ModPipe 2.2.0  11-01-2010:
 - Introduced flag to disable TSVMod calculation if needed
 - TSVMod scores are incorporated into ModPipe. Scores will be calculated
   for all structures. Additionally, when chosen as a gathering option, 
   models with a predicted no35>0.4 will be selected. 
 - PDB files are now also searched for in PDB-style subdirectories (e.g. PDB
   code 1abc will be looked for in the 'ab' subdirectory). If these PDB files
   are compressed (.Z, .gz, or .bz2) they will be automatically uncompressed
   when opened.
 - Change of the Gathering mechanism: GatherModMP.py script now has two modes:
   (i)local and global gathering using final_models_by and yaml files
   (ii)fast gathering by concatinating the local files
   ModWeb by default gathers local for every sequence and
   fast at the end of the job
 - ModBaseImport.py now inserts the run information after loading models
   and sequences, to avoid access in the middle of the loading process
 - GatherModMP.py also creates .fin files in sequence directores,
   which can be used by ModBaseImport.py and are default for ModWebd. 
 - ModWebd: jobs get moved to the current directory before running
 - ModWebd: uses enddatapath option in ModBaseImport
            Template based functionality implemented 
 - ModWeb_TemplateBased.pl submits a TemplateBased job to the cluster
 - StrucImpact.pl has been renamed to TemplateBased.pl
   It has been modified to separate the template and target
   part (different tmp directories and configuration files). 
   It can also be called with an option to only model the 
   sequences (from uniprot or input) using the input template. 
 - ModWeb.pl deletes any running sequence based SGE job if it is killed.
 - ModBaseImport.py: New option to copy relevant data from network storage to a permanent disk

ModPipe 2.1.3   06-03-2009:
 - Insertion codes (e.g. residue numbers such as 6A) should now be handled
   properly in PDB structures.
 - Bugfix: in MPModules.pm: Changed HitsPrfSeq.pl to HitsPrfSeq.py and
   adjusted options.

ModPipe 2.1.2   04-06-2009:
 - read_hits_file() and read_models_file() in the modpipe.serialize module
   now return generators, rather than lists. Hits and models files can contain
   multiple YAML documents.
 - Bugfix: GatherModMP.py now correctly clusters models by region.

ModPipe 2.1.1   03-31-2009:
 - main/AddSeq.pl has been renamed to main/AddSeq.py, and src/ConvertSeq.pl
   to src/ConvertSeq.py.
 - Bugfix: ModWeb no longer crashes if other than 3 options are given for
   'select models by'.

ModPipe 2.1.0   02-23-2009:
 - Changed GatherModMP.py to check whether the .mod file exists. 
   This could potentially get changed to print out which .mod files
   are missing (for resubmission)
 - Generated .mod, .fin, .sel and .hit (model and hit) files are now in
   YAML format.
 - main/BenchMark.pl has been renamed to main/BenchMark.py and
   main/GatherModMP.pl to main/GatherModMP.py.
 - PDB files generated by ModPipe now contain information on the ModPipe
   version used to build them.
 - Remove MODELLER option from configuration files; it is not used (ModPipe
   has its own copy of MODELLER in the ext/mod directory).
 - Several scripts now take positional arguments rather than "mandatory"
   options; e.g. "MakeChains.py [-p DIR] [-o FILE] pdblist" rather than
   "MakeChains.py [-p DIR] [-o FILE] -f pdblist".
 - Structure impact / Leverage. For a given new PDB structure ("template of 
   interest"), find a candidate set of UniProt sequences and model each with
   ModPipe. StrucImpact.pl is main routine; AugmentPDB.pl and GetFullSeqs.pl
   are subsidiary scripts; StrucImpactResults.py collates output.
 - Structure impact related change: add option to ModPipe to do modeling only
   if template of interest is among hits, and to retain template of interest
   after clustering.  Also accommodate option in WriteSGEMP() 
   (in lib/perl/MPLib/MPUtils.pm).
 - Structure impact related change: add options to GetProfile() 
   (lib/perl/MPLib/MPModules.pm).
 - Structure impact related changes: add FULLSEQDB (full UniProt database),
   XPRF_PIR (PDB95 structure sequences), and XPRF_DATDIR (directory of PDB95
   profile data) to conf file -- all optional (though required for
   StrucImpact.pl).
 - Structure impact auxiliary program: UniqueSeq.py - determines which sequences
   in file are unique within a specified percent identity.

ModPipe 2.0.2   12-09-2008:
 - It is no longer necessary to set the MODPIPEBASE environment variable or
   to run Modeller's modpy.sh script to use Python scripts; this is all set
   up automatically by ./Setup now.
 - MD5 sums of generated model (PDB) files no longer include the EXPDTA
   line. (This is because the EXPDTA line contains the time the model
   was generated, which changes on each run.)
 - Scripts use regular long options (-- prefix) by default, and all scripts
   should understand the standard --help and --version options.

ModPipe 2.0.1   12-05-2008:
 - Choose SEQID and MPQS as mandatory gathering options in MODWEB. 
 - Add ModWeb queue status page, and allow multiple jobs to run simultaneously.
 - Update Modeller to correctly handle sequence databases containing more than
   2^31 residues.
 - Add basic test suite ('make' in tests directory) to run as part of the
   nightly builds. Currently only reference outputs on synth are present.

ModPipe 2.0     10-09-2008:
 - Latest code from Eashwar. Version history prior to this point is unknown.
