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CaGe V0.3

Tutorial --- Tour de CaGe

Let's suppose you have started CaGe. If you do not know how to do this, have a look at the README file which is provided together with CaGe. After you have started the program, a message appears. After a few seconds either a window or the frame of a window appears. In the first case new windows are placed automatically, in the second case you must place every new window yourself by moving the frame (this is done by moving the mouse) and pressing the left mouse button afterwards.

There are two windows which appear: The main window and the selection window. The main window is titled "CaGe V0.3" while the selection window is just titled "CaGe".
  • Main window:
    The main window will stay on the screen as long as CaGe is running. You can always exit CaGe by clicking the "Quit" button in the main window (clicking a button on the display means that you press the left mouse button while the mouse pointer is located on that button). You should exit CaGe only this way. You should never make use of the window options which are offered by your window manager (close, delete, destroy...). When a generation program is running, the main window provides some information about the state in which the generation program is.
  • Selection window:
    You can choose a graph generation program via the selection window. All generation programs which are provided and the kind of graphs which they generate are listed in the selection window. Actually, there are five different programs which will be discussed later. There is a little space between the third and the fourth entry in the list because the last two programs are intended to support not only chemical applications, but various tasks.
  • Let's choose the first program as an example. So we want to generate fullerenes, and the program which does this is called fullgen. As soon as you click the "Fullerenes (fullgen)"--button, the selection window disappears and another window appears which is called the option window:

    Here you can change some parameters which determine what kind of fullerenes shall be generated and where the output shall be sent to. To change the parameters, different widget types are supported. One widget type you have already used is the button. By clicking a button you invoke a certain process (e.g. entering a new window). There are some other types:
  • Slider:
    A slider contains a button which can be moved and a container in which the button can be moved. By moving the button you change the value of a parameter. This value is shown either above the button or to the left of the container. To move the button, put the mouse pointer on it, press the left mouse button and hold the left mouse button while moving the mouse. To change the parameter value for the smallest possible unit, put the mouse pointer on the container and press the left mouse button. If the parameter value becomes smaller or bigger depends on the position of the mouse pointer in relation to the slider button.
  • Checkbutton:
    A checkbutton is a small light with a label at its right side. The light can be either on (red) or off (grey). You can turn the light on or off by clicking it. A checkbutton is used to mark something.
  • Entry:
    An entry can be used to show text. You can change this text by clicking the entry. In this case a cursor appears and the program accepts keyboard input. If the text is long, then it might happen that the entry is too small to show the whole text. But it is nevertheless there, it will not be cut.
  • Radiobutton:
    Radiobuttons always appear in groups. They look like checkbuttons, but the light is a rhombus instead of a square. Only one radiobutton in each group can be switched on. Whenever you turn one radiobutton on, all other radiobuttons in this group will be turned off automatically.
  • Label:
    Labels are used to show text. If the text represents a parameter, then it might change. But different to an entry the user cannot change the text himself.
  • Most widgets that can be used interactively will highlight (with white colour) whenever the mouse pointer is put on them. By pressing the left mouse button you invoke the widget. For example, you do not need to put the mouse pointer exactly on the checklight to invoke a checkbutton. It suffices to put the pointer somewhere on the related label.

    The parameters can be split into three categories:
  • Basic options: In fullgen, there is only one basic option. It is the number of vertices (atoms) each generated fullerene must have. In the first row of the window there are two sliders. By moving one slider button you can change the minimum number of vertices or the maximum number of vertices each generated fullerene must have. Note that the other slider moves simultaneously whenever you move one slider. This is because the "min=max"--checkbutton at the right of the sliders is switched on. When the checkbutton is turned off you can move the two sliders separately of each other. By default, CaGe switches on the "min==max"--checkbutton because it assumes that you want to generate fullerenes with a fixed number of vertices. As you will see, CaGe often does such assumptions to minimize the amount of changes you need to do (especially if you change output options). So sometimes it switches checkbuttons on or off automatically when you invoke another widget. Another reason for automatical changes is that not all parameter values fit to each other. Whenever there is a combination of values which is not allowed, CaGe tries to change the values itself.
  • Output options: The output options are the same for all generation programs. So the option window for every generation program contains the same frame named "Output". For each generated graph there are basically three output styles: You can have the simple adjacency information of the graph, you can have an embedding into the two--dimensional Euclidean plane (such embeddings are called "Schlegel--diagrams") and you can have an embedding into the three-dimensional Euclidean space. While the adjacency information can only be stored into a file or sent into a pipe, the embedded graphs can also be shown on the display. You can invoke some of the options simultaneously, some others you can't. We will discuss this in detail in section fullgen (see "output options" there).
  • Extra options: Like the basic options, extra options are different for every generation program. Extra options are handled separately from basic options because in most cases they are not needed. Sometimes the extra options are so sophisticated that you cannot use them without having a deep impression of how the generation program works. So we will discuss extra options later.

