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First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Re-branching for JUNG2 development
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object; updated reconstruct.java to make use of the new TinkerRunner method; updated GraphAverager: now assigning edgetype and cutoff to consensus graph
Fixed (yet again) the report output, now also outputting size (number of residues) of protein
Now parsing tinker's error function value, changed report file format (again!!)
Changed name of native output pdb file
Now writing also original pdb file Fixed output of rmsd: now only few decimal figures output
Now tinker.log has also baseName in file name
Writing report to file instead of standard output Catching unknown errors in runDistgeom (all other non-zero exit values)
Doing more input error checks In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used
cathing InterruptedException from TinkerRunner
Fixed the output
Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason! Throwing less exceptions in ConstraintsMaker
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