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refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
new class for some evolution
distance map and contact map error function
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
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.
Now printing restrains viols and bounds viols.
Now Reconstructer can also take RIGraphs with "unobserved" residues (i.e. with missing nodes). Model pdb files that Reconstructer creates now contain strictly only CA atoms.
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.
Made Bound[][] bounds a member, thus changing the signature of most methods. Refactored getBoundsAllPairs(bounds) to better name computeTriangleInequality: now it uses as input the bounds member variable and updates it as output.
Fisrt full implementation of metrization
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
Introduced scaling of the embedded coordinates (first good embedding ever!!) Make the random generation more consistent. Also introduced for debugging a fixed seed.
Fixed in BoundsSmoother: now the lower bound will be set to the triangle inequality value only if the newly found lower bound is bigger than the hard spheres bound. Now we also introduce contiguous CA distance constraints (3.8) In main now checking for violations to the full bounds matrix. New method in Pdb for getting distance matrix as Jama object
New method in Pdb to set atoms for all coordinates of a given atom. Used in BoundsSmoother and Embedder mains. Changed slightly how parameters are passed in BoundsSmoother.
Lower bounds bounds-smoothing now also implemented (using Dijkstra's shortest path algorithm and offsetting to avoid negative weights).
First implementation of BoundsSmoother. Does only bounds smoothing through triangle inequality for the upper bounds (for lower bounds just takes a hard-spheres distance value)
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