Now elimination of redundant interfaces not based only on count of edges, but also on identity of each of the contacts (atom's serials, atom codes, residue serials, residue types). Added more test cases. Seems to be working fine.

added some javadoc

First implementation of enumeration of interfaces (based on crystal transformations), equivalent to PISA's. This is still a very rough implementation (far too slow) and not totally correct: some of the interfaces are duplicated. Needs more work but still good as a starting point. 

Scoring:KendallsTau-method added to  Statistics

Implemented inter-chain contact calculation (using same hashing algorithm as in intra-chain).

Implementation of class for KendallsTau Correlation Calculation
Implementation of class for Check for Correctness of Casp server model files
Implementation of class for Calculation of geometric scoring

actual version

Method to get translated and rotated coordinates.

adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.

HahpMap keytype changed to Pair instead of String

print function

PrintOut method ion RIGGeometry

Check for consistency in translation rotation framework.

Additional method for coordinate transversion.

New Residuescoringfunctionimplementation

Rotation and translation procedure transfered into extra class GmbpGeometry

RIGGeometry: class that computes and stores geometry information for graph based on rotation and translation invariant framework.

new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()

fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public

Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph

revert. wasn't the best idea.

adding phi/psi constraints to edges

new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)

adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()

New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.

refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker