View Database Workbench Databases Menu

Databases Menu

select a command

Commit 1D Changes To Database

Append/Replace Database Compounds...

Create Database...

The Databases menu contains commands for updating 1D property data and adding and replacing 2D and 3D topologies in a database. The menu also lets you set up a background process for building a database.

Commit 1D Changes To Database...

The Commit 1D Changes To Database command permits you to update 1D values in a database that you created (i.e., to which you have write access). First you must make your changes in a spreadsheet derived from a database you own by searching/browsing in the View Database workbench or by sampling a compound from the StockroomDB to the Generate Hypothesis workspace. Then you must save the changed spreadsheet with the Save Report To Lab As Spreadsheet... command and follow the steps outlined in "Updating a Property's 1D Values in Your Database" to use the Commit 1D Changes To Database command.

Note: In The Generate Hypothesis workbench, the Commit 1D Changes To Database command appears on the Data menu.

Append/Replace Database Compounds...

The Append/Replace Database Compounds... command lets you use a Catalyst spreadsheet to update a database by adding new compounds to it or by replacing compounds in it with revised ones. To use this command you must have created the database; that is, you must have write access to it. The command also allows you to update a compound's 2D and 3D structures without altering its 1D property data already in a database. The Append/Replace Database Compounds... command has the following requirements:

To append a compound and its associated 1D, 2D, and 3D data to a target database, the compound's name must not match the name of any compound already in the database.
To replace a compound's 2D and/or 3D structures in a target database while preserving its associated 1D data in the target database, the replacement compound's name must be of the form UPD-compoundname in which you substitute the name of the compound to be replaced for compoundname.
To replace a compound completely in a target database, the replacement compound's name must exactly match the name of the compound to be updated. Catalyst overwrites all data (1D, 2D, 3D) associated with the compound name in the database with that of the replacement compound. Note that the replacement compound will have the union of the 1D properties defined in your StockroomDB property dictionary file (.../catdata/StockroomDB.bpd) and the target database.
Compounds being added to a target database or replacing those in the target database must be in a saved spreadsheet in the report area of the View Database workbench when you execute the Append/Replace Database Compounds... command.
The target database must be installed in your current Catalyst session and selected on the shelf of the View Database workbench when you execute the Append/Replace Database Compounds... command.
The Append/Replace Database Compounds... command is intended for adding or replacing 2D and 3D topologies in a target database. If you want to update 1D property data in a database, follow the procedures outlined in "To Update 1D Values in a Database". Follow these steps to append or replace compounds in a database you own:

If necessary, use the Install Database... command in the Stockroom Databases menu to bring the database into your current Catalyst session.
Open a View Database workbench and search or browse the target database to retrieve compounds you want to alter. Catalyst displays a local spreadsheet containing them in the report area. For detailed information on searching and browsing, see
· "To Browse a Database or Spreadsheet"
· "To Search a Database"
Click on the row number of a compound you want to edit and from the Data menu select Save to Lab As... to save a copy of the compound. If you want to edit several compounds, extend select their row numbers and then select Save to Lab As... from the Data menu. Catalyst saves copies of the compounds on the shelf.
To change a compound's 2D or 3D structure, drag and drop the compound on the View Compound QuickTool and edit the compound. Alternatively, to create a compound you want to add to the target database, click on the View Compound QuickTool and draw the molecule. For additional information, see "How to Use the View Compound QuickTool".
From the QuickTool menu select Return from QuickTool. Catalyst displays a local icon for the compound on the shelf. By default the local compound is called UPD-compoundname with the name of the compound substituted for compoundname if you edited a saved compound. If you drew a new molecule, the default name is Local-n where n is an integer.
Click once to deselect and then once to select just the local compound and then select Save to Lab As... from the Data menu to display the Save To Lab As dialog box.
If you want to replace an existing compound's 2D and/or 3D structures in the target database with the ones you have just edited and you want to preserve the compound's associated 1D property data in the target database, select the Save button. Catalyst saves the compound with a name of the form UPD-compoundname. The UPD- characters preceding the compound's name are important: they signal the Append/Replace Database Compounds... command to preserve the existing 1D data.
If you want to replace a corresponding compound in the target database with edited structures and overwrite its existing 1D data with default 1D property data (compound name and molecular weight), click in the Name text box and use the Backspace key to remove the UPD- characters preceding the compound's name and then select the Save button.
If you want to append a new compound you drew in the View Compound QuickTool, save it with a name that does not already exist in the target database.
Repeat steps 4 through 7 until you have finished editing compounds you want to update and new compounds you want to add to the target database.
Now you need to put your new and edited compounds in a spreadsheet to use with the Append/Replace Database Compounds... command.

Select Clear All Report Rows from the Edit menu and then drag and drop compounds from the shelf onto the report area.
From the Data menu select Save Report to Lab as Spreadsheet... and save the local spreadsheet that results from the previous step.
Select the target database, extend select the spreadsheet containing compounds you want to add to add and/or replace, and then select Append/Replace Database Compounds... from the Databases menu. Catalyst displays the Append/Replace Database dialog box.
Catalyst automatically selects the machine on which the target database resides to run the background process that appends and replaces compounds. That is, Catalyst automatically selects Run Locally or Run Remotely on under Job Options and fills in the Remote Host text box if applicable. You cannot alter these selections because the background process must run on the host machine that owns the target database. For detailed information on how to set up the other options for the process, see the description for the Create Database dialog box in "Building a Default Database from Your StockroomDB".
After you have made all your specifications in the Append/Replace Database dialog box, select Append/Replace to submit the background process.
When you schedule the background process for now in the Job Options dialog box invoked by selecting the More Job Options... button, Catalyst displays an Alert message advising you that the target database is closed for use within this Catalyst session until the process has completed. If you or others ignore this message and use the database while the background process is in progress, the process will terminate prematurely. That is, you will see DIED next to its name in the Process Information dialog box if you check on its status with the Process Information... command from the Data menu in the Stockroom. (See "When a Background Process Starts" under "What Happens if There Are Not Enough Tokens?" for additional information.)
Catalyst also issues an Alert message to advise you that the setup for the background process is complete and that the process is scheduled or running according to your instructions. For detailed information about checking on the status of a background process and cleaning up residual temporary data files, see "Process Information".

Create Database...

You can build your own Catalyst database with the default configuration and 2D and 3D indexes from a spreadsheet with the Create Database... command. The command displays the Create Database dialog box that lets you specify such parameters as the database's name, type of conformational model generation, maximum number of conformers, the machine on which to run the background database construction job, and so on. For detailed information on how to use the command, see "Building a Database from a Subset of Another Database".

For background information on Catalyst databases and the various ways of creating and maintaining them, select from the following topics:

· Background information

· Building a default database from a StockroomDB in Catalyst

· Building a custom database from a StockroomDB with catDB

· Building a single-conformer database

· Building a multiconformer database

· Maintaining databases

· The catDB utility program and its command options

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Last updated April 16, 1996 at 02:14pm PDT.