Abbreviated (Superatom) Groups

Abbreviated groups are used to represent (sub)structures with a text abbreviation and are useful tools for drawing large, complex structures or structures which have the same substructure, that is, functional groups.

MarvinSketch contains a default library of commonly abbreviated groups which can be accessed through Insert > Group.

To display the available abbreviation groups in the upper left corner of the canvas, start typing the name of the abbreviation groups.

Abbreviated Groups on the Canvas

To insert an abbreviated group, follow the steps below.

  1. Start typing the name of the abbreviation.

  2. To complete the name hit Enter or End.

  3. As the desired group appears on the cursor, simply click on the canvas with it.

Group abbreviations are case sensitive, for example, typing either NO or no leads to the nitrosyl (NO) functional group. On the other hand, typing No displays the atom symbol of nobelium.

Abbreviations having a number as a first character can be displayed by typing the entire abbreviation or by navigating to Insert > Group.

If the cursor is placed over an atom, the atom automatically changes into the abbreviated group.

To expand an S-group before placing it to the canvas, press Shift before clicking the mouse button.

The following group-related context menu actions are available in MarvinSketch:

  • Edit Group: This action is only available in the context menu if the context menu was invoked inside or on a group. You can change the following parameters on the Edit Group dialog:

    • Type

    • Name

    • Polymer repeat pattern

    • Bracket style

  • Ungroup: Removes all abbreviated groups from the selected area or the whole canvas. Structures remain, but they are no longer associated with their abbreviations.

  • Contract Groups: If there is a group selected, contracts the selected group to its abbreviation. Otherwise, contracts all groups on the canvas.

  • Expand Groups: If there is a group selected, expands the selected group from its abbreviation. Otherwise, expands all groups on the canvas.

Marvin gives priority to the user-defined abbreviated groups and overwrites the default groups after redefinition.

Create an Abbreviated Group

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.

Add or Remove Attachment Points to Abbreviated Groups

To add an attachment point to an abbreviated group, right-click an atom of the abbreviated group and select Add S-group Attachment from the context menu. Alternatively, you can select the desired atom and navigate to Atom > Add S-group Attachment.

The attachment point is marked by a number in a green rectangle. The display of the attachment points can be switched on or off by using View > Advanced > S-group Attachments.

There is no limit on how many attachment points can be added to an abbreviated group. The added attachment points are numbered in the order of their creation. Similarly, an atom of the abbreviated group can have more attachment points.

Bonds are connected to group atoms through their first free attachment point (except amino acids).

Only attachment points not involved in bonds are marked by numbers in the expanded abbreviated group.

To remove an attachment point, select the Remove S-group Attachment option either from the context menu or from the Atom menu. If the selected atom has more than one attachment point, they are deleted in descending order.

Add Abbreviated Groups to the Template Library

To add abbreviated groups to the templates, select the group to be added, and click Add to My Templates on the context menu.

The structure is added to the Advance Template Toolbar.

Format Default and User-defined Abbreviated Groups

The Atom Label Editor can be used to change the characters to bold, italic, super- and subscript and insert symbols.

Color, font type, and size can be set by choosing Format from the context menu.

User-defined Abbreviated Groups

MarvinSketch stores its default groups in the following formatted TXT file:

default.abbrevgroup

You can create your group file. While assembling a .abbrevgroup file you must strictly follow the abbreviated group file format.

The newly defined file must be named user.abbrevgroup and must be stored in the ChemAxon folder of your home directory in your file system.

The process of creating user-defined abbreviated groups is described in the following steps:

  1. Open MarvinSketch.

  2. Draw the desired structure on the canvas.

  3. Select the structure and by using the Create Group dialog name your structure.

  4. Add attachment points as needed.

  5. Copy the content of the Source dialog box (Edit > Source) to the text editor of your choice. The text must be copied in ChemAxon SMILES Abbreviated Groups format. Navigate to View > SMILES > ChemAxon SMILES Abbreviated Groups to change it.

  6. If you do not have a user.abbrevgroup file, then create it in your ChemAxon folder and paste the text into it. If you already have the file, simply paste the text into it.

Formatting User-defined Abbreviated Groups

The label of the abbreviated groups can be formatted, by adding the graphicalMarvinProperty::FormattedLabel property to the abbreviated group atom.

Example:

i-Bu CC(C)C 1 abbrevAtomProperties=graphicalMarvinProperty::FormattedLabel.\ii\n\-Bu

In the property name the ’:’ character must be replaced to : because the ’:’ character has a special meaning in the abbrevAtomProperties value.

Syntax of the abbreviated group name

Numbers are automatically subscripted unless "\n" is used or at the start of a string. Charges (+, -, ++, --, 3+, and so on) are automatically superscripted at end of string or if the following character is a closing parenthesis.

Allowed control sequences in the abbreviated group name are as follows:

  • italic: \i

  • small: \m

  • bold: \b

  • underline: \u

  • subscript: \s

  • superscript: \S

  • reset (normal): \n

  • escape (escaping autoformatting): \

Block restriction: [format]{[text]} Besides the default abbreviated groups, you can also set up user-defined groups (or redefine the default ones).