | Play a music file. | ||
SONGSTOP | Fmod | Stop the music. | ||
SONGVOL | Fmod | Set the music volume. | ||
SRFCALC | Std | Calculate and show the molecular surface. | ||
SRFCOLOR | Ogl | Change the surface color. | ||
SRFCOLORBY | Ogl | Color the surface by a specific method. | ||
SRFSAVE | Std | Save the molecular surface. | ||
STRINGBOX | Gen | Open the string dialog box. | ||
TEXT | Gen | Show a message in the console. | ||
TORSION | Ogl | Measure a torsion angle. | ||
TRANSLATE | Ogl | Translate the active object. | ||
TRJANIMPLAY | Ogl | Start the trajectory animation playback. | ||
TRJANIMSET | Ogl | Set the trajectory animation range. | ||
TRJANIMSPEED | Ogl | Set the trajectory animation speed. | ||
TRJANIMSTOP | Ogl | Stop the animation playback. | ||
TRJGRAPHENE | Ogl | Show the energy data in the Graph Editor. | ||
TRJOPEN | Std | Open a trajectory file to analyze it. | ||
TRJSEL | Std | Select the trajectory frame by number. | ||
TRJSELFIRST | Std | Select the first frame of the trajectory. | ||
TRJSELLAST | Std | Select the last frame of the trajectory. | ||
UNSELECT | Ogl | Hide the atoms using the pattern matching. | ||
UNSELRANGE | Ogl | Hide an atom range or a residue range. | ||
VDWPROP | Ogl | Change the VDW visualization properties. | ||
WIREPROP | Ogl | Change the wire frame visualization properties. | ||
WKSCHANGE | Ogl | Change the current workspace | ||
WKSLOCK | Ogl | Lock the current workspace | ||
WKSNEW | Ogl | Create a new workspace and select it | ||
WKSNEXT | Ogl | Go to the next workspace | ||
WKSPREV | Ogl | Go to the previous workspace | ||
WKSREM | Ogl | Remove a workspace | ||
WKSREMALL | Ogl | Remove all workspaces | ||
WKSREMCUR | Ogl | Remove the current workspace | ||
WKSSETNAME | Ogl | Set the workspace name | ||
WKSUNLOCK | Ogl | Un lock the current workspace | ||
ZCLIP | Ogl | Set the Z clipping. | ||
ZOOM | Ogl | Set the zoom factor. |
Dbase | = Database commands. | |
Fmod | = FMod commands. | |
Gen | = General purpose commands. | |
Ogl | = OpenGL commands. | |
Std | = Standard commands. |