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r869
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Bound.java 802 (10 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
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.
Reconstructer.java 831 (10 years ago) by duarte: New experimental class Distiller
SetScore.java 835 (10 years ago) by duarte: Changed scoring: from sum(upi-ui)2 to sum of max(0,upi-ui). New methods to write subsets to files in table (tab delimited) format. Now main() writes out all scores/subsets to two files instead of only outputting best, worse and ensemble of bests. Moved ScoreSet to its own file, new static methods to read subsets from db.
Distiller.java 853 (10 years ago) by gmueller: distance map and contact map error function
BoundsSmoother.java 855 (10 years ago) by gmueller: new class for some evolution
Scorer.java 855 (10 years ago) by gmueller: new class for some evolution
Population.java 858 (10 years ago) by gmueller: new class to deal with arrays of Individuals class, provides methods to generate new arrays of Individuals
CorrelationFunction.java 860 (10 years ago) by gmueller: class to estimate the correlation function to a given error function, deals onlz with Population arrays
Individuals.java 861 (10 years ago) by duarte: Fixed +1 issues
(Current path doesn't exist after revision 950)
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