R-Group Creator Panel

Create and edit R groups, and manage R-group libraries.

To open this panel: click the Tasks button and browse to Enumeration and Ideation → Create R-Group Library.

  • Features
  • Additional Resources

R-Group Creator Panel Features

Create R Groups tab

Create new R groups by sketching them, defining them from an existing set of structures, or analyzing a set of ligands to extract R groups.

Choose method for creating new R-groups options

Select a method for creating new R groups, from the following:

  • Sketch R groups—Sketch R groups in 2D using the 2D sketcher.
  • Get from fragments—Create a set of R groups from a set of structures by automatically assigning the attachment bond by use of a SMARTS pattern.
  • Analyze R groups from ligands—Analyze a set of congeneric ligands to locate a common core and extract R groups that are attached to the common core from each ligand.
Sketcher tool

Sketch an R group using the standard 2D sketching tools (see 2D Sketcher Panel for more information). You should add a terminal atom to designate as the attachment point, which you can do by right-clicking on this atom and choosing Set as attachment point.

When you have finished sketching, use the Add R-group to library tools to add the new R group to the desired libraries. To clear the sketcher for another (unrelated) R group, click Reset Sketcher. You can also continue on with the current structure to create another, related R group.

The name in the R group in the R group base name text box is used to name the R group when it is added to a library. The name in the text box is updated each time you add an R group to the library, by adding a numeric suffix (if it doesn't have one) or incrementing the suffix (if it does). You can change the name before adding an R group to a library, and it is named with the name you provide; this name is then the one that is updated for the next R group. (This feature works in the same way as for job names.) The R-group name is used in enumeration to construct entry titles for the resultant structures.

Fragments tools

These tools are used to create fragments from a set of structures, by defining the attachment bond in the structures using a functional group or a SMARTS pattern.

Use structures from option menu

Choose the structure source for the fragments. The structures are added to the Fragments table as soon as you choose the menu item.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entries)—Use the entries that are currently included in the Workspace, treated as separate structures.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box. The structures are imported into the project and the first one is displayed in the Workspace.

Fragments table

This table displays the input structures before the fragments are created, and displays the fragments after they are created. You can select fragments to be added to R-group libraries, once R groups have been created from the fragments.

Number of columns box

Set the number of columns in the fragments table.

Reset R Groups button

Clear the R groups from the table and redisplay the source structures. This allows you to easily change the functional group and reuse the same structures to create more R groups.

Define attachment bond from option menu

Choose a method for defining the attachment bond. The choices are:

  • SMARTS—Define the attachment bond by entering a SMARTS pattern or loading it from the Workspace.
  • Functional Groups—Define the attachment bond by selecting from a predefined set of functional groups. When you choose this method, the Define button is displayed so you can choose the functional group.
Define button

Define the functional group SMARTS pattern and the leaving and attachment atoms by selecting from a predefined set of functional groups. Opens the Select Functional Group Dialog Box, which displays 2D structures for the functional groups that you can pick. When you click OK in the dialog box, the SMARTS text box, the Position of leaving atom box, and the Position of attachment atom box are populated. You can then modify the SMARTS pattern and the atom positions if you want.

SMARTS text box and Get from Workspace Selection button

Enter the SMARTS pattern for defining the attachment bond in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Get from Workspace Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace. The SMARTS pattern does not need to define the entire leaving group (the one that is removed to create the R group), but it must contain the bond that is broken to create an R group and a leaving group. This bond is specified by the indices of the leaving atom and the attachment atom.

Position of leaving atom box

Specify the index of the leaving atom in the bond that is broken to form the R group and the leaving group. The index is the index of the atom in the SMARTS pattern. The leaving atom is removed along with all other atoms attached to it (the leaving group); the atoms that remain form the R group.

Position of attachment atom box

Specify the index of the attachment atom in the bond that is broken to form the R group and the leaving group. The index is the index of the atom in the SMARTS pattern. The attachment atom is the atom in the R group by which it will be attached to a scaffold when doing an enumeration of R groups.

Evaluate SMARTS and Create R-Groups button

Once the SMARTS pattern is defined and the leaving group is specified, click this button to create R groups from the selected fragments. The number of R groups is reported next to the button. You can then add the selected fragments to a library.

Select All button

Select all the fragments in the table.

Ligand analysis tools

Analyze a set of ligands in terms of a common core and attachments to the core. Once the core is identified, the attachments are listed and can be used as R groups. The core can be identified either by a search for the maximum common substructure or by matching a SMARTS pattern.

