Skip to main content


Showing posts from November, 2008


On the mean streets of CDK-city, one massive tower block dominates the skyline in the renderer district - the Renderer2DModel tower...

Masak pointed me to this site due to Richard Wettel which is about a static-analysis tool for making so called 'code cities'. 
Basically, the parking lots (like SMARTSParserConstants) have lots of attributes (in fact, this class only has attributes) while skyscrapers (like in the debug package) have many more methods than attributes (most of the debug classes have no attributes except inherited ones).
There's an eclipse plugin from here called MooseBrewer, and I think there are other tools there I haven't explored. It's great to have a map to this busy code metropolis, as I wondered what my workplace looked like :)


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.

Seeing Double?

Comes from too much screen-time:
although refactoring often seems like running on the spot (you get nowhere fast), things happen behind the scenes..
A short code snippet.

More Annealing

Some more detail here:
Here is a larger molecule, cembrane (pubchem link) which has 20 carbons. The run is longer, too, with 2,000 steps. It finds a spectrum with 100% match within 300 steps, in this case.
An even larger example is lanosterol (pubchem link) which has 30 carbons. This actually seems to be too large for C-NMR prediction using NMRShiftDB. It doesn't get the answer within 2,000 steps, and does not look like it is on course to do so:
The highlighted step (1928) is shown as a molecule in the box marked "final", but the score graph has levelled off by about the 400th step.

Adaptive Annealing Engine Test Screenshot

So, finally, some work that I am meant to be doing (click for bigger, as usual):

It's crude, but it is starting to work. The screenshot shows only the first 100 steps of a run, but clearly you can get the right answer (almost by chance, actually) for such a small molecule when you are essentially just permuting the atoms.
Now to test more fully...