[Owl-devel] new interface ResidueContactScoringFunction

Henning Stehr stehr at molgen.mpg.de
Fri Apr 30 03:27:12 EDT 2010

Hi Dan,

> Not sure if this is the right list to get into details on this, but anyway...
I always knew this would cause some confusion. Basically, you can assume
that any CMView developer will also be subscribed to owl-devel, because
CMView is so much based on the owl library. Since scoring functions are
of general interest, this is exactly the right place.

> 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?
That's exactly right.

> 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.

> My goal is to be able to implement residue-residue scoring functions
> from the literature.
Thanks for contributing to open source software :)


> 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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