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).

 

11.1.1 Command index

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.