Three-Dimensional Scheme Windows

You construct, modify and operate on Kinetiscope's reaction schemes using scheme windows. Each scheme window includes a Scheme Page tailored for its particular type of reaction scheme.

The Scheme Page of a three-dimensional scheme window looks like this:

This page contains a scheme diagram of the reaction scheme. On the scheme diagram, compartments are represented by labeled cubes and transfer paths are represented by diamonds or labeled arrows. You may also add text annotations to the diagram.

Above the scheme diagram is a tool bar with a row of push buttons that allow you to edit compartments and transfer paths, start a simulation of the reaction scheme, or create a new results window, a separate window that presents the output of the last simulation.

A single click of the right mouse button in an empty area of the scheme diagram displays a context menu listing more available actions.

The current status of the reaction scheme is indicated by the status bar along the bottom of the window.

Creating a Three-Dimensional Reaction Scheme

To create a new three-dimensional reaction scheme:

  1. Select File | New Scheme | three-Dimensional Model... from the menu bar of Kinetiscope's main window
    click the push button on the main window's tool bar.

  2. A Create Three-Dimensional Scheme Dialog appears.
  3. Using the Create Three-Dimensional Scheme Dialog, in sequential steps you
    • choose the units you wish to use;
    • enter the initial dimensions of the compartments, and
    • specify the size and characteristics of the array of compartments and transfer paths.
  4. Click the Finish push button on the Create Three-Dimensional Scheme Dialog.

A new three-dimensional scheme window displaying a scheme diagram of the specified array of compartments and transfer paths is added to Kinetiscope's main window.

You now use the tool bar and context menus to configure the reaction scheme.

Using the Tool Bar

For a number of these actions, you first select one of the objects in the scheme diagram, and then click the appropriate push button on the tool bar.

To select an object:

  • Single-click the object with the left mouse button.
  • The selected object appears cross-hatched to indicate its state.

The push buttons and their functions are as follows:

Add a new annotation.
Clicking this push button inserts a new text annotation in the upper-left area of the scheme diagram. You may then move, edit, change text attributes or delete the annotation.
Copy the selected object.
When this push button is clicked, a copy of the currently selected object is placed on Kinetiscope's internal clipboard. That copy may be pasted into this reaction scheme, or into another reaction scheme that is loaded into memory.
Paste an object.
This button is only enabled when a valid compartment, transfer path or annotation is on Kinetiscope's clipboard from a previous Cut/Copy action.

The action taken depends on whether an object in the scheme diagram is selected:

  • If the selected objects are the same type as the clipboard object, then all selected items in the scheme diagram are replaced with the copy on the clipboard.
  • If the selected object's types are different from the clipboard object, then no action takes place.
  • If no object is selected, and the object on the clipboard is an annotation, then the Paste operation adds a copy of the annotation on the clipboard to the scheme diagram.

Delete the selected object.
This push button is only enabled when an annotation is selected.

This action deletes the selected annotation from the scheme diagram and discards it.

Edit the selected object.
This action opens the appropriate Editor Dialog for the selected object. This same action may be initiated by double-clicking the left mouse button on the object. If multiple objects are selected when this button is clicked, then an Attributes Editor Dialog appears that allows you to modify names and colors for all selected objects.
Search the scheme for species usage.
This action searches for usages of a species you specify. When triggered, an initial menu allows you to choose whether you want to search in all compartments, all transfer paths, or in a subset of these objects you have previously selected. A Search Objects Dialog then appears where you can specify search critera and scan the objects.
Zoom in.
This action increases the scale of the scheme diagram. You may also zoom in and out using the mouse wheel.
Zoom out.
This action decreases the scale of the scheme diagram. You may also zoom in and out using the mouse wheel.
Zoom to full scale.
This action resets the scale of the scheme diagram to its original scale.
Zoom to show all.
This action sets the scale of the scheme diagram to ensure all objects are visible.
Create a new simulation results window.
This button is only enabled when a simulation has been successfully run and simulation results are available.

To create a new results window:

  1. Select the compartments to be plotted.
  2. Click this button.
A results window displaying a graph of simulation results will be added to the main window.

The type of plot depends on the form of the array of compartments that you have selected.

