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.

Delta Rank

Fixed bug with notifier (only used from CMView). Now if null it will be skipped.

merged tinker changes into trunk

Fixed bug: was not handling correctly sequences with 'X' in reconstruction
Fixed bug: Pdb.getPhi/Psi were failing because hasCoordinates(int,String) was NullPointing for unobserved residues. 
Added test case for getAllPhiPsi

Major change: now hydrogens are read in Pdb and subclasses
New getChirality method in Residue.
Added some more unit tests.

Introduced some more checks for validity of contact types.

Introduced a delay between runProtein and runXyzpdb in reconstruct to make sure when we run xyzpdb the file is there: we try to find xyzFile a few times with a delay between retries.

Fixed bug: wasn't checking exit value of protein, xyzpdb and pdbxyz. Now throwing exception when exit value not 0.

Fixed bug (hopefully): was not closing drmaa session after every runParallelDistgeom, only in the shutdown hook. We need to close it always in case there is more than one run within the same instance of the JVM.

Implemented a more robust approach to failure of jobs in parallel distgeom. Now we send 1.1*n jobs and require that only n of them finish successfully. These solves many issues: even if 0.1*n jobs fail the whole thing will be successful, if a jobs hangs forever we will not wait for it to finish.

Fixed bug: now parallel distgeom works even if a relative path  specified in caller script.

Implemented shutdown hook. Now all jobs killed upon CTRL-c.
Now submitting directly the distgeom binary without needing writing a shell script. That removes the dependency on java6 (needed for set execution permission on the shell script). 
Introduced (but not in use yet and not fully implemented) the submission of more jobs for failure tolerance.

Some minor fixes and cleanup. Changed timeout to 2hours.

Better error messages

Fixed bug: now correctly capturing exit state. Correctly cleaning up (killing jobs) after a failure. Closing the drmaa session properly.

Implemented first version of a parallel (using distributed distgeom jobs through sge) reconstruction. Experimental so far, not well tested.

New method geometrizeContactMap

Better implementation of getViolatedEdges

Added static method to report violations.

Removing test commit

Test commit

New option -s to do split output. 
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)

Initial commit of script and classes to interface with gromacs.

New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond.
New method in Pdb: getOmega

Changed default force constants to tinker's defaults ones (100.0 for distances and 1.0 for torsions). Reconstruction from averaged graphs was not working well sometimes, with really bad clashes. We think the distance force constant=10 was causing this.

Fixed bug: can't assign phi/psi torsion angle restraint to first and last residues.

Added phi/psi angle constraints to the reconstruction pipeline. New option -F in averageGraph for using phi/psi angle constraints

Added members and method to ProtStructGraph and Pdb to write AUTHOR and METHOD fields to Casp files. Added missing reconstructFast methods to TinkerRunner.

Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

Introduced another check in runMinimize: now we check for CHKXYZ warnings, that happened when the xyz file is somehow not well formatted. In some cases that leads to strange output in minimize.

New feature in TinkerRunner: now it can run "analyze" and "minimize" programs from the tinker package
Fixed some bugs and improved TinkerRunner: 
- flushing instead of closing the log PrintWriter when throwing TinkerError exception. Before it would close and nothing more would get logged after the first error.
- now writing command line to log
- now flusing at the end of each runXXX() method
New script computeEnergies for calculating energies of a set of decoys using tinker.

Added a FAST switch to reconstruct and a reconstructFast method in TinkerRunner: without simulated annealing tinker runs much faster.

Fixed mega-nasty bug: after introducing the PRMType enum, there was still one instance of the "type" variable being compared to a String in getCorrectedPdbAtomName method

some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)

New option in reconstruct: -f force constant. New constructor in TinkerRunner that takes the force constant, previous constructor will work as before with the default constant.

Copied the aglappe-jung branch into trunk.

T

Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph
Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise
Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0

Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)

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

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)

Doing more input error checks
In ConstraintsMaker createConstraints won't throw Exception anymore, we only assery that ALL can't be used

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

Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"

Now does correct atom mapping for any atom of any residue ONLY for amber prm files
createConstraints does not work yet with multi atom contact types
Got rid of all the commented out mapAtoms code + some refactoring

First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo

Moved tinker stuff to its own package