R-group Representation and Editing Options

An R-group query can involve several derivatives that differ in one or more substituents (fragments). These are as follows:

• R-group label
• R-group attachment point
• R-group definition

For the R-group search, some conditions (R-logic) can also be set during the R-group query.

Creating R-group Labels

Smart R-group Tool

1. Select the Smart R-group tool.
2. Click on a clear place on the canvas, or on the right place in the molecule (sprout drawing is also possible).

In this case, the default setting is that the auto numbering is active, which means that R1, R2, and so on, groups will automatically appear in the place of the clicking in the right order.

Shortcut

Hitting R+Space opens the R-group dialog window, where you can set the number of the R-group (or you can leave the field empty to get an R-group without any number). After closing the window, the chosen R-group appears on the tip of the mouse pointer and this can be added to the root structure in the same way as atoms are inserted. Hitting the R key places an R on the tip of the cursor; it can be placed on the canvas with a left-click or pressing Enter as many times as needed.

Editing R-group Labels

There is an option to add or change R-groups to the required number by clicking on an R-group (when the Smart R-group tool is active). Clicking on an existing R-group opens the R-group dialog window, here you can turn off the auto numbering by unchecking the box and set the number of the R-group. When you check the auto numbering box again, the numbering will carry on from the first number that is not yet represented on the canvas.

To change other symbols to R-group label (without number), hover over an atomic symbol or select it by the Selection tool, and hit R. Existing atoms can be replaced by R-group labels using the Atom properties dialog as well, where the R-group type should be chosen instead of Element. In this case, you can set the number, alias, or map to the R-group.

Adding Attachment Points

R-group Attachment Point Button

Select the R-group attachment point button and then click on the atom. You can add more attachment points by clicking successively on the selected atoms.

Context Menu

Right-click on the selected atom then choose + R-group attachment from the menu. The attachment points on every separate fragment are automatically numbered, beginning with 1.

The bond type of the R-group attachment points can be changed using either the R-group attachment point tool or any of the bond tools.

Create R-group Definitions

To create the definition for an R-group, draw the substituents from which the R-group should stand for, then you can choose from two options.

{info} R-group definition import and export are supported only in Chemaxon Marvin Document (MRV) format in Marvin JS; besides, you can choose other formats if the relevant web service is available.

Selecting with the Smart R-group tool results that the R-group label will be given to the fragment (or fragments), which appears on the canvas. When there is more than one R-group in the scaffold, the label of the fragment will get the smallest R-group number, which has not got a definition yet.

Alternatively, select the substituents with one of the Selection tools, and then hit R+Space shortcut. The R-group dialog opens, and you can set the relevant R-label.

Adding Elements to the Definition

Selecting the substituents together with the Smart R-group tool results that the same R-group label will be given to the fragments.

If you want to add one or more fragments to an R-group definition, select these fragments (with the Selection tool), right-click on the relevant R-group label, then choose the Add to this group option.

Removing Elements to the Definition

You can remove fragments from the definition by selecting it with the Smart R-group tool. In this case, the selected element will get a new label.

To remove a fragment from a group, select this fragment, right-click on the R-label of the group, and select Remove from this group option.

Ungrouping an R-group Definition

Ungrouping the definition results that the fragments will not be erased, but they will not belong to an R-group definition any longer. Right-click on the R-group label, and use the Ungroup option in the pop-up menu.

Deleting an R-group Definition

In that case, the definition and all of its contents will be erased from the canvas. Deleting the definition can happen as with any other objects, by the Delete tool, or by the Delete keyboard button.

Adding R-logic

Right-click on the label of the R-group definition, then select the R-logic item from the context menu. Set the appropriate values and press OK. R-logic data appears on the top left corner.