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).
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. |
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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. |
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VGLENABLE | Ogl |
Enable a function used in the rendering pipeline. |
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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. | |