Changes from 2.32 to 2.33

-->  2.33 released 2013/01/09

Helper Scripts

  bin/calcSARDC
    added -singleEns option 

  bin/contactMap
    a new helper to visualize intramolecular contacts.

  bin/ens2pdb
    added support for EnsembleSimulation members specified using a wildcard

  bin/getBest
    added the -wildcard option to specify ensemble simulation members

  bin/pyXplor
    fix to allow empty string command-line arguments

  bin/pbsxplor
    -modified to get log file in the current working directory.
    -added the -jobs_per_node option to be able to manually control
     the number of processes run on each node.
    -now support Torque -f option for fault tolerance.
    -updated to work on Altix under PBSPro using the SGI-specific
     cpuset command.  On that platform, jobs should be launched using
     the ncpus resource to specify the number of cores.

  bin/ramaStrip
    a new helper to help quickly evaluate Ramachandran quality of a
    large number of structures. Based on torsionDBPot.

  bin/xplor
    -fixup for bad versions of ``which'' which print errors places other
     than stderr  
    -fixup in allLocal determination logic
    -fix to allow empty string command-line arguments

Example scripts

  eginput/gb1_rdc/refine.py
    replace RAMA with torsionDB

  eginput/pre/refine/newRefine.py
    change tuples to lists s.t. things work if only a single expt. 

  eginput/PSF_generation/genLigand.py
    fixed so that it works with the HEME example in the tutorial

Python Interface

  python/ensembleSimulation
    added memberFromSimulation - to subclass a Simulation ->
    EnsembleMemberSimulation 

  nmrPot/nbTargetPot.cc
    bug fix in the neighbor search. This should prevent a progressive
    degradation in performance during a calculation.

  python/noePotTools.py
    create_NOEPot: added optional verbose argument

  common/potList.cc
    PotList::rms(): fix treatment when all terms are negative

  python/prePotTools.py
    -getNucleusType: change heuristics to query residue name. Now much
     more robust.
    -create_PREPot: added verbose argument

  python/prePot
    instantiate the base case Restraint<PREPot> to get its methods

  python/protocol.py
    updatePseudoAtoms: better handling for default sim values 

  nmrPot/psolPot
     -now uses SurfTesselation, surface integral integral evaluation,
      instead of volume integral.
     -working approximate surface integral gradient

  python/pyXplor.cc
    when handling -c from the command-line: now correctly include the
    rest of argv - needed by idle

  nmrPot/rdcPot1
    -showViolations: now print contribution from each atom pair in all
     ensemble members 

  python/regularize.py
   fixupCovalentGeom: changed default sel argument to omit pseudoatoms

  python/restraintStats.py
    RestraintStats now supports to optional potential term members:
    noPotSummary and noViolationStats to suppress unwanted output.

  python/selectTools.py
    added threeToOne function for residue name conversion.

  python/simulation.i
    -rationalized derived/base relationship between Simulation and
    classes which derive from it.
    -__eq__, __ne__: now handle case of simulation compared with other type 


  python/simulationTools.py
    -StructureLoop: 
      *new argument: pdbFilesIn: if specified, a coordinate file
       will be read in before each call to structLoopAction. This allows
       easier parallelization over a list of arbitrarily named input
       files, for analysis and validation. 
      *added mechanish to pass back arbitrary (pickable)
       data from structLoopAction to process 0 by writing to the
       sharedData member.  
      *added the pdbFileIn method, returns the current input structure
       file name.
    -StructureLoop.makeFilename: added optional memberNum argument to
     override default  
    -StructureLoop.run: change behavior if calcMissingStructs and
     doWriteStructures are specified: now read in pre-existing
     structure and rewrite them, to make re-analysis
     easier. 
    -StructureLoop.writeStructure: extraRemarks can now be a sequence
     of strings  

    -flattenPotList: 
      *added argument: includePotLists. If true, return
      (non-toplevel) potlists in addition to individual pot terms.
      *now flattens any type of potential which is iterable (instead
       of only PotLists).

