Hi Dan<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
> Below you mention that you have two scoring functions almost ready...<br>
> which classes are they in? I'd like to work on trying to make them<br>
> implement the interface.<br>
</div>The package owl.decoyscoring contains some scoring functions,<br>
which were implemented by Jose based on your BMCBI paper.<br>
<div class="im"><br></div></blockquote><div><br>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. <br>
<br>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.<br>
<br>Whenever I get some time I will try to adapt the existing code to the new interface. It shouldn't be difficult.<br><br>Good luck<br><br>Jose<br><br></div></div>