  • We will now do some example calls of fullgen. For the first call, please change the number of vertices to 60 and leave all other options unchanged. So, what we want to do is to generate all fullerenes with exactly 60 vertices. The default output option is to save the adjacency information of the generated graphs into a file. The name of this file is determined automatically and depends on the options we use. You can see the filename in the related entry box ("Full_codes_60"). The code which is used for saving is called writegraph2d. When you click the "Start"--button at the bottom of the option window, then the generation will begin. The option window vanishes. Since there is no output for display the only window which remains open is the main window. The main window provides some information to the user about what the generation program is doing. Like every other generation program fullgen performs two steps:
  • Preparing generation
  • Generating graphs
  • The program will need about 20 seconds to generate all fullerenes with 60 vertices. After the generation has finished, a window called "Fullerenes --- Logfile contents" appears. Fullgen generates a so--called logfile into which it writes information about the performed generation that might be useful for the user. For example, the number of generated fullerenes is written into the logfile. If the logfile contents does not fit into the text display, you can use the slider on the right side of the display to scroll up and down inside the text. Except the slider, the "Logfile contents"--window has only one more button. By clicking this button (named "Continue") you close the window and return to the option window.

    The purpose of this call was to generate and store simple adjacency information. Since (like all other generation programs) fullgen already provides this information we could have got it without the use of CaGe. We could have called fullgen directly. However, calling fullgen is much easier using CaGe since CaGe provides buttons, sliders etc. for the options. If you want to have a look at the generated file "Full_codes_60", you can load this file into an editor. We will give a description of the code in section codes .

    We are now back at the option window. For the second call of fullgen, please change the number of vertices to 44. Now we try to get embedded graphs. We try to get two--dimensional and three--dimensional embeddings in one go. Please switch off the checkbutton named "Adjacency information". This means that pure adjacency information will not be stored. As you see, all related checkbuttons and radiobuttons are switched off automatically. Now, please switch on the radiobuttons named "File" which are positioned in the same lines as the checkbuttons named "2D representation" and "3D representation". The latter two checkbuttons are automatically switched on. So, the checkbuttons named "3D representation", "2D representation" and "Adjacency information" are used to mark that the related generation will be done at all. To avoid one generation you can just switch off the related checkbutton. If you want to include a generation you can choose between various output directions (e.g. file and display) and it suffices to switch on the related radiobutton. If you switch on the related checkbutton instead, CaGe chooses a default output direction.

    The names of the files into which the embedded graphs are written are determined automatically. There is one file for 3D representation and one file for 2D representation. The names are similar to those determined for files which contain adjancency information. Only suffixes ".3d" and ".2d", respectively, are added. Now, please click the "Start"--button. Now the same action as in the first example call will take place. The only difference is that it takes much more time to generate embedded graphs than to generate pure adjacency information (that is why we wanted you to reduce the number of vertices to 44). For this reason CaGe tells the user about the number of already embedded graphs. CaGe shows this number in the main window. In this example, 89 graphs will be generated and embedded. Finally the logfile contents will be shown. After clicking "Continue", you will return to the option window.

    Let us now have a third example. This time we want to generate embedded graphs and have a look at them on the display. We suppose you have already returned to the option window. Note that the parameters you have changed in the second example keep their values (e.g. the "Adjacency information"--checkbutton is still switched off). So the parameter changes we will now perform base on the second example. Please switch on the radiobuttons named "RasMol" (only if a program with this name is provided on your computer, otherwise you cannot have 3D embeddings on the display in this example) and "Display". The radiobuttons named "File" are automatically switched off. Furthermore, please change the number of vertices to 36. By clicking the "Start"--button fullgen will be called.

