 ../
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Bound.java
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802
(13 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
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BoundsSmoother.java
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825
(13 years ago)
by duarte:
Fixed bug: this time really fixed bug from last revision. Now references of the bounds arrays are properly handled (hopefully!). Tests seem correct: now the output models when metrizing seem not to be correlated anymore
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Distiller.java
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832
(13 years ago)
by duarte:
Changed the scoring so that is an error function: now it is the average sum square upper bounds deviation from the contact map. A perfect fit to the contact maps is err=0.
Cleaned up, refactored and documented.
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Embedder.java
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821
(13 years ago)
by duarte:
New classes Reconstructer and ModelPdb. Reconstructer is a one-stop solution for reconstructing from contact maps (RIGraph) using BoundsSmoother and Embedder. At the moment doesn't support reconstruction of contact maps with non-observed residues.
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Reconstructer.java
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831
(13 years ago)
by duarte:
New experimental class Distiller
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