Extended commands

VEGA can interpret commands with extended syntax  that can be send trough the standard windows class port (OpenGL) and/or trough the TCP/IP.  The syntax of each command is:

COMMAND_NAME   ARG1    ARG2 ...

The command name can be in upper case or lower case and the number of arguments is tipical 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").
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.
MCHAR Multiple selection string. The MCHAR argument must be a specific keyword (string).

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).

 

Standard commands

CHARGE   (CHAR)Mode
It assigns the partial atomic charges using the specified Mode. At the present time, the only supported mode is Gasteiger. For more inforamtion, click here.
e.g.    CHARGE    Gasteiger

FORCEFIELD   (CHAR)Template    (BOOL)Quiet
It assigns the atom types using the specified Template. If Quiet is true, no warning messages are showed if a problem was found during the force field attribution. For more inforamtion, click here.
e.g.    FORCEFIELD    CVFF   1

GET   (CHAR)Variable
The command GET returns the value of a specific internal variable. The argument name is case-insensitive and the returned value is always a character string. The result can be read from clipboard or from Result item of VGP_VEGAINFO structure if the command is sent by a plugin (see plugin.h). SendVegaCmd retrives the result automatically from the clipboard.

Standard variables:

Variable Type Description
CURLANG CHAR Current language for string translation.
DATADIR CHAR Directory path of data files (e.g. templates, preferences, etc).
ERRCODE UINT Last error code.
ERRSTR CHAR Last error string.
PRFLANG CHAR Language for string translation in prefs file.
TOTATM UINT The total number of atoms of the current loaded molecule.
TRJBESTENERGY FLOAT The energy of the best frame in the trajectory file.
TRJBESTFRM UINT The number of the best frame.
TRJCURFRM UINT The current frame number selected in the trajectory.
TRJSIMTIME UINT Lenght (in ps) of the simulation.
TRJSTARTTIME UINT Start time (ps) of the simulation.
TRJTEMP UINT Simulation temperature (Kelvin).
TRJTIMESTEP UINT Time step.
TRJTOTFRM UINT Total number of frames in the trajectory.
TRJWORSEENERGY FLOAT The energy of the worse frame in the trajectory file.
TRJWORSEFRM UINT The number of the worse frame.
VEGADIR CHAR Directory path where VEGA is installed.
VERSION CHAR Full VEGA version.

OpenGL variables:

Variable Type Description
PORTNUM UINT Communication port number.
ROTX FLOAT X rotation of the scene (degree).
ROTY FLOAT Y rotation of the scene (degree).
ROTZ FLOAT Z rotation of the scene (degree).
SCALE FLOAT Visualization scale.
TRANSX FLOAT X translation of the scene.
TRANSY FLOAT Y translation of the scene.
TRANSZ FLOAT Z translation of the scene.
WINSIZEX UINT Width of the main window.
WINSIZEY UINT Height of the main window.
WINPOSX UINT X screen position of the main window.
WINPOSY UINT Y screen position of the main window.


MSGERRMODE
   (MCHAR)Mode
This command sets the Mode that VEGA uses to show an error message. The keywords allowed, are:

Console shows the errors in the console window (default for command line operation mode).
Quiet no errors are showed.
Window all errors are showed in a standard request window (default for OpenGL operation mode).

e.g.    MSGERRMODE     Console

NEW
It cleans all objects, removing molecules, surfaces, selections, etc from the memory, without to ask a confirm. Use mNew if you want that this operation must be confirmed.
e.g.    NEW

OPENMOL   (CHAR)File_Name
It opens a molecule and a trajectory file.
e.g.    OPENMOL     "C:\Documents\Molecules\MyMolecule.pdb"

SAVEMOL   (CHAR)File_Name   (CHAR)Format  (CHAR)Compression  (BOOL)Connectivity
This command allows to save the current molecule in the file File_Name, using a specific Format (see -f command line option), Compression (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS) and Connectivity (0 no connectivity, 1 connectivity).
e.g.    SAVEMOL    MyMolecule.pdb   PDB    BZIP2   1

TRJOPEN   (CHAR)FileName    (BOOL)OpenDialog
It opens a trajectory file (FileName) and the analysys dialog box if OpenDialog is 1 (true).
e.g.    TRJOPEN    "Simul.DCD" 1

TRJSEL (UINT)Number
Select the frame by number (0 < Number <= LastFrameNumber). The trajectory must be opened with TRJOPEN command.
e.g.    TRJSEL    25

TRJSELFIRST
Select the first frame of the trajectory. The trajectory must be opened with TRJOPEN command.

TRJSELLAST
Select the last frame of the trajectory. The trajectory must be opened with TRJOPEN command.