  python/socketComm.py
    collect/distribute: added calls to barrier() at start to update keys

  python/torsionDBPotTools.py
      -Removed class TargetTorsionPot from torsionDBPotTools module
      -torsionDBPotTools module: added TargetTorsionPot class
  python/torsionDBTools.py
      -python/torsionDBTools.py: some fixes associated with the
      introduction of nucleic info 
      -python/torsionDBTools.py: added definitions of nucleic
       (pseudo)torsion angles 

  python/torsionDBPotTools.py
      create_TorsionDBPot: got rid of reporting # of terms generated
      if SimulationWorld_world().logLevel()==none  

  python/torsionDBPotTools.py
      torsionDBPotTools module: added analyze function

  nmrPot/torsionInterpolPot.cc
  nmrPot/torsionInterpolPot.hh
  python/torsionDBPotTools.py
  python/potList.i
  python/restraintStats.py
      Added noPotSummary member data to torsionInterpolPotND (N=1,2,3)
      and torsionDBPotTools.TDBPotl 
      Merge from /home/schwitrs/xplor

      python/torsionInterpolPotTools.py
  python/varTensorTools.py
      torsionInterpolPotND (N = 1,2,3) added violations() member function

  python/torsionDBPotTools.py
      torsionDBPotTools: subclassed potList.PotList and used instances
      to pack the terms; this is to facilitate violation analysis 

  python/torsionDBPotTools.py
      Added elevel entries to torsionDBPot database files and modified
      create_TorsionDBPot and setup_pot functions (torsionDBPotTools
      module) to read them and set thresholds 

  nmrPot/torsionInterpolPot.cc
      TorsionInterpolPotND constructor initializes threshold() to
      1e30; TorsionInterpolPotND_Restraint energy member funct. sets
      diff_ to the unscaled energy (N = 1,2,3) 

  nmrPot/torsionInterpolPot.cc
      TorsionInterpolPotND_Restraint (N = 1,2,3) now uses name()
      member function inherited from Restraint; relative to the
      previous commit this one works 

  nmrPot/torsionInterpolPot.cc
  nmrPot/torsionInterpolPot.hh
      TorsionInterpolPotND_Restraint (N = 1,2,3) now uses name()
      member function inherited from Restraint 

  python/torsionTools.py
     -setTorsions function no longer accepts
      reference to angles by name (e.g. phi)

  python/varTensorTools.py
    calcTensor_ensemble: added the optional selection argument updated
    to work for inhomogeneous ensembles with nonuniform weighting
    updated to support pairwise averaging  

  python/waterRefineTools.py
    buildShell: fix to deal with >10 water boxes in a dimension. 
    Also now gracefully exits if too many water boxes are required. 

  python/xplorInit.py
    added the -- option to stop command-line option processing

  python/xplorSimulation
    getXplorSimulation: fixed to work for EnsembleMemberSimulations


Architecture-specific changes

  arch/Linux_x86_64/include/alignof.h

  arch/ARCH/include/alignof.h
    added platform-specific alignof.h which implements __alignof__

  arch/Darwin_10_x86_64/intVar/Makefile
     reduce optimization for 2011 and 2012 versions of Intel
     compiler. This may not be necessary for 2013 version...  

  arch/Linux_x86_64/source/Makefile
    update (optimization downgrade) to get gcc-4.7 working

  arch/Darwin_8_ppc/Makefile.defs
  arch/Darwin_8_x86/Makefile.defs
    added excluded (system) libraries

  arch/Linux_x86_64/Makefile.defs
    do substring match for easier alternate gfortran/gcc version spcification



Low-level Functionality

  common/atom
   added bondedTo method; added cdsMapConvertToInt so Atoms can be CDSMap
   keys

  common/atomSel.hh
    added (read-only) iterator support

  CDSlib/cdsComplex.cc
    add unary minus

  CDSlib/cdsIterator.hh
    Iterator: changed _container type to pointer; added default
    constructors; partial documentation 
  
  common/modified.hh
      Modified- now allow argumentless constructor- for use without
      ModifiedBase 

  common/pot
    Pot::violations now floating point value s.t. AvePot can report on
    EnsembleSimulation violation averages

  common/relAlloc.cc
    a very simple heap allocator to be used for shared memory
    allocations. 

  common/xplorSimulation.cc
    pad4: now use snprintf instead of sprintf to avoid very unlikely
    buffer overrun.  