Analyze structures from option menu

Choose the structure source for analysis into a core and fragments.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entries)—Use the entries that are currently included in the Workspace, treated as separate structures.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
File name text box and Browse button

Enter the file names in this text box, or click Browse and navigate to the files. The names of the files you selected is displayed in the text box. The allowed file types are: Maestro.The structures are imported into the project and the first one is displayed in the Workspace.

Core definition from option menu

Choose the method for defining the common core.

  • Maximum common substructure—Determine the maximum common substructure using Canvas MCS. This method searches for the largest substructure that is common to all structures, using a scheme that defines which atoms are considered to be equivalent for matching purposes.
  • SMARTS—Determine the core from a single SMARTS pattern. In this method, a structure is skipped if a match to the SMARTS pattern is not found.
Settings button

Open a dialog box in which you can make settings for the atom equivalences for the maximum common substructure method. The atom equivalences are described in Table 1 in canvasFPGen

SMARTS text box and Get from Workspace Selection button

Enter the SMARTS pattern for the core in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Get from Workspace Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace. Only available if you choose SMARTS for the core definition.

Analyze button

Analyze the structures to locate the core by the chosen method, and populate the table with the attachments to the core (R groups) that are found for each structure.

View Core button

Opens a panel that displays the 2D structure of the core, with the R-group labels at the attachment points.

R-group table

Displays the R groups found for the analyzed structures. Each column shows the unique R groups found at a particular attachment point (including hydrogen). Click View Core to show the locations on the core of each attachment point. You can select all the R groups in a column by clicking on the column heading. To select R groups in the table, you can drag over cells, use control-click (command-click) to add or remove single cells from the selection, or use shift-click to add multiple cells to the collection.

Select All button

Select all the R groups in the table.

Add R group to library option menu and Add button
Add R groups to library option menu and Add button
Add selected R groups to library option menu and Add button

Add the current R group or R groups, or the selected R groups, to the library chosen from the option menu. Click Add to add the group to the library. You can choose an existing library or create a new library, and you can add the R group to the libraries that are selected in the Manage R Groups tab.

Manage R Groups tab

In this tab you can create, view, delete, and edit R-group libraries.

R-Group Libraries section

This section provides tools for managing the libraries themselves and selection of libraries for other actions. The total number of libraries and selected libraries is reported next to the heading.

List of R-group libraries

The available libraries are listed in this area. Each library has a check box, which you can use to select libraries for actions. When you select a library, its members are displayed in the R-group display area below. You can select multiple libraries The All check box allows you to select or deselect all libraries. To clear the selection, use the All button twice. By default the built-in libraries (Diverse R-Groups and Solubilizing R-groups) are shown.

You can rename a library by right-clicking on the name and choosing Rename.

New button

Create a new empty library. Opens a dialog box in which you can name the library. The new library is automatically selected, and the R-group display area provides links for creating or adding R groups to the library, that take you to the Create R-Groups tab or open a file selector to add R groups from file.

Import button

Import R-group libraries from file. These must be pre-existing libraries. The libraries are added to your library set and are shown in the list.

Export button

Export the selected R-group library to a file, in Maestro format. Only one library must be selected. A file selector opens so you can navigate to a location and name the file.

Delete button

Delete the selected libraries from your library set, after confirmation.

R-Groups section

This section displays the R groups in the selected libraries and allows you to add or remove R groups.

Display area

The 2D structures of the R groups are displayed in a grid in this area. You can select R groups with click, shift-click, and control-click, or by dragging. Shift-click selects all R groups in the rectangle between the previous click and the shift-click: it does not fill entire rows. To clear the selection entirely, click in a cell, then control-click the same cell.

Number of columns box

Set the number of columns to show in the grid of R groups.

Select All button

Select all R-groups shown in the display area.

Add button

Add R groups to the selected libraries. Opens a file selector so you can locate and read R groups from file. All the R groups are added to each selected library.

Duplicate button

Duplicate the selected R group. Only one R group must be selected. Opens a 2D sketcher so you can make modifications before saving the R group as a new group. When you save the R group, it is added to all selected libraries.

Delete button

Delete the selected R groups from their libraries.

More Actions option menu

This option menu offers other actions that you can perform on the selected R groups.

  • Export—Export the selected R groups in Maestro format. Opens a file selector so you can navigate to a location and name the file.
  • Copy—Copy the selected R groups to the clipboard.
  • Paste—Paste the R groups from the clipboard into the selected libraries.
  • Edit—Edit an R group. Opens a 2D sketcher panel so you can edit the group. The group is replaced with the modified version when you click Update R-Group.

Reset button

Reset the panel to its default state, clearing all data.

Tutorials

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