Alternative JCP architecture

Soooo. I have been messing around with what I've optimistically been thinking of as an 'alternative' JChemPaint renderer rather than just a botched refactoring. I started with the code by Niels Out (blog) and messed around with it a bit. Here is a diagram of part of where it is at:

This is meant to be valid UML, but the message is the same : "Overly. Complex." The basic idea is that the parent SymbolTreeFactory handles the logic of what bonds to create, and the child factory creates a tree suitable for AWT.

There's a name problem here, as "AWT" is not right for Java2D; also I'm not sure why I decided on "SymbolTree" as it's not really a tree as such. It could be, using a Composition pattern perhaps, but that seems unnecessary.

Anyway, the point of this is to make separate AWT and SWT renderers, while sharing as much code as possible. This may not be the way to do it, but it is a way to do it.

Comments

Egon Willighagen said…

Arvid implemented this basic design yesterday...

2 October 2008 at 09:23

gilleain said…

Oh, I should have said, this diagram was made from the implementation, not the other way round!

So, I have a version. There are still problems with the design; mainly due to having to render text (font sizes are always the problem).

Not sure where to put the code...

2 October 2008 at 10:13

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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