Edit Reactive Group Dialog Box

Edit the SMARTS pattern that defines a reactive group, or add a new SMARTS pattern. The dialog box is named New Reactive Group if you are adding a new pattern.

To open this dialog box, click Edit or New in the Reaction Type tab of the Covalent Docking panel.

  • Using
  • Features
  • Additional Resources

Using the Edit Reactive Group Dialog Box

You may want to edit the SMARTS pattern to create a more specific pattern, as the default SMARTS pattern for the ligand is generic. For example, you might want to use more specific SMARTS patterns to apply additional criteria beyond the actual reactive functional group.

  1. (Optional) Display a ligand in the Workspace, on which you can select atoms that define the functional group.

  2. Click Edit or New in the Covalent Docking Panel, to open the Edit Reactive Group Dialog Box.

     

  3. Do one of the following to change the SMARTS pattern:

    • Edit the pattern in the SMARTS text box.

    • Pick atoms in the Workspace that include the functional group and any other atoms you want to include, then click Get From Selection.

      The atoms you choose must at least match the default SMARTS pattern. The SMARTS pattern for the selection is displayed in the SMARTS text box.

  4. Choose an atom in the SMARTS pattern from the Position option menu to define the atom that forms a bond with the receptor.

    This option menu only displays the indices of the atoms that are capable of bonding to the receptor for the chosen reaction chemistry, so it might only contain one item.

  5. Click OK.

Edit Reactive Group Dialog Box Features

Smarts text box

Lists the SMARTS pattern for the reactive group. This text box can be edited directly. The text is replaced when you click Get From Selection.

Get From Selection button

Create a SMARTS pattern from the atoms that are selected in the Workspace, and display it in the SMARTS text box.

Position option menu

Lists the available atom positions in the SMARTS pattern that can be selected for the atom that forms a bond to the receptor. Choose the desired position to use from this option menu. You can use the SMARTS Index Panel to determine what the SMARTS index of a particular atom in the Workspace is.

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