11.2 Standard commands
These are the VEGA standard commands:
ADDHYDROG (MCHAR)MolType (MCHAR)HPos
(BOOL)IupacNames (BOOL)ActiveOnly
Add the hydrogens to the molecule. If the hydrogens are already present,
they will be removed before the adding procedure.
Parameters: | ||
MolType |
Molecule type. It must be GEN (generic organic), NA (nucleic acid) and PROT (protein). |
|
HPos |
Hydrogen position in the file. It must be HEAVYATM (the hydrogens are placed after each heavy atom) or RESEND (the hydrogens are placed at the end of each residue). |
|
IupacNames |
If it's true (1), IUPAC hydrogens name convention is used. |
|
ActiveOnly |
If it's true (1), the hydrogens are added to active (visible) atom only. |
Return values:
The number of added hydrogens.
Example:
ADDHYDROG GEN RESEND 1 0
See also:
AddIons.
ADDIONS (CHAR)Element (INT)Charge
(UINT)Ions (FLOAT)ExclAtomRad (FLOAT)ExclIonRad
(FLOAT)GridStep (FLOAT)BoxThick
With this command is possible to add one or more counter ions to the active
molecule. For more information about the method, please click
here.
Parameters: | ||
Element | Counter ion element (e.g. Na, K, Mg, Cl, etc). | |
Charge | Ion charge (e.g. 1, 2, -1, etc). | |
Ions | Number of ions to add. | |
ExclAtomRad | Atom-ion closest distance. | |
ExclIonRad | Ion/ion closest distance in order to reduce the electrostatic repulsion. | |
GridStep | Grid step to build the grid used to place the ions. | |
BoxThick | Box thickness surrounding the molecule. |
Return values:
Error code if it fails.
Example:
ADDIONS Na 1 5 6.5
11 0.5 10
See also:
AddHydrog.
CHDIR (CHAR)Directory
Change the current directory. Use CURDIR variable to get it.
Parameters: | ||
Directory | New directory path. |
Return values:
Error code if it fails.
Example:
CHDIR "C:\My Documents\Molecules"
See also:
None.
CHARGE (CHAR)Method (BOOL)ActiveOnly
Assign the atomic partial charges using the specified method. For more information, click here.
Parameters: | ||
Method |
Method to assign the atomic partial charges. At the present time, the only supported method is Gasteiger. |
|
ActiveOnly |
If it's true (1), the force field is assigned only to the active (visible) atoms. If it's false (0), the force field is assigned to all atoms (visible an invisible). |
Return values:
Error code if it fails.
Example:
CHARGE Gasteiger 0
See also:
FORCEFIELD, mCalcCharge.
CPUFINDFILE (CHAR)FileName
Check if the specified executable or DLL file exists and return a new file name
if an executable with better performances is present.
Parameters: | ||
FileName |
Method to assign the atomic partial charges. At the present time, the only supported method is Gasteiger. |
Return values:
An empty string if the file doesn't exist or the executable file name optimized
for the installed CPU.
Example:
CPUFINDFILE BioDock.exe
If your system has got an AMD Athlon and the specific executable is installed,
the command returns BioDock_k7.exe.
See also:
None.
ERRMSG (UINT)ErrorCode
Return the error description (standard C format) from the error code.
Parameters: | ||
ErrorCode | .Error code. |
Return values:
Error string.
Example:
ERRMSG 201
See also:
MSGERRMODE.
FORCEFIELD (CHAR)Template (BOOL)ActiveOnly
(BOOL)Quiet
Assign the atom types using the specified template. For more information, click here.
Parameters: | ||
Template |
Template name used to assign the atom types. |
|
ActiveOnly |
If it's true (1), the force field is assigned only to the active (visible) atoms. If it's false (0), the force field is assigned to all atoms (visible an invisible). |
|
Quiet |
If it's true, no warning messages are showed if a problem was found during the force field attribution. |
Return values:
Error code if it fails.
Example:
FORCEFIELD CVFF 0 1
See also:
CHARGE, mCalcCharge.
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
retrieves the result automatically from the clipboard.
If you call the GET command from a plugin, please use PLUGINGET instead of it.
