Symbols and Elements

I have made attempts over the years to draw triangles and circles like, for example, this:

(in fact, this was drawn by David Westhead's code). There is a small design decision to be made between representing drawing elements as basic geometry or as symbols. A symbol may be the same as a geometric element (like a circle), but it might be a combination of them. Consider the 'N' and 'C' in boxes, above. Or this image:

where the mass number and charge are separate text elements on the left, and part of the whole symbol on the right. Neither is a 'better' way of doing things; they each have their advantages - and disadvantages.

It can be a lot clearer to use symbols, as each model object (atom, bond, helix, gene, cell) has a corresponding representation, and then a diagram composes the symbols into a manageable whole. On the other hand, you can re-use elements in different combinations for diagrams. A general vector drawing package would have Line, Text, Rectangle, Triangle, and so on.

So my vote would be to use symbols for the CDK/JCP renderer. The JCP application is not intended to be a full vector drawing package, but a specialised chemical editor.

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Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin...

chalky

I wanted to show something that hints at the things that the new architecture can afford us: This is using a Java2D graphics Paint object to make it look like chalk...kindof. It's a very simplistic way of doing it by making a small image with a random number of white, gray, lightgray, and black pixels. edit: it doesn't look so good at small scales some tweaking of stroke widths and so on is essential.

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the ...

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