14.1 Introduction to extended commands

VEGA ZZ can interpret commands with extended syntax that can be sent trough the console window, the  windows class port and the TCP/IP port (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 of each command. The arguments must be separated by one or more spaces. As shown in the following table, the argument types can be:

 

Type Description
BOOL Boolean value (0 = false, 1 = true).
CHAR ANSI 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 format (the decimal separator must be a dot (.) and not a comma (,)).
UFLOAT Unsigned floating point number.
INT Integer number.
UINT Unsigned integer number.

 

In order to interpret much easier the syntax of the commands present in this guide, each argument is highlighted indicating 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 ZZ that a new AMMP calculation being to start.
AMMPUPDATEFREQ Ogl Set the AMMP update frequency for output files.
ANGLE Ogl Measure the bond angle.
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 Bind/unbind 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.
ATMINVCHIRALITY   Std   Invert the chirality center.
ATMSET Std Set an atom property.
BACKCOLOR Ogl Change the background color.
BALLSTICKPROP Ogl Change the ball & stick visualization properties.
BEGINCALC   Ogl   Notify to VEGA ZZ that an asynchronous calculation being to start.
BIODOCK Ogl Start a BioDock background calculation.
BUILD3D   Ogl   Convert a structure to 3D.
BUILDDNA   Std   Build a nucleic acid from its nucleotide sequence.
BUILDPEPT   Std   Build a peptide from its amino acid sequence.
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.
CONREC   Ogl   Record the console output as log file.
CONRECPAUSE   Ogl   Pause the log recording.
CONRECRESUME   Ogl   Resume the log recording after pause.
CONRECSTOP   Ogl   Stop the log recording.
CONSAVE Ogl Save the console output to text file.
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 analysis, 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).
DBGETMOLNAME   Dbase   Get the molecule name by database handle and molecule ID.
DBGETROWID   Dbase   Extract a molecule from the database specifying its primary key (row ID).
DBINFO Dbase Obtain the value of a database variable.
DBLOCK   Dbase   Lock/unlock an existing database.
DBOPEN Dbase Open an existing database.
DBPUT Dbase Put the current molecule to the database.
DBREOPEN   Dbase   Open a database already open and return the handle.
DBSETMOLNAME   Dbase   Set the molecule name by database handle and molecule ID.
DBSORTMOLNAMES   Dbase  

Sort alphabetically the molecule names of a database.
DBSQLEXEC   Dbase   Execute SQL commands.
DNSQLTABLEINFO   Dbase   Return the table structure of a SQL database.
DBUPDATE   Dbase   Update the current molecule in the specified database.
DEPTHCUE Ogl Enable/disable the depth cueing.
DIRDLG Gen Show the directory dialog box.
DISTANCE Ogl Measure the distance between two atoms.
ENDCALC   Ogl   Notify to VEGA ZZ that an asynchronous calculation is finished.
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 message.
FINGERPRINT   Std   Calculate the fingerprint of the molecule in the current workspace.
FIXAROM Std Fix the aromatic rings replacing the conjugated bonds with partial double bonds.
FORCEFIELD Std Assigns the atom types.
FPSIMILARITY   Std   Compare two fingerprints and return the similarity index.
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 to 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 to a file.
GRAPHSET Ogl Set the point values.
GRAPHSETCUR Ogl Set the current Graph Editor window.
GRAPHSPECTRUM Ogl Calculate the frequency spectrum using the Discrete Fourier Transformation (DFT).
GRAPHTITLE Ogl Set the chart title.
GRAPHTOCLIP Ogl Copy the plot to 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.
IONIZE   Std   Ionize the molecule according to its acid/base groups and the specified pH.
ISODIST   Std   Calculate the isotopic distribution of a molecule formula.
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.
MOLDELETE   Std   Delete a molecule in the current workspace.
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 by file name or URL.
OPENDATADIR   Ogl   Explore the data directory.
OPENEX   Std   Open molecules/surface/trajectory by file name or URL (extended version),
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 plug-in 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.
REMINVATOMS   Std   Remove the invisible atoms.
REMVISATOMS   Std   Remove the visible atoms.
RESETVIEW   Ogl   Reset the current view, resetting rotations, translations and scale factor.
ROTATE Ogl Rotate the active object.
ROTATEVIEW   Ogl   Rotate the point of view.
SAVE Std Save the molecule.
SAVEDLG Gen Show the requester to save a file.
SAVEMOLDLG   Gen   Show the requester to save a molecule.
SAVEIMG Ogl Save the current view as bitmap or vector graphics.
SAVEIMG2D   Ogl   Save the current molecule as 2D sketch.
SCORE   Std   Evaluate the interaction energy of a complex.
SECSTRUCT   Std   Change the secondary structure of a peptide.
SELECT Ogl Show atoms using the pattern matching.
SELPROX   Ogl   Show atoms or residues included in a sphere around specified atoms.
SELRANGE Ogl Show an atom or a residue range.
SELSMARTS   Pgl   Show atoms according to the SMARTS string.
SETLASTFILENAME   Ogl   Set the pre-defined name used to open a file.
SEGDELETE   Std   Delete a segment of a molecule in the current workspace.
SHUTDOWN Ogl Shutdown the system.
SMARTMOVE Ogl Enable/disable the SmartMove operation.
SMARTMOVEATM Ogl Change the atom threshold to auto enable the SmartMove.
SMARTSCOUNT   Std   Count the number of recurrences in the current molecule for a given SMARTS query.
SMILES   Std   Convert a SMILES string to a 3D structure.
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.
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.
SRFRENAME   Std   Rename the current surface.
SRFSAVE Std Save the specified surface.
SRFSETCUR   Std   Make current 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.
TRJCLUSTCOORD   Std   Perform the cluster analysis of the conformers included into the current trajectory by their atom coordinates.
TRJCLUSTTOR   Std   Perform the cluster analysis of the conformers included into the current trajectory by their values of the torsion angles.
TRJCLUSTTORRMSD   Std   Perform the cluster analysis of the conformers included into the current trajectory by RMSD differences of their torsion angles.
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.
TURBO   Ogl   Enable/disable the turbo mode.
TURBOEX   Ogl   Enable the turbo mode changing the default message.
UNDOENABLE   Ogl   Enable/disable the undo buffer.
UNDOPOP   Ogl   Pop from the undo buffer.
UNDOPUSH   Ogl   Push the current molecule into the undo buffer.
UNSELECT Ogl Hide the atoms using the pattern matching.
UNSELPROX   Ogl   Hide atoms or residues included in a sphere around specified atoms.
UNSELRANGE Ogl Hide an atom range or a residue range.
UNSELSMARTS   Ogl   Hide atoms according to the SMARTS string.
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.
WKSCPYATM   Ogl   Copy the atoms from a workspace to another one.
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 = Generic commands.
Ogl = OpenGL commands.
Std = Standard commands.