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 plug-in).  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
ACTIVATE Ogl

Activate the main window giving the input focus on it.

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.

AMMPSETFF Ogl

Set the AMMP force field.

AMMPSTARTCALC Ogl

Notify to VEGA that a new AMMP calculation being to start.

AMMPUPDATEFREQ Ogl

Set the AMMP update frequency for output files.

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.

BUILD3D   Ogl   Convert a structure to 3D.
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 current molecule to the clipboard.

COPYTEXT Ogl

Copy a string to 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.

CTORCLEAR Ogl

Clear all torsions.

CTORFIND Ogl

Find the torsions to perform a calculation (conformational search, trajectory alalysis, etc).

CTORGET Ogl

Get the properties of a torsion angle.

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.

FIXAROM Std

Fix the aromatic rings replacing the conjugated bonds with partial double bonds.

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).

GRAPHTYPE   Ogl   Set the chart type (bar, line, pie and mass).
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.

MENUENABLE   Ogl   Enable/disable the main menu.
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).

MOVIEADD   Ogl   Add a new frame to the movie file.
MOVIECLOSE   Ogl   Close the movie.
MOVIECREATE   Ogl   Create a new movie file (AVI, MPEG1 and MPEG2-VOB).
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.

UPDATELASTFILE Ogl

Enable/disable the update of the last file menu.

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 from the stack.

VGLPUSHMATRIX Ogl

Push the current matrix to the 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.