9.2 Database explorer

The Database explorer is a tool useful to manage the molecular databases, allowing some basic operations that can be classified in two main groups: the first one includes the database operations (open, synchronize, close and close all) and the second one includes the molecules management functions (find, get, put, remove, rename and update). These functions are accessible trough buttons and popup menus.
 

9.2.1 Usage

The Database explorer is shown automatically when the database is opened with the Open/create file requester or selecting File -> Database -> Explorer main menu item. Its window is full resizable and the Database and Molecule boxes are resizable inside the window also.

The left box shows the gadgets for the database management: the Database list to select the current database, the Open button to open/create a database, the Close button to close the selected database and the Close all button to close all databases.  The user can also open the database using the drag & drop operation. Clicking with the right mouse button on the database items, a popup menu is shown: it replicates the button functions (Open, Close and Close all) and it include the Synchronize item that allows to synchronize the large databases (LDB, see below).
The right box includes all controls for the molecule data manipulation. To extract a structure from the database you must select one or more molecules in the Molecule list (the multiple selection is permitted), choose the Get mode in order to add/replace the molecule in the current workspace or to place the molecule in a new workspace, and finally click the Get button. Instead of the Get button click, you can double click the molecule name or use the popup menu or hit the return key and it will be extracted automatically. The Next and Previous button are useful for the database scanning, because they allow to get sequentially the structures in the database.
To insert a molecule in the database, you must open its structure in the current workspace and thus click the Put button: a dialog box will shown to specify the name of the molecule. Clicking the Ok button, the molecule will be added into the database using the default parameters (molecule format, compression, connectivity and constraints) defined when the database is created.
A structure in the database can be updated selecting it in the molecule list and clicking the Update button. This structure will be replaced by the molecule in the current workspace.
A molecule in the database can be renamed, selecting it and clicking the Rename button, but remember that the molecules included in a Zip file can't renamed.
In similar way, a molecule can be removed from the database selecting it and clicking the Remove button. The multiple selection is allowed.
The Update button is useful to force the update of the molecule list when the database was changed by another application.
To find molecules inside the active database, you can use the find function (Find button, or Find item in the popup menu). The search is case-insensitive and it allows the wildcards (*, ? characters). Another method to find molecules inside the database is available trough the keyboard: typing a character on the keyboard, the molecule with the name starting with that character is automatically selected.
The status bar placed on the bottom of the window shows the total number of opened databases, the total number of molecules, the number of molecules in the active database and the database type indicator (SDB, LDB, see below).
The Done button closes the Database explorer.

 

9.2.2 Context menu

Clicking with the right mouse button on the Database list or in the Molecule list, the context menu is shown:

Database context menu
Item Accelerator Description
Open Ctrl+O Open a new database.
Close Ctrl+C Close the database.
Close all - Close all databases.
Synchronize Ctrl+S Synchronize the database (see the next section).

 

Molecule context menu
Item Accelerator Description
Get Ctrl+G Get the molecule.
Put Ctrl+P Put the molecule in the database.
Update - Update the molecule.
Rename F2 Rename the molecule.
Find Ctrl+F Find a molecule in the list.
Rescan - Rescan the database to update the molecule list.
Save list - Save the molecule list to a file.
Copy list - Copy the molecule list in the clipboard.

 

9.2.3 Small database and large database

VEGA ZZ can operate with the molecular databases in two modes:

The status bar highlight the operation mode showing the SDB or LDB labels. The LDB label could have a star (*) indicating that the selected database isn't synchronized. If the database is read-only, the Remove, Rename, Put, Synchronize and Update functions are disabled and in the status bar the RO label appears at the left of SDB/LDB word.

 

9.2.3 Notes: