Combi-Chem

3b. Importing libraries into Cerius2

Importing the benzodiazepine library

If you have just finished the previous section, start a new session by selecting the File/New Session menu item in the Visualizer. Click Confirm in the Re-initialize All message window. You could also start from a brand new Cerius² session.

2.   Open an empty study table

Go to the LIBRARY ANALYSIS card located in the COMBI-CHEM I deck and select Show Study Table.

3.   Select and add default descriptors to the study table

Choose the default set of combinatorial chemistry descriptors by selecting Preferences/Defaults Set/COMBICHEM from the menu bar in the Study Table control panel. Add these descriptors to the empty study table by selecting Descriptors/Add Default on the menu bar in the Study Table control panel.

As the descriptors are added, they automatically become part of the independent (X) group. This is the set of columns that participate in later diversity and similarity studies.

Note

4.   Set the molecule import defaults

Open the Molecule Preferences control panel by selecting the Preferences/Molecules... item from the menu bar in the Study Table control panel. Uncheck Add Hydrogens and Minimize Energy using.

5.   Select the SD file to import

Open the Add Molecules from SD File control panel by selecting Molecules/From SD File... from the menu bar in the Study Table control panel to open the Add Molecules from SD File control panel. Select the file benzo_720.sd that you created in the previous library-building example and click the SELECT pushbutton.

The SD file is read, and the number of structures in the file is posted as 720 near the top of the Add Molecules from SD File control panel.

Alternatively, if you did not complete the earlier part of this tutorial, select the file ./Cerius2-Resources/COMBICHEM/demos/benzo_720.sd and click the SELECT pushbutton.

6.   Set the SD file import preferences

Click the Preferences... pushbutton in the Add Molecules from SD File control panel to open the SD File Preferences control panel. Check the Delete Model After Adding checkbox.

The Delete Model After Adding check box allows you to delete structures after descriptors have been computed, while maintaining a link to the structure from the study table. This provides a semi-file-based system capable of handling large libraries while operating on common study tables.

7.   Import the library in the study table

Click the IMPORT MOLECULES pushbutton in the Add Molecules from SD File control panel.

You can follow the progress of the import process in the interrupt message window. Importing the structures and calculating the default set of 50 descriptors takes about 10 minutes on an Indigo2 R10000 work station.

After the import process has finished, close all control panels except for the Study Table control panel.

8.   Working with the study table

Even though the structures are not loaded, you can still manipulate the study table and recall structures as you need them.

Select a few rows from the study table and open the Show Selected Molecules control panel by selecting the Molecules/Show Selected... item from the menu in the Study Table control panel. Click the Show Selected Molecules in Models Window action button.

The system goes back to the original SD file and restores the models. Note that the models were not minimized at library building time and therefore may have distorted geometries.

9.   Save the study table

Open the Save Study Table control panel by selecting the File/Save item from the menu bar of the Study Table control panel. Save the table as benzo.tbl.

Importing compounds from WDI

If you have just finished the previous section, start a new session by selecting File/New Session from the Visualizer menu bar. Click Confirm in the Re-initialize All message window.

You may also start from a brand new Cerius² session.

2.   Open an empty study table

Go to the LIBRARY ANALYSIS card located in the COMBI-CHEM I deck and select the Show Study Table menu item.

3.   Set the molecule import defaults

Open the Molecule Preferences control panel by selecting the Preferences/Molecules... item from the menu bar in the Study Table control panel. Uncheck Add Hydrogens and Minimize Energy using.

4.   Set the SD file import options

Open the Add Molecules from SD File control panel by selecting Molecules/From SD File... from the menu bar in the Study Table control panel. Check the Read Data Fields check box. Select the file ./Cerius2-Resources/COMBICHEM/wdi/wdi-400.sd and then click the SELECT pushbutton.

The SD file is read and the number of structures in the file is shown as 399 on the Add Molecules from SD File control panel. The available data fields also appear in the control panel.

Select NAME in the data field list box (on the right of the control panel) . Click the Set mol name from selected data field action button.

The MolName field now appears as NAME.

Click the Select all action button above the list box.

5.   Import the WDI structures into the study table

Click the IMPORT MOLECULES pushbutton on the Add Molecules from SD File control panel.

You can follow the progress of the import process in the interrupt window. Importing the structures with data fields takes under a minute on an Indigo2 R10000 work station.

After the import process has finished, you can close the Add Molecules from SD File control panel.