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CaGe V0.3

HCgen

HCgen is a generation program which generates hydrocarbon structures. Each carbon atom has bonds to exactly three other atoms where these atoms are either carbon atoms or hydrogen atoms. Carbon atoms are always part of either pentagon or hexagon rings (compare section fullgen ).

Basic options: Choose the number of carbon atoms by using the slider "Number of C atoms" or the "C-Atom" entry. Choose the number of hydrogen atoms by using the slider "Number of H atoms" or the "H-Atom" entry. Choose the exact number of pentagon rings by using the slider "Number of pentagons" or the "Pentagons" entry.

The three numbers interact so that not every combination is possible. Two of the three numbers determine the minimal and maximal number of the third. CaGe shows these minimal and maximal numbers for the C-Atoms, the H-Atoms and the pentagons. Let us look at one example.

After we have choosen 60 C-Atoms and 5 Pentagons the input area looks this way :


This means :
  • 12-16 C-Atoms 6 H-Atoms and 5 Pentagons are legal combinations.
  • 60 C-Atoms 10-30 H-Atoms and 5 Pentagons are legal combinations.
  • and with 60 C-Atoms 6 H-Atoms no value of Pentagons cause a legal combinations.
    (this is indicated by negative min. and max. values or by a min. value that is greater than the max. value).

    • The second case means that e.g. 60 C-Atoms 10 H-Atoms and 5 Pentagons is a legal combinations. So we choose 10 H-Atoms and the input area looks this way :

    An other illigal combination is the following

    60 C-Atoms 11 H-Atoms and 5 Pentagons

    The number of C-Atoms and the number of C-Atoms have to be both even or odd, so we have to choose:

    61 C-Atoms 11 H-Atoms and 5 Pentagons
    or
    60 C-Atoms 10 H-Atoms and 5 Pentagons

    If no error is indecated we can start the generation program by using the "Start"--button.

    Output options: See section fullgen .
    Extra options: The following options are options which are rarely used.

  • Isolated pentagons: If this checkbutton is switched on, only hydrocarbons with isolated pentagons are generated, i.e. no two pentagons share an atom.
  • Include H atoms: Exactly if this checkbutton is switched on, hydrogen atoms are included into the graphs. If hydrogen atoms are not included, then their positions can be uniquely determined by looking at atoms which have only bonds to two other atoms. The third bond is an implicit bond to a hydrogen atom. If hydrogen atoms are included, the size of the output becomes a bit larger and the computation of 2D and 3D embeddings takes more time. Besides, 2D output looks rather ugly.
  • Peri--condensed: If this checkbutton is switched on, no two carbon atoms which lie on the outer cycle must have bonds to each other except this bond (represented by an edge) is itself part of the outer cycle.
  • Maximum size of a gap: A gap is a sequence of two or more carbon atoms on the outer cycle of the hydrocarbon which do not have bonds to a hydrogen atom. The maximum size of such a gap can be determined by this slider.