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 ../ 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 821 (11 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. 825 (11 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 831 (11 years ago) by duarte: New experimental class Distiller 835 (11 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. 843 (11 years ago) by duarte: One more command line argument: contact percent sampling
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