General Concepts

There are some key concepts that are helpful for understanding how to interact with VIDA. Individual objects in VIDA can be in various states, including Focused, Visible, Locked, Marked, and Selected. Each of these states carries some special behaviors which are described below. These states also provide a way to refer to specific molecules or sets of molecules. For example, one could apply a coloring scheme or rendering style to all Marked objects, or to the Focused object.

VIDA’s “Scope” determines which objects will be affected by operations within the program, based on their states, and is discussed in the “Scope” section below.

Focused State

The Focused state is a property of a single object in the application; there can be only one Focused object at any given time. Being Focused indicates that that particular object is the current object of interest and is therefore the primary focus of all relevant windows. If the Focused object is not already Visible (see below), it will behave as if it were Visible for as long as it remains Focused.

In addition, when a molecule is the Focused object, its SMILES representation is displayed in the application’s status bar (which can be found at the bottom of the application window). If any of the molecule’s atoms are selected, that selection will be indicated in the SMILES display by the coloring of relevant atoms. Selected atoms are colored using the current selection color (the default is orange) and are also in a bolded font while all of the unselected atoms will be displayed in their usual normal black font.

For large molecules (>100 atoms in this case), no SMILES representation is displayed as it would not fit in the status bar.

Visible State

The Visible state is an indicator of whether or not the associated object is drawn in the 3D display. Multiple objects can be Visible simultaneously. If VIDA is operating in tiled mode (see Tiled Display), each Visible object will be displayed in its own individual pane.

If the 2D display is also shown and VIDA is in tiled mode, Visible molecules will be drawn in the 2D display as well as the 3D display.

Locked State

The Locked state is essentially the same as the Visible state except in the situation where the application is in tiled mode, in which case each Locked object will be displayed in every pane of the 3D display. However, a Locked object can also be simultaneously Visible and/or Focused in which case it will be displayed in its own individual pane as well as every other pane in the 3D display.

Marked State

The Marked state is simply an indicator of user interest in the associated object. The Marked state can be used to help filter data as well as to specify the desired input to application functions. For instance, the Marked state can be used to specify which molecules out of a large list are saved. Finally, when certain operations generate too many results to be displayed at one time, the Marked state can be used to indicate the results of those operations.

Selected State

The Selected state is a special property of the Visible state. Only objects that are Visible, Focused, or Locked can be Selected. Much like the Marked state, the Selected state is an indicator of interest and provides an input set to application functions. Unlike, the Marked state, the Selected state is more transient and is easily cleared. The act of selection is usually performed in either the 3D or 2D display. Selected objects are usually indicated by a change of color (the default is orange) in the 2D display, and by a colored outline in the 3D display. More details on the actual process of selection can be found in the chapters on 3D and 2D displays.