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:
Small database mode (SDB).
The small databases are updated in real time. If a molecule, is renamed,
removed or updated, the database is automatically rebuilt with the changes.
This operation requires a lot of time and so is applicable to small database
only.
Large database mode (LDB).
When you open a large database (its size is greater than 20 Mb), VEGA ZZ
scans it in order to build an index that accelerates the database access.
The obtained information is stored in a special IFF file called SDI (.sdi
extension). If you reopen the database, no rescan is required because VEGA
ZZ read the SDI file dramatically reducing the waiting time. When you
rename, remove or update a molecule, the database remains unchanged and the
modification are stored in the SDI file. In this way, the user obtains a
fast feedback without wait. If the database must be used with another
software, it must be synchronized with the SDI file and to do it, the user
must select Synchronize clicking with the right mouse button on the
database name.
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:
The database list is shared with the Add Fragment dialog. The fragment libraries are databases in zip format and so they appears in the database explorer. You can do all operations but not close theirs.
The database engine stores the file offsets in 64 bit integers breaking the limit of 2 Gb file size.
The maximum number of molecules for each database is 2^32 (4.294.967.296).
The maximum number of databases is 2^32 (4.294.967.296).
The maximum number of manageable molecules is 2^64 (18.446.744.073.709.551.616).
At this time, the SDF databases only are treated as SDB and LDB. The other database formats are SDB always.