14.1 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 shown 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).

 

14.1.1 Command index

Command     Type     Description
ADDHYDROG Std Add hydrogens.
ADDIONS Std Add ions.
AMMPSEND   Ogl   Send a command string to AMMP.
AMMPSENDMOL   Ogl   Send the molecule in the current workspace to AMMP.
AMMPSTARTCALC   Ogl   Notify to VEGA that a new AMMP calculation being to start.
ANGLE Ogl Measure the bond angle between three atoms.
ANTIALIAS Ogl Enable/disable the anti-aliased visualization.
ASSIGNBNDORD Std Assign the bond order. 
ATMADD Std Add a new atom.
ATMBEGINUPDATE Std Notify to the system a massive atom update.
ATMBOND   Std   Bond/unbond two atoms or change the bond order.
ATMDELETE   Std   Delete one or more atoms.
ATMENDUPDATE Std Notify to the system that the update is finish.
ATMFIND   Std   Find an atom by element, atom name and atom type.
ATMGET Std Get an atom property.
ATMSET Std Set an atom property.
BACKCOLOR Ogl Change the background color.
BALLSTICKPROP Ogl Change the ball & stick visualization properties.
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.
CONNBUILD Std Build the atom connectivity.
CONNDESTROY Std Destroy the atom connectivity.
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.

CURSOR Ogl Change the mouse cursor.
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.
DBPUT   Dbase   Put the current molecule in the database.
DEPTHCUE Ogl Enable/disable the depth cueing.
DIRDLG Gen Show the directory dialog box.
DISTANCE Ogl Measure the distance between two atoms.
ENEPARGET   Gen   Get a parameter used for the MM energy evaluation.
ENEPARSET   Gen   Set a parameter used for the MM energy evaluation.
ERRMSG Std Return the error description.
FORCEFIELD Std Assigns the atom types.
GET Std Get the value of a specific internal variable.
GRAPHACTIVATE Ogl Activate the current graph window giving the input focus to it.
GRAPHADD Ogl Add a point value in the chart.
GRAPHBEGINUPDATE Ogl Notify to the graph window that it will be massively updated.
GRAPHCALC Ogl Calculate a statistical value.
GRAPHCLOSE Ogl Close the Graph Editor window.
GRAPHDELETE Ogl Delete a point.
GRAPHDERIVATIVE Ogl Calculate the derivative of the plot.
GRAPHENDUPDATE Ogl Notify to the graph window that the update is finish.
GRAPHEXCEL Ogl Export the data to Microsoft Excel.
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.
GRAPHMAXIMIZE Ogl Maximize the graph window.
GRAPHMINIMIZE Ogl Minimize the graph window.
GRAPHNEW Ogl Clear all data in the chart.
GRAPHNR Ogl Remove the noise from the plot signal.
GRAPHOPEN Ogl Open the Graph Editor window.
GRAPHPRINT Ogl Print the current plot.
GRAPHRESTORE Ogl Restore the position and the size of the graph window.
GRAPHSAVE Ogl Save the graph data into a file.
GRAPHSET Ogl Set the point values.
GRAPHSETCUR Ogl Set the current Graph Editor window.
GRAPHSPECTRUM Ogl Calculate the frequency spectrum using the DFT.
GRAPHTITLE Ogl Set the chart title.
GRAPHTOCLIP Ogl Copy the plot in the clipboard (Enhanced WMF).
GRAPHWIN Ogl Change the position and the size of the Graph Editor window.
LIGHT Ogl Enable/disable the lighting.
LIGHTAMB Ogl Enable/disable the ambient light.
LIGHTAMBCOLOR Ogl Change the ambient light color.
LIGHTCUR Ogl Set the current light source.
LIGHTCURDIFCOL Ogl Change the diffuse color of the current light source.
LIGHTCUREN Ogl Enable/disable the current light source.
LIGHTCURPOS Ogl Set the position of the current light source.
LIGHTCURSPECCOL Ogl Change the specular color of the current light source.
LOGOPOS Ogl Enable/disable the VEGA ZZ logo visualization and set its position.
LOGOSCALE Ogl Set the VEGA ZZ logo scale factor.
MAINWIN Ogl Change the position and the size of the main window.
MATSHINY Ogl Change the material shininess.
MATSPECULAR Ogl Change the material specularity.
MATVECTSPEC Ogl Enable/disable the vector specularity.
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 Ogl Change the monitor power status (CRT).
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.
MUSICPLAY Fmod Play a music file in .mod, .s3m, .xm, .it, .mid, .rmi, .sgt and .fsb format.
MUSICSTOP Fmod Stop the music.
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.
SHUTDOWN Ogl Shutdown the system.
SMARTMOVE Ogl Enable/disable the SmartMove operation.
SMARTMOVEATM Ogl Change the atom threshold to auto enable the SmartMove.
SONGPLAY Fmod Start the streaming of a song file in in MPEG layer 2/3, Wav, WMA, ASF and RAW format.
SONGSTOP Fmod Stop the streaming.
SONGVOL Fmod Set the music volume.
SOUNDEFFECTS   Ogl   Enable/disable the sound effects for event notification.
SRFALPHA Ogl Enable/disable the alpha blending (transparency) of the current surface.
SRFALPHAVAL Ogl Set the alpha blending value (transparency level) to the current surface. 
SRFCALC Std Calculate and show the molecular surface.
SRFCOLOR Ogl Change the surface color.
SRFCOLORBY Ogl Color the surface by a specific method.
SRFCOLORGRAD Ogl Color the surface by property using a gradient.
SRFCUR Std Make current the specified surface.
SRFDOTSIZE Ogl Set the dot size of the current surface.
SRFGRAD Ogl Define a new color gradient that can be used to color a surface by property.
SRFGRADAUTORNG Ogl Enable/disable the automatic range detection of the surface property values.
SRFGRADRANGE Ogl Define a range of property values to perform standardized gradient colorizations.
SRFREMOVE Std Remove the current surface from the current workspace.
SRFREMOVEALL Std Remove all surfaces from the current workspace.
SRFSAVE Std Save the specified surface.
SRFVISIBLE Ogl Make the current surface visible or not.
STICKPROP Ogl Change the stick visualization properties.
STRINGBOX Gen Open the string dialog box.
TEXT Gen Show a message in the console.
TORSION Ogl Measure a torsion angle.
TRACEPROP Ogl Change the trace visualization properties.
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.
TRJCLOSE Std Close a trajectory stream.
TRJCREATE Std Create a new trajectory stream.
TRJGRAPHENE Ogl Show the energy data in the Graph Editor.
TRJOPEN Std Open a trajectory file to analyze it.
TRJSAVE Std Save the current trajectory converting it into the specified file format.
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.
TRJWRITE Std Write a frame into the trajectory stream.
TUBEPROP Ogl Change the tube visualization properties.
UNSELECT Ogl Hide the atoms using the pattern matching.
UNSELRANGE Ogl Hide an atom range or a residue range.
VGLBEGIN   Ogl   Begin a new graphic primitive.
VGLCOLOR   Ogl   Change the current color.
VGLCOLORRGB   Ogl   Change the current color using the RGB scheme.
VGLDISABLE   Ogl  

Disable a function used in the rendering pipeline.

VGLENABLE   Ogl  

Enable a function used in the rendering pipeline.

VGLEND   Ogl   End the VGLBEGIN section.
VGLGROUPBEGIN   Ogl   Begin a group of primitives.
VGLGROUPEND   Ogl   End the group of primitives.
VGLGROUPHIDE   Ogl   Hide a group of objects.
VGLGROUPREMOVE   Ogl   Remove a group of objects.
VGLGROUPSHOW   Ogl   Show a group of objects.
VGLINIT   Ogl   Initialize the rendering pipeline.
VGLLABEL   Ogl   Add a new text label.
VGLLINEWIDTH   Ogl   Change the line width.
VGLLOADIDENTITY   Ogl   Replace the current matrix with the identity matrix.
VGLNORMAL   Ogl   Change the current normal vector used to calculate the lighting effects.
VGLPOINTSIZE   Ogl   Change the point size.
VGLPOPMATRIX   Ogl   Pop the current matrix stack.
VGLPUSHMATRIX   Ogl   Push the current matrix stack.
VGLRADIUS   Ogl   Change the x, y, z radii at the same time.
VGLRADIUS3   Ogl   Change the x, y, z radii.
VGLROTATE   Ogl   Multiply the current matrix by a rotation matrix.
VGLSCALE   Ogl   Multiply the current matrix by a general scaling matrix.
VGLTRANSLATE   Ogl   Multiply the current matrix by a translation matrix.
VGLVERTEX   Ogl   Add a new vertex to the current primitive.
VOLUME Std Calculate the molecular volume.
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.