Skip to main content

CDK, JCP, SWT, AWT...

And other TLAs (three-letter acronyms)...

So, in trying to find out what the status of the JChemPaint code, there seems to be a lot of stuff, but not all of it works. So, in order to understand the plan, and as a suggested architecture, have this diagram:

It's not proper UML, but the package symbols are right. What this sketch suggests is that if there is graphics-independant code in the cdk.renderer package, then this package would take a molecule (or a reaction set, or a chemobject, etc) and 'render' it into graphical objects.

These would then be passed (the "renderer objects" oval) to the package (n.b.cdk.jchempaint or o.o.jchempaint) that is actually using a Graphics or GC object to draw with. Otherwise, the renderer package is really doing nothing useful.

Comments

One thing to consider is that the input for the Renderer is not just IMolecule, but also things like IReaction.

In relation to this, we likely need rendering modules, which one can easily plugin in and out... for example, a module to draw reaction boxes, and electron movement arrows...

Now, a tree or list of rendering objects is a good idea, but we need to come up with a design which integrates well with such a modular design too...
gilleain said…
I saw the IRenderer2D interface methods (paintMoleculeSet, paintReactionSet, etc).

I suppose it might be nice to have these as modules, but I can't see the use-case for it. It seems like YAGNI applies:

http://en.wikipedia.org/wiki/You_Ain%27t_Gonna_Need_It

But, I could be wrong...

In principle, there is no problem making the intermediate representation in a modular fashion, but at the moment the test implementation only renders bonds, rings, and atom symbols so there's a way to go :)
The alternative is to add many options to the Renderer2DModel, such as: drawReactionBoxes, drawElectronMovements, etc...

We do need this one way or another...

Popular posts from this blog

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

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

General Graph Layout : Putting the Parts Together

An essential tool for graph generation is surely the ability to draw graphs. There are, of course, many methods for doing so along with many implementations of them. This post describes one more (or perhaps an existing method - I haven't checked). Firstly, lets divide a graph up into two parts; a) the blocks, also known as ' biconnected components ', and b) trees connecting those blocks. This is illustrated in the following set of examples on 6 vertices: Trees are circled in green, and blocks in red; the vertices in the overlap between two circles are articulation points. Since all trees are planar, a graph need only have planar blocks to be planar overall. The layout then just needs to do a tree layout  on the tree bits and some other layout on the embedding of the blocks. One slight wrinkle is shown by the last example in the image above. There are three parts - two blocks and a tree - just like the one to its left, but sharing a single articulation point. I had