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MAJOR CHANGES: - merge the changes from the jung-branch: *Pdb loading scheme together with new methods getChains(), getModels() - different exceptions
Moved DEFAULT_FORCECONSTANT up to TinkerRunner. New member variable defaultForceConstant in ConstraintsMaker
new methods getLastModelFiles and getGdtsToNative (using MaxClusterRunner)
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
Now parsing tinker's error function value, changed report file format (again!!)
Writing report to file instead of standard output Catching unknown errors in runDistgeom (all other non-zero exit values)
fixed bug when running distgeom, now waiting for process to exit before checking exit status
added error handling for killed tinker process with error code 139 (presumably out of memory)
Now capturing exit status 137 (2 instances of tinker running in same machine) Now outputting progress per model
Initial commit of reconstruct script. Works only sometimes!! Some others doesn't run distgeom without apparent reason! Throwing less exceptions in ConstraintsMaker
Moved tinker stuff to its own package
Initial commit of TinkerRunner and exception class to go with it TinkerError
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