9.1 Open/create a database
Thanks to this file requester it's possible
to open a pre-existing database and/or create a new database that can be managed
with the Database explorer tool in order to put, get, update, rename and delete
the molecules.
To open the dialog you can select the File -> Database -> Open item
of the main menu or click the Open button in the Database
explorer window.
To open a single database, you can proceed
as a normal file requester, but if you want open more than one databases, you
can do a multiple selection.
The New database box is for the creation of a new empty database, specifying
the database format (Directory, SDF file, SQLite, Zip) the default molecule format type
and the compression (None, BZip2, GZip, Z Compress), and if the connectivity and
the constraints will be included in the file format. Putting the database file
name in the File name field and clicking the Create button, the
database will be created. To open the new database you must push the Open
button.
When you click the Open button the dialog will be closed and the Database
explorer window will be shown.
Please remember that the SD database format doesn't allow the selection of the default molecule type and its properties. The other database formats stores the default parameters in the database.dat file. This is an ASCII file that, at this time, contains two tags. The #DBASEINFO tag is placed as first line. This is used by VEGA ZZ to recognize the file and to detect its version. The second tag is #MOLFORMAT. It includes four arguments: molecule format, compression type, connectivity and constraints flags (boolean values).
If you need a molecule database and don't have the time to build it, you can download it from some Web site that allow the access to their libraries for free. The most common are:
You can download manually the whole databases or the subsets, but the VEGA ZZ package includes some scripts to do it in automatic way. These scripts are in the ...\VEGA ZZ\Data\Database\Download directory and can have the .cmd or .sh extension if you are running VEGA ZZ on real Windows PC or on Linux/Wine system. Each script is able to download and build the database in SDF format. The output file is placed in the ...\VEGA ZZ\Data\Databases directory.
WARNING:
There are huge databases (e.g. ZINC - All Purchasable, ZINC -
Everything) which size is about 35-40 Gb. For this reason, check the free
disk space before to run the download scripts. To process correctly these large
databases about 60 Gb are required.