Add Definition Dialog Box

In this dialog box, you can add a pattern definition to the list of patterns in the Functional Group Counts tab of the Ligand Filtering Panel.

To open this dialog box, click New in the Functional Group Counts tab of the Ligand Filtering Panel.

  • Using
  • Features
  • Additional Resources

Using the Add Definition Dialog Box

A new functional group definition can be built up out of the existing definitions from the Functional Group Counts tab of the Ligand Filtering Panel, or by adding new SMARTS patterns. The existing definitions are listed.

Each pattern that is added to the definition can either be "included" in the definition or "excluded" from the definition. For a chemical feature to match the definition, it must match all of the "included" patterns, and it must not match any of the "excluded" patterns. So, for example, if you wanted to match all oxygen atoms that were not in alcohols, you could include "O", and exclude "Alcohols".

To add an existing pattern to the definition, select the pattern in the list and click Include or Exclude. The pattern name is displayed in the text box above the list when you select it.

If you want to view the definition of a pattern, click View. The SMARTS string for the pattern is displayed in a dialog box.

To add a SMARTS pattern, enter the SMARTS expression in the text box above the list, and click Include or Exclude. You can add a SMARTS expression to the text box by selecting atoms in the Workspace and clicking Get From Selection.

Before you click Add to add the new definition, ensure that you have named it.

Add Definition Dialog Box Features

Name of new pattern definition text box

Enter the name of the new pattern definition in this text box. This name is used in the list in the Patterns tab of the Filtering Options dialog box.

Include and Exclude buttons

The Include button adds the pattern in the SMARTS expression or pattern name text box to the definition as a pattern that is to be matched by the chemical feature. The pattern is listed in the lower part of the panel, preceded by a + sign.

The Exclude button adds the pattern in the SMARTS expression or pattern name text box to the definition as a pattern that is not to be matched by the chemical feature. The pattern is listed in the lower part of the panel, preceded by a − sign.

SMARTS expression or selected functional group text box

This text box displays the SMARTS expression or the name of the functional group that is to be added to the definition by clicking the Include or the Exclude button. You can enter a SMARTS expression or a pattern name in the text box. The pattern name is automatically entered into this text box when you select it in the list.

Get From Selection button

This button replaces the content of the SMARTS expression or selected functional group text box with a SMARTS pattern derived from the atoms that are selected in the Workspace.

Pattern list and View button

Lists the available pattern definitions. You can select a single pattern in the list. The name is automatically displayed in the SMARTS expression or pattern name text box. You can view the definition of the pattern in terms of a SMARTS expression by clicking View Definition. The expression is displayed in a dialog box.

Pattern definition text area and buttons

The patterns that you include or exclude in the definition are listed in the text area in the lower half of the dialog box, preceded by a "+" if they were included, or a "−" if they were excluded. To delete a single pattern from the definition, select it in the list and click Delete. To clear the entire pattern definition, click Delete All.

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