12.11 PowerNet - Network Interface


12.11.1 Introduction

PowerNet is the most powerful VEGA ZZ plug-in  because it's a bridge between VEGA ZZ and the other applications trough the TCP/IP protocol. Moreover, it includes the WarpEngine Technology that allows you to distribute the calculations over the network without special skills.  These applications can run on the local machine:


Local TCP/IP connection


or on a remote machine:


Remote TCP/IP connection


PowerNet adds to VEGA ZZ a TCP/IP port that is usable to send and receive command-line instructions, working in the same way of a POP3 server. An interface application example is the REBOL scripting language that is useful to create simple scripts to automate the most common procedures. PowerNet allows to communicate virtually with all applications that include a minimalist TCP/IP client. PowerNet includes the access control in order to protect your system by hacking attacks from Internet.


12.11.2 Configuration

The configuration interface can be shown by main menu clicking Tools Plugin configuration PowerNet, or using the plug-in manager (Tools Plugin configuration Manage). The configuration parameters are stored in ...\VEGA ZZ\Config\powerner.xml file and the default parameters in ...\VEGA ZZ\Config\powerner.def.


Telnet tab

Default settings:
- Telnet service enabled.
- Port number: 2000.
- No password check. Telnet tab

In this tab, you can enable/disable the TCP/IP service (Enable telnet service), change the port number, enable/disable the password check, specify the user name and the password. Remember that you can't change the port number if the telnet service is enabled, thus you must disable it before to set the new port number. The default TCP/IP port number is 2000 and it can be automatically increased by PowerNet if the port is already in use by other applications or by other VEGA ZZ sessions. In this way you can start more than one VEGA ZZ sessions without conflicts.

Please remember that if the telnet service is disabled, no local or remote connection are possible (e.g. REBOL can't work). HTTP tab

PowerNet includes a Web server that is used to run applets and JavaScripts.
You can enable/disable the HTTP server (Enable HTTP service), change the port number, specify the Browser type for applets and scripts (Built-in = custom browser included in PowerNet, Default = default browser installed in your PC), decide to apply the browser settings to all applets (Apply to all applets), set the client window size and define if the client window is sizeable. The default port number is 4000 and it can be automatically increased by PowerNet if the port is already in use by other applications or by other VEGA ZZ sessions as explained in the above section.

Please remember that if the HTTP service is disabled,  applets and JavaScripts can't run.


It may be possible that the built-in browser is unable to run Java applets. In this case, it's strongly recommended to set the browser type to Default and check Apply to all applets. The included applets were tested to run with Internet Explore 6, 7, 8, 9 and FireFox 3.

The HTTP server is inactive until the first applet/javascript is started.

   Clients tab

Default settings:
- HTTP service enabled
- Port number: 4000.
- Browser type: Built-in.
- Apply to all applets: unchecked.
- Client size: 580x384.
- Sizeable client: checked.




Clients tab

Default settings:
- Remote access disabled.
- No IP filtering. Clients tab

In this tab, you can enable the remote access granting the VEGA ZZ control to other PCs.


It's strongly recommended to activate the password check and to put the user name and the password, when you enable the remote access.

You can permit or deny the access to specific hosts putting their IP in the IP fields and clicking Add button. On the left of each IP added in the list is present a checkbox. If it's checked, the host access is granted, otherwise it's dined. Each entry can be moved in the list using the Up/Down buttons and removed pressing Remove button. In the IP addresses, can be used the wildcards in order to control the access of more than one host. A good idea is to grant the access of all host in your domain (e.g. 192.168.0.XXX), adding the 192.168.0.* entry.
 Log Tab

In order to check the TCP/IP connections and the script execution, it's possible to enable the PowerNet event logging. The log is a text file containing client information, the time of each event, submitted commands, results and errors.
This file can be cleared at each VEGA ZZ run or kept appending the new information (see Clear the file when VEGA starts checkbox). It's possible to type the log file name, using the specific field.

   Log tab

Default settings:
- Logging disabled.
- Clear the file when VEGA starts enabled.
- Log file name points the VEGA installation directory.


PDB tab

Default settings:
- Store directory: %DATADIR%\Pdb.
- Remove PDB files after download. PDB Tab

PowerNet adds to VEGA ZZ the capability to connect to Protein Data Bank (PDB) to download structures (click here for more information). The downloaded files can be removed from the disk immediately after the download or stored in a specific folder (Store directory) in order to build a personalized local database.




Default settings:
Interpreter: %PROGDIR%\Bin\Win32\Rebol.exe.
Script path: %SCRIPTDIR%. REBOL tab

PowerNet adds to VEGA ZZ the capability to manage REBOL scripts trough the graphic interface (see script section). In this tab, you can change the REBOL interpreter and the directory path in which the REBOL scripts are placed. PowerNet includes REBOL/view package that can be used to create  graphic interfaces for your scripts in easy way. For more information about REBOL and REBOL/view, click here.


12.11.3 Testing the configuration

In order to check the TCP/IP configuration, you can use a simple telnet client (e.g. telnet.exe included in Windows), following this procedure:


12.11.4 PDB database interface

Another PowerNet feature is the interface to download the PDB structures directly into VEGA ZZ. To setup  this service, please refer to the configuration section. Picking PDB download item in VEGA ZZ File menu, you can access to the interface window:


PDB download


To download a structure, you must put the PDB entry conde in PDB Id and press Download button. Before to start a new download from PDB, PowerNet checks if the molecule is already present in the local database and ask you to proceed with the new download or to use the local file (see the configuration section to create a local PDB database). The status bar indicates the download progress and if an error occurs. When the download ends, the structure is automatically loaded in VEGA ZZ.


12.11.5 How to run a script

The scripts files must be placed in the scripts directory (or in its subdirectories), as explained in the configuration section. The scripts can be managed selecting Run script from VEGA File menu:


Script manager


This dialog box allows to create, edit, run, rename, delete and move your scripts. The structure of the Scripts directory is shown as a tree that can be explored by the keyboard (cursor arrows, home, end, pg. up, pg. down and enter keys) and mouse:


Exploring the scripts directory


Selecting a script, you can run it clicking Run button or double clicking it. The right mouse button shows the context menu:


Context menu


By the context menu, you can run and Edit the selected script, Rename, Delete and create (New) scripts and folders. You can move scripts and directories from a folder to another one by drag & drop operations. The Update item is useful to refresh the script list.
Clicking on the small > button at the left, you can expand the window, showing the description of the current script:


Expanded view


Showing the context menu on the description box, you can Add, if it's not already present, Edit with WordPad, Delete and Print the description:


Context menu


The description box can be closed clicking < button and the context menu functions are duplicated in the menu bar.


12.11.6 Description file format

The description files are stored in the same directory in which the script is placed. When a script is moved, renamed or deleted, its description file is moved, renamed or deleted also. They are in Rich Text Format (RTF) and have the .rtf file extension. It's strongly recommended to not use Microsoft Word to crate or modify them, because it adds some codes that aren't recognized by PowerNet and it increase the file size.