 

OpenGL commands

ANTIALIAS   (BOOL)Mode
Enable/disable the anti-aliased visualization setting Mode to 1 or 0.
e.g.    ANTIALIAS    1

COLOR   (CHAR)Color
Change the color of the current selection. The allowed colors are: black, white, red, green, cyan, yellow, firebirck, magenta, pink, violet, ghostgray, gray, darkgray, orange, darkgreen, blue, darkyellow, brown, skyblue, ghostpink, ghostgreen, ghostblue, ghostyellow and sand.
e.g.    COLOR    Blue

CPKPROP   (UINT)ShpereRes   (UINT)SphereScale  (UINT)CylinderRes  (FLOAT)CylinderRad
Change the CPK visualization properties: the sphere resolution (8 <= SphereRes <= 24), the sphere scale (10 <= SphereScale <= 50), the cylinder resolution (5 <= CylinderRes <= 20) and the cylinder radius (0.05 <= CylinderRad <= 0.5).
e.g. CPKPROP    12   20   10   0.10 (default settings)

DEPTHCUE   (BOOL)Mode
If Mode is 1, the depthcue is enabled, otherwise if it's 0, the depthcue is disabled.
e.g.    DEPTHCUE    1

LIQPROP   (UINT)SphereRes   (UINT)CylinderRes  (FLOAT)CylinderRad
Change the liquorice visualization properties: the sphere resolution (8 <= SphereRes <= 24), the cylinder resolution (5 <= CylinderRes <= 20) and the cylinder radius (0.05 <= CylinderRad <= 0.5).
e.g. LIQPROP    12   10   0.20 (default settings)

PLUGINABOUT   (CHAR)Plugin_Name
It shows the about information of the specified plugin.
e.g.    PLUGINABOUT    PowerNet

PLUGINCONFIG   (CHAR)Plugin_Name
This command opens the confuration dialog of the plugin.
e.g.    PLUGINCONFIG    PowerNet

PLUGINHELP   (CHAR)Plugin_Name
Show the plugin help.
e.g.    PLUGINHELP    PowerNet

PLUGINCALL  (CHAR)Plugin_Name    (UINT)Function_number
Call a plugin user function by function number (from 1 to 100).

REFRESH
Force the refresh of the main window.
e.g.    RERESH

ROTATE   (FLOAT)X    (FLOAT)Y   (FLOAT)Z
Rotate the object around X, Y and Z axis.
e.g.    ROTATE   90   45.5   0

SELECT   (CHAR)Selection
With this command it's possible to show/hide (see UNSELECT command) the atoms. The Selection uses the following format:

ATOM_NAME:RESIDUE_NAME:RESIDUE_NUMBER:CHAIN_ID

Each argument of the selection is optional and the max lenght of each field is four characters for the ATOM_NAME, RESIDUE_NAME, RESIDUE_NUMBER and one character for the CHAIN_ID. The selection is case-sensitive and you can use wildcards (?, *). The SELECT command can be used also to select by atom number.
e.g.

SELECT    H*    -> Select all hydrogens
SELECT    C*:ALA    -> Select all carbons of all alanines
SELECT    CA:*:*:B    -> Select all alpha carbon of the chain B
SELECT    *:VAL:?    -> Select all valines in the first 9 residues
SELECT    10    -> Select the atom number 10

SELECTRANGE   (MCHAR)Mode    (UINT)Start   (UINT)End
It allows to show/hide (see UNSELECTRANGE) an atom or residue range specifing the starting and the ending atom/residue number.
e.g.

SELECTRANGE    ATOM   45   101    -> Show atoms from 45 to 101
SELECTRANGE    RESIDUE   70   75    -> Show residue from 70 to 75

TRANSLATE   (FLOAT)X    (FLOAT)Y   (FLOAT)Z
Translate the object along X, Y and Z axis.
e.g.    TRANSLATE   90   45.5   0

TRJANIMPLAY
Start the animation playback.
e.g.    TRJANIMPLAY

TRJANIMSET   (UINT)Start    (UINT)End   (BOOL)Loop
Set the animation range selecting the starting (Start) and the ending (End) frames. If Loop is 1, the animation is played endlessly, otherwise if it's 0, the animation is played only once.
e.g.    TRJANIMSET   12   40   1

TRJANIMSPEED   (UINT)Speed    (UINT)Skip
Set the trajectory animation speed (0 <= Speed <= 500) and the number of frames to skip for each animation step (Skip >= 0).
e.g.    TRJANIMSPEED   200   0

TRJANIMSTOP
Stop the animation playback.
e.g.    TRJANIMSTOP

UNSELECT   (CHAR)Selection
See SELECT command.

UNSELECTRANGE   (MCHAR)Mode    (UINT)Start   (UINT)End
See SELECTRANGE command.

VDWPROP   (UINT)SphereRes    (UINT)DotSize
Change the VDW visualization properties: the sphere resolution (8 <= SphereRes <= 24) and the size of the dots (1 <= DotSize <= 4).
e.g.    VDWPROP   20   2

WIREPROP   (UINT)Tickness    (BOOL)SmoothMode
Change the wireframe visualization properties: the line tickness (1 <=  Tickness <= 5) and the line color smoothing (1 = enabled, 0 = disabled).

ZCLIP   (UINT)Value
This command set the Z clipping value (1 <= Value <= 300).

ZOOM   (UINT)Factor
Set the zoom factor (Factor > 0).

 

FMod commands

These commands are the interface to the fmod library (Music and Sound effect system).

SONGPLAY   (CHAR)FileName
It starts the playing of a music file (FileName) in MPEG layer 2/3, Wav (using ACM codecs), WMA, ASF and RAW.
e.g.    SONGPLAY    "MyMusic.mp3"

SONGSTOP
Stop the playing.
e.g.    SONGSTOP

SONGVOL   (UINT)Volume
Set the volume from 0 to 255.
e.g.    SONGVOL    128