Substructure Groups in MarvinSketch

Create Groups

To create a group, follow the steps below.

  1. Select a molecule or a part of a molecule.

  2. Click the Create Group button on the Tools toolbar. Alternatively, you can use the Ctrl+G shortcut, the Group button of the context menu (since version 5.3), or the Structure > Group > Group submenu.

  3. Edit the group properties in the dialog box.

Step 1 and Step 2 are interchangeable.

Group Types

The following group types are available in MarvinSketch:

You can only select the group types that are enabled for the actual selection in the molecule.

To enable all types during selection, navigate to Edit > Preferences > Structure tab and remove the checkmark from the Validate S-groups at Creation checkbox.

Whether the creation of a specific group type is allowed or not depends on the following factors:

  • The number of crossing bonds.

  • The embedding of groups into each other (several conditions are checked for the group to be created). These are as follows:

    • Whether it can be embedded into the groups which would contain it, for example, polymer S-groups can not be embedded into multiple S-groups.

    • Whether it can embed all the groups which would be contained by it, for example, structural repeating unit S-groups (SRU) can not embed monomers.

    • Whether it can be embedded directly into the group which would be its direct embedder, for example, component S-groups can be directly embedded only into ordered or unordered mixtures.

    • Whether it can directly embed the groups which would be embedded by it directly, for example, mixtures can directly embed only components.

  • Expandable S-groups are not allowed to be embedded into each other.

Since those group types which are allowed only for whole fragments (mixtures, components, and monomers) are always extended to whole fragments, these types are allowed even if only fragment parts were selected (if they are correct when extended to the whole fragment).

Extension to the whole fragment is not allowed if the group type is changed by editing an existing group. In this case, mixtures are not allowed for fragment parts.