Some Stuff

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.

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...

This is a better picture of what the dependencies were like in bioclipse: The dashed lines indicate some kind of vague boundary between plugin 'layers'. There's no such concept of a plugin layer, as far as I know, but still. Of course, there is the net.bioclipse.core plugin, which could be considered to be an inner core. It may be an artificial distinction to make between the 'data' and 'analysis' layers, but basically the data plugins do the open-edit-save cycle mentioned here  while the analysis plugins do more. Specifically, the seneca and medea plugins can produce spectra data from molecule data.

More pictures, mainly for my own benefit. First, a possible refactoring of some bioclipse modules: Where boxes are modules, and lines indicate dependencies. There's a lot of work in that arrow! Only the compute plugin and the seneca plugin have been ported (however incompletely) so far. The second image shows the extension points for the putative CASE plugin. One is the judge extension point that already exists in the seneca plugin, and the other is a structure source: This is more general than just a structure generator extension point, and could also include sources from files or databases. I think that this makes sense...