In brief, NonbondedListScoreState is now an abstract class and the corresponding class is AllNonbondedListScoreScoreState. I don't like the name, so if you have a better one, please suggest it. I needed to have a base class for the lists so that I can implemented one which handles particles with varying radii nicely.
In more depth: 1) Better string handling in the exception base class
2) added bounds check on vector access
3) Refactored the non-bonded list code. There is a new internal class which implements a voxel grid for particles. There is also a base class for non-bonded lists which AllNonbondedList and BipartiteNonbondedList both inherit from. I also got rid of the subdir for the bonded lists and fixed various documentation. SConscipt files and IMP.h changes are not submitted.
Daniel Russel wrote: > In brief, NonbondedListScoreState is now an abstract class and the > corresponding class is AllNonbondedListScoreScoreState. I don't like the > name, so if you have a better one, please suggest it. I needed to have a > base class for the lists so that I can implemented one which handles > particles with varying radii nicely.
I guess one of us screwed something up with this refactoring, because the unit test for the bipartite nonbonded list fails now, at least on my Mac.
Ben
Strange, that test worked when I generated the patch :-) I'll see what is up.
On Feb 18, 2008, at 12:41 AM, Ben Webb wrote:
> Daniel Russel wrote: >> In brief, NonbondedListScoreState is now an abstract class and the >> corresponding class is AllNonbondedListScoreScoreState. I don't >> like the >> name, so if you have a better one, please suggest it. I needed to >> have a >> base class for the lists so that I can implemented one which handles >> particles with varying radii nicely. > > I guess one of us screwed something up with this refactoring, because > the unit test for the bipartite nonbonded list fails now, at least > on my > Mac. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
I must have just gotten luck (or unlucky to have the tests pass before). Here you go.
On Feb 18, 2008, at 12:41 AM, Ben Webb wrote:
> Daniel Russel wrote: >> In brief, NonbondedListScoreState is now an abstract class and the >> corresponding class is AllNonbondedListScoreScoreState. I don't >> like the >> name, so if you have a better one, please suggest it. I needed to >> have a >> base class for the lists so that I can implemented one which handles >> particles with varying radii nicely. > > I guess one of us screwed something up with this refactoring, because > the unit test for the bipartite nonbonded list fails now, at least > on my > Mac. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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