[Owl-devel] new interface ResidueContactScoringFunction

Matthias Winkelmann matthias.winkelmann at gmail.com
Fri Apr 30 03:13:27 EDT 2010

Hi Dan,

I've implemented the DeltaRank scoring function which predates the new  
interface and is therefore not (yet)  using it. The code is scattered  
in a few classes in owl and CMView all having 'deltaRank' in the name.  
It does however require access to our DB.

You could probably more easily implement a simple statistical pairwise  
potential. I've calculated that data before and could mail it later  
(on the road right now).



On 30.04.2010, at 01:38, Dan Bolser <dan.bolser at gmail.com> wrote:

> Not sure if this is the right list to get into details on this, but  
> anyway...
> Sorry for the noob questions, I'm very new to Java / Eclipse. I have
> checked the project into my workspace, and navigated to the
> ResidueContactScoringFunction interface. When marked I hit ctrl-t to
> list the implementors (I'm very much at the stage where I need to
> stare at example code), however, nothing is listed. Is this because
> nothing yet implements the interface?
> 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.
> My goal is to be able to implement residue-residue scoring functions
> from the literature.
> Sorry for the basic questions!
> Dan.
> On 26 April 2010 12:22, Henning Stehr <stehr at molgen.mpg.de> wrote:
>> Hi all,
>> folllowing a discussion on cmview-devel:
>> There is now an interface ResidueContactScoringFunction in the new
>> package owl.core.structure.scoring.
>> The idea is to implement different scoring functions in this package
>> such that they can be used in a standard
>> way in CMView and any other projects which can make use of contact
>> based protein scoring. We have two such
>> scoring functions almost ready (in owl.decoyscoring) and DeltaRank  
>> and
>> GMBP could at least potentially also be
>> used in the same way. The nice thing is that once the basic
>> visualization code is implemented in CMView (which
>> is also in principle there and just needs to be adapted to use the
>> interface), new scoring function could easily
>> be plugged in and could then also be reused in other projects such as
>> decoy scoring.
>> So, please consider using this interface if you are working on  
>> scoring
>> functions in CMView or other projects.
>> Cheers,
>> Henning
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