Scaffold Decomposition of jobname Panel

This panel displays the results of a scaffold decomposition job. The scaffolds are displayed, sorted by the number of rings or ring systems, along with a representation of the property distribution of the structures that contain the scaffolds.

  • Using
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Using the Scaffold Decomposition of jobname Panel

The Scaffold Decomposition of jobname panel shows the 2D structures of the scaffolds in a table. The scaffolds can be classified by the number of rings in each scaffold, or by the number of ring systems. The scaffolds for a given classification are shown on the same table row. You can select scaffolds in the table, and limit the display to show only those scaffolds. Each time you limit the display (or remove the limits), that view of the table is stored, and you can use the arrow buttons to step through these views. If you want to see all the subscaffolds or superscaffolds of a particular scaffold, right-click in its table cell and choose the appropriate command.

The table also shows the property distribution of the structures that contain each scaffold, for a property that you can choose from the Property option menu. The average, standard deviation, minimum, and maximum values of the property are displayed to the right of the option menu. The property distribution is displayed for each scaffold as a "stick spectrum" in a bar that represents the full range of the property. For each structure there is a vertical line at the property value for that structure. The average property value is marked, and the region outside one standard deviation from the average is colored if it contains vertical lines for property values.

You can export the scaffolds to a structure file. The scaffolds are stored internally as canonical SMILES strings, so if you choose Maestro or SD format for the file, they are exported as 2D structures without hydrogens, except where the hydrogens are part of the SMILES string.

If you want to see the source structures for a set of scaffolds, select them in the table and click Show Source Structures. The Source Structures panel opens, and displays the structures for those scaffolds, arranged in rows with the same classification as for the scaffolds, and including the property distribution display. You can export selected structures or all structures to a file. You can run an R-group analysis on the selected structures or on all structures in the panel. If the structures have more than one scaffold in common, you are prompted to choose the scaffold you want to use for R-group analysis.

Scaffold Decomposition of jobname Panel Features

View navigation buttons

Use these buttons to step through the selections of scaffolds that you have made.

Show buttons

Choose which scaffolds to display in the table. Click Selection Only to display only the selected scaffolds; click All Scaffolds to display all scaffolds.

The number of scaffolds selected and the total number of scaffolds is reported to the right of these buttons, along with the number of structures represented in the scaffold selection and the total number of structures.

Property option menu

Choose the property whose values are graphically represented for each scaffold. The average, standard deviation, minimum, and maximum values of the selected property are shown to the right of the option menu.

Order rows by options

Select one of these options to determine how the scaffolds are assigned to rows in the table.

  • Number of rings—Assign scaffolds to rows by the number of rings that they contain, counting fused rings as multiple rings. For example, naphthalene is considered as containing two rings.

  • Number of ring systems—Assign scaffolds to rows by the number of ring systems they contain, counting fused rings as a single ring system. For example, naphthalene is considered as containing a single ring system.

Show Source Structures button

Show the source structures for the selected scaffolds, in a table similar to the scaffolds table. Opens the Source Structures panel.

Scaffolds table

This table displays the 2D structures of all the scaffolds, sorted by the Order rows by options. The more condensed ring systems are on the left if ordering by number of rings; the scaffolds with fewer rings are on the left if ordering by number of ring systems.

Each cell contains a scaffold 2D structure and a graphical representation of the property chosen from the Property option menu. In this representation, the minimum property value is at the left, and the maximum is at the right. The property value for each structure that contains the scaffold is marked by a vertical line. The average value over all properties is marked with an arrow at the top. The regions outside one standard deviation from the average are colored if they contain property values for one or more structures.

The table cells have a shortcut menu, which allows you to select all the subscaffolds of the scaffold in the table cell, all its superscaffolds, or both.

Legend button

Display a description of the property display in the scaffold table cells.

Cell size slider

Use this slider to adjust the size of the cells in the scaffolds table.

Export Scaffold buttons

Export all scaffolds (All) or the scaffolds selected in the table (Selected) to a file, in Maestro, SD, CSV, or SMILES format.

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