Standard variables:
Variable | Type | Description |
CPUFEATURES | INT | 32 bit integer containing the CPU features (only for x86 CPUs). |
CPUNAME | CHAR | Installed CPU name. |
CPUS | UINT | Number of the installed CPUs. |
CPUTYPE | CHAR | Type, family, model and stepping of the installed CPU (only for x86 CPUs). |
CPUVENDOR | CHAR | CPU vendor. |
CURDIR | CHAR | Current directory. |
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. |
OS | CHAR | Operating system (e.g. AmigaOS, Linux, Irix, Unix, Windows 95/98/ME, Windows NT/2000/XP). |
OSFAMILY | CHAR | Operating system family (e.g. amigaos, unix, windows). |
PRFLANG | CHAR | Language for string translation in prefs file. |
TMPDIR | CHAR | Temporary directory. |
TMPFILE | CHAR | Full path and file name to use as temporary file. |
TOTACTATM | UINT | Total number of active (visible) atoms. |
TOTATM | UINT | Total number of atoms of the current loaded molecule. |
TOTMOL | UINT | Total number of molecules loaded un memory. |
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 | Length (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 |
CONBUFSIZE | UINT | Console buffer size (lines). |
CONHISTSIZE | UINT | Max. number of commands stored in the history buffer. |
CONPOSX | UINT | X screen position of the console window. |
CONPOSY | UINT | Y screen position of the console window. |
CONSIZEX | UINT | Width of the console window. |
CONSIZEY | UINT | Height of the console window. |
CONVISIBLE | BOOL | True if the console is open. |
GLASSWIN | BOOL | True if the glass windows are enabled. |
GLRENDERER | CHAR | OpenGL rendering subsystem (hardware/software). |
GLVENDOR | CHAR | The vendor of the graphic card. |
GLVERSION | CHAR | OpenGL subsystem version. |
GRAPHID | UINT | The ID of the current Graph Editor window |
GRAPHLABELX | CHAR | X axis label. |
GRAPHLABELY | CHAR | Y axis label. |
GRAPHPOINTS | UINT | Number of the points in the current graph. |
GRAPHPOSX | UINT | X screen position of the Graph Editor window. |
GRAPHPOSY | UINT | Y screen position of the Graph Editor window. |
GRAPHSIZEX | UINT | Width of the Graph Editor window. |
GRAPHSIZEY | UINT | Height of the Graph Editor window. |
GRAPHTITLE | CHAR | Chart title. |
GRAPHVISIBLE | BOOL | True if the Graph Editor is open (obsolete, only for backwards compatibility. |
ISRUNNING | BOOL | True if a background calculation is running (e.g. Mopac). |
MAINSIZEX | UINT | Width of the main window. |
MAINSIZEY | UINT | Height of the main window. |
MAINPOSX | UINT | X screen position of the main window. |
MAINPOSY | UINT | Y screen position of the main window. |
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. |
SCREENDEPTH | UINT | Screen depth in bit per pixel. |
SCREENX | UINT | Screen width. |
SCREENY | UINT | Screen height. |
TRANSX | FLOAT | X translation of the scene. |
TRANSY | FLOAT | Y translation of the scene. |
TRANSZ | FLOAT | Z translation of the scene. |
WKSCURNUM | UINT |
Progressive number of the current workspace. 0 is the main workspace and it's always present. |
WKSCURNAME | CHAR | Name of the current workspace. |
WKSTOT | UINT | Number of the workspaces. It's at least greater or equal to 1. |
Return values:
The value of the specified variable.
Example:
GET TOTATM
See also:
PLUGINGET.
MERGE (CHAR)FileName (INT)Flags
(BOOL)ActiveOnly (BOOL)Force
Merge the loaded molecule with one or more parts of another molecule. For more
information click here.
Parameters: | ||||||||||||||||||||||||||||
FileName |
File name of the object to load (molecule, surface, trajectory). |
|||||||||||||||||||||||||||
Flags |
This argument allows to specify the molecule fields/elements that are merged with the atoms already in memory. The following values can be combined through the "or" operator (or addition): |
|||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||
ActiveOnly |
If it's true (1), it merges the molecule with the active (visible) atoms only, otherwise (false, 0) it merges the molecule with all atoms in memory. |
|||||||||||||||||||||||||||
Force |
If it's true (1) and the molecules are different (but with the same number of atoms), the merging is forced. |
Return values:
Error code if it fails.
Example:
MERGE "C:\Documents\Molecules\MyMolecule.pdb"
10 0
See also:
NEW, SAVE, mMerge, mNew, mOpen, mSave.
MSGERRMODE (MCHAR)Mode
This command sets the mode used by VEGA to show the error messages.
Parameters: | ||||
Mode | Error message mode. It can be: | |||
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). |
Return values:
Error code if it fails.
Example:
MSGERRMODE Console
See also:
ERRMSG.
NEW
It cleans all objects, removing molecules, surfaces, selections, etc from the memory,
without confirm. Use mNew if you want that this operation must be confirmed.
Parameters:
None.
Return values:
Error code if it fails.
Example:
NEW
See also:
OPEN, MERGE, SAVE,
mNew, mOpen, mSave.
OPEN (CHAR)FileName
Open a molecule or a surface or a trajectory file.
Parameters: | ||
FileName | File name of the object to load (molecule, surface, trajectory). |
Return values:
Error code if it fails.
