The Dendogram panel and its operations

The Dendogram panel graphically visualizes the common substructure hierarchy of the compounds in the library. It provides possibility to mark nodes and leaves. The marked elements are displayed in the view panel. The bottom level of the dendogram contains the leaves, that is the chemical structures of the library. The upper levels contain the common substructures. The highest level contains the scaffolds. Some examples are highlighted on the picture below: nodes by orange, leaves by green color.

Mouseover on the dendogram evokes showing the actual structure with/without data according to the setting of the Display/Properties on tooltips menu option. The following operations are supported:

• Single click on a node marks the actual node.

• Double click on a node marks the actual node and its children.

• Right click on a node provides four possibilities: Mark node, Mark leaf nodes, Mark children, and Copy to clipboard.

• Horizontal selection: structures of one or simultaneously more levels can be marked by single click on the arrays at the left side of the panel.

• Application of the Ctrl button makes possible multiple selection.

There are special sizeable scrollbars on the top and on the right side of the dendogram. They serve not only for moving the dendogram but - by dragging their parts highlighted by red color on the picture below - for zooming it as well.

Fig. 2 Dendogram panel and its parts

The View panel and its modes

The View panel offers different view modes to view the clustering results.

MCS options

The minimum allowed size of any MCS found can be set with Minimal MCS size. When set, for instance to 5, possible common structures smaller than 5 atoms are dropped.

The Maximum level count parameter defines the maximum number of hierarchy levels. For instance, there are cases when only first level clusters are interesting, that is, the common substructures of the input molecule are sought for, but these common structures are not clustered further. In such cases there is no point in generating higher levels of hierarchy. In order to stop libmcs after the first level is created (ie. all input structures are clustered), 1 has to be set in the parameters dialog.

Clustering options

Fig. 5 MCS options

The Required cluster count parameter defines the minimal number of clusters required on the top level of the hierarchy. If the number of clusters gets smaller than this limit, the search terminates.

Keep rings means that the clustering process handles whole rings, does not break rings.

Colouring molecules

Visualization options can be set in Color molecules dialog.

Color molecules

The Dendogram will be highlighted by the selected Action (Mark or Color) with the selected Color at the points representing the structures the selected Property values of which are between Minimum and Maximum.