  CDSlib/mat3.hh
  CDSlib/vec3.hh
  nmrPot/utils.hh
      moved crossMat from vec3.hh to mat3.hh; moved outerProd from
      utils.hh to mat3.hh; these changes forced additional includes 

  surfD/
     -removed unused methods, functions
     -clean up
     -Surf:
        *renamed Max_Tess_Len to maxTessLen accessor
        *renamed struct SurfacePointOut to AtomPoints
         in this struct replace in At_nmbr member with atom 
        *renamed out_spt member to atomPoints
        *new method calcSA for calculating surface area for an existing
         tessellation. 
     -converted Surf::atoms to CDSList, removed Num_atoms member
     -changed type of SurfacePointOUT::Sum
     -SurfacePoint:
       *added delta member, dCoord method
       *replaced At_nmbr index with Atom 
     -Tessel::gen_tris: 
        removed calculation of surface area. 

  nmrPot/relaxRatioPot
      added use of retessellateIfNecessary instead of direct call to calcSurf


  nmrPot/diffPot
     -calcEnergyAndDerivs: now increment retessellateCount
     -now use SurfTesselation helper methods to reduce code duplication
     -removed surfDiff member from SurfTessellation, added to DiffPot,
      RelaxRatioPot 

  nmrPot/surfTessellation
     -SurfTessellation: shuffled members to simplifiy retessellation,
      cuttoff recalculation logic 
     -added retessellateIfNecessary method to encapsulate normal
      calling logic 
     -removed use counter stuff
     -added verbose member

 bin/findSwig
    added 2.0.8 

  tcl/Makefile
    swig fixes

  tcl/findTCL
      added logic to use $tcl_library to search for the include dir 

Databases

  databases/torsions/protein/top8K_bb/
      Added databases/torsions/protein/top8K_bb/ for protein backbone
      validation with multiple elevels in each file

  databases/torsions/protein/top8K_v0
     Renamed files in databases/torsions/protein/top8K_v0/ and
     explained elevel in databases/torsions/README.format 





		     Changes from 2.31 to 2.32

-->  2.32 released 2012/09/06

Documentation

  helplib/faq/node0600.txt
    include final resid in dimer restraints

  doc/python/index.html
    updated base Python documentation link 

  doc/xplor/manual_ypress.tex
    again corrected switching function definition (eq. 4.9 in the
    XPLOR manual)  


Example Scripts

  eginput/gb1_rdc/analyze_ProbDistPot.py
    fixed typo in atom selection

  eginput/saxs_EI/testCalcTensor
    added calcTensor test with segid-less restraints for symmetric dimer

  eginput/PSF_generation/genCircPep.py
    modernized and made to work

Topology/Parameters

  toppar/CNS/
    added recent CNS topology/parameter files

Python Interface

  python/findPython: now support version 2.7

  python/atom.i
    added __ne__ method

  nmrPot/noePot
    to the Restraint class, added method:
      bestPair() - for ASSIgn ... OR restraints, the (zero-offset) index of the
                   selection pair which gives the smallest energy contribution.

  python/pcsTools.py
    added pcsTools module (contributed by M. Stanton-Cook)
    This includes the calcXTensor function for calculating the delta
    chi tensor (alignment tensor and paramagnetic center).

  python/protocol.py
    initParams: added optional string argument

  nmrPot/psolPot
    fixed setRp() accessor to calls setRadii()
    changed restraints to be rc pointers

  nmrPot/rdcPot1
    added Restraint::setErr() accessor

  python/residueAffPotTools.py
    added reference 

  nmrPot/sardcPot
    added optimizeScale accessor, allow avectorScale to be set

  python/simulationTools.py
    StructureLoop:
      -added doWriteStructures to obviate the need for writeStructure in
       structLoopAction.
      -added calcMissingStructs boolean to indicate that only non-present
       structures are to be calculated.
      -pdbTemplate now takes a default value.
  
        eginput/gb1_rdc/refine.py now uses these three changes.

