R-Group Analysis Panel

The R-Group Analysis panel identifies the groups that are attached to a core and provides tools for displaying properties of the R groups and for exporting them to files. The core can be specified by a SMARTS pattern, or determined by the maximum common substructure obtained from a Canvas MCS run.

To open this panel: .

  • Using
  • Features
  • Additional Resources

Using the R-Group Analysis Panel

As well as running from Maestro, you can open the R-Group Analysis panel from the command line with the following command:

$SCHRODINGER/run r_group_analysis.py [input-file]

The use of SMARTS or Canvas MCS to determine the core can result in cores with different atomic composition, multiply bonded R groups, R groups that are attached to the core in more than one location, and multiple core structures. In cases where the results are unexpected, the following actions are taken.

  • R groups that are attached with multiple bonds are treated as any other group. You might, for example have a carbonyl group (XC=OX') in one structure where there is a substituted methylene group (e.g. XCHCH3X') in another. In the first structure the R group is =O, in the second it is –CH3. The core in both structures involves the X-C-X' framework.

  • Attachment points on the core that have no R groups at all for some input structures can arise when different atom or bond types are treated as equivalent. For example, the core might contain a pyridine ring in one structure, but a benzene ring in another. An attachment point in the benzene ring might be at the carbon atom corresponding to the nitrogen in the pyridine. In this case, the attachment at the nitrogen is considered a “null” attachment, and a dummy atom is added, bonded to the nitrogen, with the label “Null”.

  • R groups can be attached in multiple positions (forming rings). An R group connected at multiple attachment points is displayed in the fragment viewer for each attachment position. At each position, the attachment bond is displayed with the same orientation and color shown for the corresponding attachment bond on the core and the other fragments in the current fragment display. The additional attachment bonds on the fragment are displayed with colors corresponding to those shown in the core display, but their orientations might not match those in the core display.

  • Attachment bonds can be found within a ring. An example is two attachment bonds within a ring pointing toward the same ring atom. This means that the discovered MCS includes the remaining ring atoms; the atom pointed toward is not part of the core, but is a multiply connected R group. This situation can be avoided by setting an option.

When using these two methods, the program must decide which mapping to use for each input structure if the core substructure maps to some input structures in several ways. The program picks the best set of mappings chiefly by optimizing the fingerprint similarity of the side chains for pairwise alignments of the input structures. This choice usually also minimizes the number of R-group positions defined on the core.

R-Group Analysis Panel Features

Analyze structures from option and menu

Select this option to analyze structions, and choose the source of structures to analyze from this option menu.

  • File—Use the structures in a specified file. If you choose this option, the File name text box and Browse button become available.
  • Project Table (selected entries)—Use the structures that are selected in the Project Table.

If you select this option, the View Results and Save Results buttons are unavailable until you have run the analysis.

Read results from previous run option

Select this option to read in a set of saved results from a previous run, by using the Browse button. If you select this option, the Core definition from options and the Start button are made unavailable, because the analysis has been done previously. The View Results and Save Results buttons are available.

File name text box and Browse button

If you are analyzing structures from a file, enter the name of the structure file in the text box, or click Browse and navigate to the file in the file selector that opens. The file must be in Maestro or SD format, and can be compressed or uncompressed. The file name is displayed in the text box when you click Open. Only available when you choose File from the Analyze structures from option menu.

If you are reading results from a previous run, enter the name of the results zip file into the text box, or click Browse and navigate to the results file in the file selector that opens.

Core definition from options

Select an option for the definition of the core of the molecule. The analysis determines the R groups that are attached to this core. See Using the R-Group Analysis Panel (above) for information about the results of using Canvas MCS and SMARTS options for defining the core.

  • Canvas maximum common substructure—Use the maximum common substructure as determined from a Canvas MCS calculation. If you choose this option, the Atom equivalences option menu becomes available, and you can choose a definition of equivalent atoms when determining the core. The options are described in the help message for canvasMCS Command Help and also in canvasFPGen. To ensure that the rings in the core are not broken when finding the substructure for the core, select Do not allow partial rings in the core.

  • SMARTS—Specify a SMARTS pattern for the core in the text area, or select atoms in the Workspace and click Get SMARTS from Workspace Atom Selection.

Start button

Start the job that determines the core and the R groups. When the job finishes, the R-Group Viewer Panel opens.

View Results button

Opens the R-Group Viewer Panel, in which you can view and examine properties of the R groups that you read from a previous run.

Save Results button

Save the results of the analysis in a zip file. Opens a file selector, in which you can navigate to a location and name the file. The results can subsequently be read in by using the Restore state from previous run option.

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