[Owl-devel] new interface ResidueContactScoringFunction

Dan Bolser dan.bolser at gmail.com
Fri Apr 30 16:39:14 EDT 2010

On 30 April 2010 08:13, Matthias Winkelmann
<matthias.winkelmann at gmail.com> wrote:
> 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).

Cheers Matthias,

Sorry for the basic question, but is there a way to search for classes
with 'deltaRank' in the name from within eclipse? I can't seem to find
a way! (I've found DeltaRank.java)

Right now I'm more interested in learning about code rather than
generating scores, however, I would be interested in looking at your
pairwise potential data if you don't mind :-)

> Best,
> Matthias
> 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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