Example:
OPEN "C:\Documents\Molecules\MyMolecule.pdb"
See also:
MERGE, NEW, SAVE,
mMerge, mNew, mOpen, mSave.
REMATOMS (CHAR)Selection
Remove one or more atoms using the pattern matching.
Parameters: | ||
Selection | It's the atom selection in standard VEGA format. For more information, see the SELECT command. Please remember that if you want remove a single atom, you can put the atom number only instead of the standard string selection. |
Return values:
The number of the removed atoms.
Example:
REMATOMS *:HOH
See also:
SELECT, mRemoveHydrog,
mRemoveInvisAtm, mRemoveWater.
SAVE (CHAR)FileName (CHAR)Format
(CHAR)Compression (BOOL)Flags
This command saves the current molecule or assembly.
Parameters: | ||||||||
FileName | File name of the output molecule (the file extension is added automatically if not present). | |||||||
Format | File format (see -f command line option). | |||||||
Compression | Compression mode (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS). | |||||||
Flags | Special flags that can be combined through the OR logical operator (or addition): | |||||||
|
Return values:
Error code if it fails.
Example:
SAVE MyMolecule.pdb PDB
BZIP2 1
See also:
MERGE, NEW, OPEN,
mMerge, mNew, mOpen, mSave.
SRFCALC (MCHAR)SurfaceType (UFLOAT)ProbeRadius
(UINT)Density (BOOL)SelectedOnly
Calculate and show (in OpenGL mode) the molecular surface. The MEP and ILM
calculations ignore the ProbeRadius and the MLP ignores both ProbeRadius
and Density.
Parameters: | ||
SurfaceType | Surface type (ILM, MEP, MLP, PSA and VDW). | |
ProbeRadius | Probe radius in Å. | |
Density | Dot density in Ų. | |
SelectedOnly | true (1), to consider the visible atoms only, false (0) to calculate the surface for all atoms. |
Return values:
The command returns the total surface area in Ų, the surface diameter in
Å,
the minum value and the maximum value of the calculated property. If the SurfaceType
is ILM, it returns the Virtual LogP value also, if the SurfaceType is PSA and it
returns the positive and the negative surface areas in Ų.
If it fails, the error code is returned.
Example:
SRFCALC PSA 1.4 20
See also:
OPEN, SRFCOLOR, SRFCOLORBY,
SRFSAVE, mOpen, mSrfCalc, mSrfColor, mSrfSave, mSrfRemove.
SRFSAVE (CHAR)FileName (MCHAR)Format
(CHAR)Compression
This command saves the surface.
Parameters: | ||
FileName | Output file name (the file extension is added automatically if not present). | |
Format | Surface format (CSV, INSIGHT, QUANTA, Raw, VrmlDotted, VrmlSolid). | |
Compression | Compression mode (NONE, BZIP2, GZIP, POWERPACKER, ZCOMPRESS) |
Return values:
Error code if it fails.
Example:
SRFSAVE "Molecules\MySurface" QUANTA NONE
See also:
OPEN, SRFCALC, SRFCOLOR,
SRFCOLORBY, mOpen, mSrfCalc, mSrfColor, mSrfSave, mSrfRemove.
TRJOPEN (CHAR)FileName (BOOL)OpenDialog
Open a trajectory file to analyze it.
Parameters: | ||
FileName | Trajectory file to analyze. | |
OpenDialog | If 1 (true), the analysis dialog box is opened. |
Return values:
Error code if it fails.
Example:
TRJOPEN "Simul.DCD" 1
See also:
OPEN, TRJSEL, TRJSELFIRST,
TRJSELLAST, TRJSELLAST,
mOpen, mAnalysis.
TRJSEL (UINT)Number
Select the frame by number. The trajectory must be opened with TRJOPEN command.
Parameters: | ||
Number | Frame number .(0 < Number <= LastFrameNumber) |
Return values:
Error code if it fails.
Example:
TRJSEL 25
See also:
OPEN, TRJOPEN, TRJSELFIRST,
TRJSELLAST, TRJSELLAST,
mOpen, mAnalysis.
TRJSELFIRST
Select the first frame of the trajectory. The trajectory must be opened with TRJOPEN
command.
Parameters:
None.
Return values:
Error code if it fails.
Example:
TRJSELFIRST
See also:
OPEN, TRJOPEN, TRJSEL, TRJSELLAST, TRJSELLAST, mOpen, mAnalysis.
TRJSELLAST
Select the last frame of the trajectory. The trajectory must be opened with TRJOPEN
command.
Parameters:
None.
Return values:
Error code if it fails.
Example:
TRJSELFIRST
See also:
OPEN, TRJOPEN, TRJSEL, TRJSELFIRST, mOpen, mAnalysis.