  • If a single compartment is selected then this action creates a new line plot window in the main window's workspace. That window initially displays a plot of the concentrations of all species as a function of time for the selected compartment. You may then modify the view to present other parameters.
  • If a one-dimensional array of compartments is selected (e.g. a row or a column of compartments) then you are shown a Waterfall Plot Style Dialog from which you select the parameter to be plotted and the plot style to be used.
  • If a two-dimensional array of compartments is selected (i.e. a plane of compartments) then you are shown a Surface Plot Style Dialog from which you select the parameter to be plotted and the plot style to be used.
  • If a three-dimensional array of compartments is selected (i.e. all compartments in a three-dimensional array) then you are shown a Volume Plot Setup Dialog from which you select the parameter to be plotted.
  • If no compartments are selected then Kinetiscope selects the plot type that will display all compartments and presents you with the appropriate Style/Setup Dialog.

For more details, see the section on Viewing the Simulation Results.

Start a simulation.
When this push button is clicked, Kinetiscope performs some internal tests of the reaction scheme to ensure that the simulation will start successfully.

If these tests are successful, a simulator window opens and Kinetiscope starts the calculation. The current reaction scheme is locked to prevent editing during the simulation, but you may continue to work with other reaction schemes while simulations are in progress.

If the reaction scheme fails one of the pre-simulation tests, a message box appears to notify you of the issue.

Context Menus

For each object in the diagram, you may invoke a context menu by single-clicking the right mouse button over the object. See the descriptions of the context menus of compartments, transfer paths and annotations for details.

The scheme diagram itself has a context menu, invoked by single-clicking with the right mouse button over any empty area in the scheme diagram. This menu can initiate the actions listed here:

The first six entries provide an alternate means of triggering the functions already assigned to the tool bar push buttons. The remaining five actions are

Lock the Scheme Layout
selecting this menu item toggles a lock on the layout of the scheme diagram.

When locked, the positions of all the objects are fixed. The locked state is indicated by a check mark next to this menu item. The locked state is preserved when the reaction scheme is saved to file.

Copy Diagram Image to Clipboard
When this menu item is selected, a bitmap image of the scheme diagram is placed on the system's clipboard.

This image may be pasted into other applications.

Export Diagram Image to File...
When this menu item is selected, a File Save Dialog appears that allows you to save an image of the scheme diagram to a disk file.

The image is saved in Portable Network Graphics (.png) format.

Show Text Listing of Reaction Scheme...
This menu item opens a new Show Text Listing Dialog displaying all details of the reaction scheme.
Show Selection Frequencies of Entire Scheme
This menu item creates a new Selection Frequency Histogram Window displaying a frequency spectrum of that includes each step defined in the reaction scheme.
Hide the Coordinate System Icon
A small icon that indicates the positive-going directions of the X(Columns), Y(Rows) and Z(Layers) axes is normally placed in the lower left quadrant of the scheme diagram. Selecting this menu item toggles the visibility of that icon.

The hidden state is indicated by a check mark next to a menu item.

Show a Scaled View of the Diagram
This menu item creates a new Scaled Diagram Window displaying in a correctly scaled format the Scheme Diagram of the current reaction scheme.

Selecting Objects in the Diagram

You must select arrays of compartments or transfer paths as you construct your reaction scheme by copy-and-paste operations, and when you create a results window.

Three different methods for selecting objects are available in a three-dimensional reaction scheme:

Selection Using the Mouse

To select one or more compartments or transfer paths:

  1. Press and hold the left mouse button while resizing the rubber-band box that appears so that it contains the desired items.

    The selected items are highlighted with a cross-hatched pattern while you resize the rubber band box.

  2. Release the left mouse button and the items remain selected.

The type of item selected depends on the type of object most recently placed on the clipboard. If a compartment is on the clipboard then only compartments in the diagram are selected; if a transfer path is on the clipboard then only transfer paths are selected.

To clear a selection:

  • Click the left mouse button on any empty area of the scheme diagram.

Selection Using the Compartment Context Menu

Each compartment's context menu has Selection sub-menu accessed by choosing the Select... menu item. On three-dimensional reaction schemes, that Selection sub-menu lists the following selection options:

You may use these actions to select one-, two- and three-dimensional arrays of objects. When you select using one of these actions, the selected objects are indicated by crosshatching.

Selection Using the Advanced Selection Dialog

The last entry on the compartment context menu is the Based on Characteristics... menu item. Selection of this action opens an Advanced Selection Dialog. From that dialog you may select compartments of transfer paths based on selection criteria such as name, ordinal location in the array, and coloring.