HahpMap keytype changed to Pair instead of String

print function

PrintOut method ion RIGGeometry

Getter for Atoms-TreeMap.

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.

Now getPdbResSerFromResSer and getResSerFromPdbResSer will return null/-1 whenever there's no mapping. Allows then for checking from the caller.

Deep copy method for Pdb, Residue and Atom. Tested only minimally, likely to have issues now or in the future. Needs a proper test case.

Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.

renamed  conflicting ContactMap class.

fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()

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

add psi/phi constraints from secondary structure to tinker reconstructions

New example implementation of ResidueContactScoringFunction

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

removing @Override annotations which were causing compilation errors for me

SecondaryStructure now implements Iterable after refactoring of getIterator

JPredConnection now returns a SecondaryStructure object; some updated javadocs

New interface ResidueContactScoringFunction to be used in CMView and for decoy scoring.

New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)

New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.

revert. wasn't the best idea.

adding phi/psi constraints to edges

Extracted the EC data parsing code to its own connection class.

Extracted Scop parsing code to its own connection class.

Extracted the CSA parsing code to its own connection class.

Extracted the calc-vol and calc-surf runner code to its own Runner class.

Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.

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.

bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found

Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 

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: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl

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

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core