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r829
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Reconstructer.java 826 (10 years ago) by duarte: Now printing statistics for both lower and upper violations.
Embedder.java 821 (10 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.
BoundsSmoother.java 825 (10 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
Bound.java 802 (11 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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