[Owl-devel] new interface ResidueContactScoringFunction

Jose M. Duarte jose.m.duarte at gmail.com
Fri Apr 30 06:34:08 EDT 2010

Hi Dan

> Below you mention that you have two scoring functions almost ready...
> > which classes are they in? I'd like to work on trying to make them
> > implement the interface.
> The package owl.decoyscoring contains some scoring functions,
> which were implemented by Jose based on your BMCBI paper.
You can try to run the scoreDecoys class from the default package (right
click and Run As Java Application). That will give you a taste of what the
decoys scoring does.

Actually you will first need to compile the scoring matrices. For that you
need to run ResCountScorer or ResTypeScorer classes from the decoyScoring
package (you'll need pdbase but you can tunnel that). Once you have the
scoring matrices you can then run the scoreDecoys executable.

Whenever I get some time I will try to adapt the existing code to the new
interface. It shouldn't be difficult.

Good luck

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