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There are a number of general concepts that are important to discuss early in order to explain how user interaction with VIDA works. VIDA is a stateful application and employs many special states (or properties) in its interaction with the user. The most important of these are: Focused, Visible, Locked, Marked, and Selected.
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 Section 3.1.2), 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.
The Visible state is an indicator of whether or not the associated object is drawn in the 3D display (see Chapter 5). Multiple objects can be Visible simultaneously. If VIDA is operating in tiled mode, each Visible object will be displayed in its own individual pane.
If the 2D display (see Chapter 6) is also shown and VIDA is in tiled mode, Visible molecules will be drawn in the 2D display as well as the 3D display.
The Locked state is essentially the same as the Visible state (see Section 3.1.2) 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 (see section 3.1.1) in which case it will be displayed in its own individual pane as well as every other pane in the 3D display.
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.
The Selected state is a special property of the Visible state (see Section 3.1.2). Only objects that are Visible, Focused (see Section 3.1.1), or alternatively Locked (see section 3.1.3) can be Selected. Much like the Marked state (see Section 3.1.4), the Selected state is a 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 (see Chapter 5) or 2D (see Chapter 6) display. Selected objects are usually indicated by a change of color (the default is orange) in these displays. More details on the actual process of selection can be found in the 3D and 2D display chapters.
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