    The next task is to arrange the new windows which appear on the screen. One of these windows is called "RasMol Version xxx".

    RasMol is an external program which is very useful for displaying three--dimensional representations of graphs. It has various options which are not to be discussed here. Just notice that every 3D representation is sent to RasMol. Every 2D representation is sent to the window called "Schlegel diagram". The third window is called "Output panel".

    It contains buttons to control which graph is displayed. The numbers of the currently displayed graphs are printed in red. Normally the 2D and the 3D numbers are equal. It takes some seconds until the first graphs appear on the screen. To make the first graph appear in the RasMol window, it is necessary to move the mouse pointer inside this window (this is a peculiarity of RasMol).

    You can change the view of both representations. To change the view in the RasMol window, use the sliders on the right hand side and at the bottom of the window. To change the view in the "Schlegel diagram" window, click inside a face of the 2D representation.

    This face is surrounded by an alternating cycle of vertices and edges, and after a few seconds a new 2D representation will appear where this cycle becomes the outermost cycle. If you click the button named "Show numbers", then every vertex will be numbered. Unlike for the other windows of CaGe, here it is useful to enlarge the window (how this is done depends on your window manager). The "Show numbers"--button is now relabeled. Its label is now "Hide numbers". If you click on the "Hide numbers"--button, the vertex numbers will vanish. If you want to save the Schlegel diagram in PostScript style, then click the button named "Save as PostScript file". Before doing that, first enter the name of the destination file in the "Filename"--entry below. Default is "unnamed.ps".

    If you want to have a look at another graph, you can type the number of this graph directly into the entry named "Show graph no." in the output panel. Or you can use the "+1" or "+10"--buttons to approach to the next graphs: If x is the number of the currently displayed graph, then after clicking the "+1"--button it will be x+1 and after clicking the "+10"--button it will be x+10. If the number of available graphs is lower than x+1 or x+10, respectively (so that the desired graph does not exist), then CaGe will cancel the output and move to the logfile window. You can perform the same step by clicking the "Cancel"--button.

    When graph x is shown on the display, you cannot turn to graphs with lower numbers than x, with one exception: All graphs that were shown on the display are stored in an internal list. You can go through this list using the buttons "<" and ">". Doing this, you enter the review mode (actually there is no hint on the display which says that you are in review mode). The first graph which is shown after entering the review mode is always the last graph in the list. Clicking "<", you go to the previous graph, clicking ">", you go to the next graph in the list. You leave the review mode by invoking one of the widgets described above (apart from "<" or ">").

    There are two checkbuttons named "Save 2D" and "Save 3D". When you switch on the ``Save 2D''--button, the 2D representation which is currently displayed is saved in a file. Furthermore, every new 2D representation which appears on the display is also saved as long as the checkbutton remains switched on. The name of the file depends on the default name which is determined in the option window. A suffix ".s2d" is added. Switching on the "Save 3D"--button has the same effect for 3D representations. However, there is one difference when entering review mode: a 3D representation is only saved once even if it is reviewed several times, while a 2D representation is saved each time it is reviewed. This is necessary because you can change the 2D representation substantially by clicking a face, and you might want both the old and the new representation to be saved.

    The last checkbutton which needs to be explained is the "skip"--button. While this checkbutton is switched on, all graphs that come in from the generation program are skipped. When you switch off the checkbutton, CaGe continues in the usual way: It embeds the next graph which comes in and displays it. This checkbutton is useful only if you know that the list of generated graphs is very large.

    Let us suppose you have finished the generation process. There are three ways to do that:
  • You have clicked the "Cancel"--button
  • You have skipped over the last incoming graph
  • You wanted to see a graph which did not exist (i.e. the number of the graph which should be shown was too high; in this example, there are 15 graphs)

  • After finishing the generation process, the "Logfile contents"--window appears as usual.

    With these three examples you have got an impression about what CaGe is good for. After clicking the "Continue"--button, the option window reappears. If you click the "Cancel"--button there, you return to the selection window where you can choose another generation program. To quit, you do not need to return to the selection window. You can click the "Quit"--button in the main window whenever you want. If other programs are running which were called by CaGe (e.g. the generation program or RasMol), then CaGe will stop them automatically.