../

Bound.java

802
(12 years ago)
by duarte:
Some big changes: now internally we use the data structure Bound[][] for all steps. We only use graphs for when we need to calculate shortest paths.
Define some static functions for printing info.
Made the scaling method an option passed as an argument to embed()
Extracted to separate file the Bound class.
Drafted an implementation of metrize

BoundsSmoother.java

824
(12 years ago)
by duarte:
Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization.
In metrize() final sampled matrix is now always reinitialising seed.

Embedder.java

821
(12 years ago)
by duarte:
New classes Reconstructer and ModelPdb. Reconstructer is a onestop solution for reconstructing from contact maps (RIGraph) using BoundsSmoother and Embedder. At the moment doesn't support reconstruction of contact maps with nonobserved residues.

Reconstructer.java

824
(12 years ago)
by duarte:
Fixed bug: was reusing the same bounds after every metrization in reconstruct(), now restarting from the initial bounds for each metrization.
In metrize() final sampled matrix is now always reinitialising seed.