    StructureLoop.genAveStats: initial barrier: disable the
     timeout. Will now block for all processes to compute structures.

    added sortFilesByEnsMember- used to match ens weights with proper
    filename 

  python/socketComm.py
    Comm.barrier: fixed logic problem for timeout==None 

  python/torsionDBPotTools.py
      create_TorsionDBPot: 
        optimized for much faster initialization.

        parse_metaselection now returns smaller selection string (when
        resid=False) and handles input list (when resid!=False)

        now counts and reports potential types.

      The format of the database files has changed. See
          databases/torsions/README.format


  python/torsionInterpolPotTools.py
    new module to be used for splined torsion angle energy terms.

  python/torsionDBPotTools.py
    create_TorsionDBPot: increase verbose verbosity

  nmrPot/varTensor.cc
    setDa: make error message more informative

  python/varTensorTools.py
    calcTensor: 
      -added the optional svdTolerance argument
      -fixes for dealing with RDC averaging, deal with singular SVD
       values; will now work for symmetric dimers with a single set of
       restraints  

TCL Interface

  tcl/findTCL
    added tcl/tk version 8.6

Helper Scripts/Programs

  bin/calcSARDC
    added a helper program for calculating steric alignment rdcs given
    table and structure 

  bin/calcSAXS
   -when -exptPointsSpline is specified, now compute the second chi^2
    value using just these points using splined calculated
    values. Previously, we always evaluated chi^2 at the calculated
    points, linearly interpolating the data. The new approach is much
    more stable with respect to changing numQ.  
   -input files are now sorted by ensemble member so that weights can
    be matched to structures.

  bin/pbsxplor.in
    mod to allow = character in filenames

  removed bin/xplor_mpi 
    it was not used for anything

Low-Level Libraries

  alloc
    quieted test output

  cminpack
    tests updated to self-test results and be quieter by default.

  common/atomSelLang
    allow + characters in atom selection strings

  common/atomSelLangYacc.y
    fixed bug where single # was not recognized as a wildcard

  bin/findSwig
    updated for swig 2.0.7


Architecture-specific changes

  arch/Darwin_12_x86_64
  arch/equivList
    added entries for Darwin 12 - thanks P. Mercier

  parallel.txt
    updated for current situation on modern Darwin

  arch/Darwin_10_x86_64/Makefile.defs
    OMITTED_SHARED_LIBS: many additions due to change in toplevel Makefile

		     Changes from 2.30 to 2.31

-->  2.31 released 2012/05/16


Python Interface

  nmrPot/atomProb
   now expose the val(i,j,k) method to Python
   autoExtent: now include a list of coordinates (corresponding to an
   	    ensemble of structures) to check when generating grid
   	    extent.

  nmrPot/distSymmPot.cc
    showViolations: fix the id field in the output

  nmrPot/noePot
    changed members d, dMinus, dPlus and comment to accessors to allow
    setting 

  nmrPot/posSymmPot
    -now supports EnsembleSimulations
    -added variance tensor (ORTEP) component for ensembles
       (enabled by setVarScale(1))
    -removed the single-atom selection sets for simplification.
    -added addEquivAtoms - 
      takes selection strings for arguments, needed for 
        inhomogeneous ensembles 
    -added member gamma, and made fixes to always maintain proper rotation
         matrices (determinant=1)

  nmrPot/relaxRatioPot
    -added Restraint subclass
    -renamed some accessors:
      getMedianTmp --> medianTmp
      get/setFr --> freq/ setFreq
      change name rot_Mtrx --> rotMat
    -added cutoff() read accessor
    -removed selection() accessor- this can be obtained from
     selection()->string() 
    -added violations(), showAllRestraints - violated_ is now set
    -now cache more values to prevent recalculation
    -now pairwise due averaging over atom selections

  nmrPot/sardcPot
    added Restraint::setErr and test

  python/cdsMatrix.i
    added SymMatrix +-* methods

  python/diffPotTools.py
    RelaxData: now support NOE field and leading hash comments

  python/ensembleSimulation.i
    added __eq__ and __ne__

  python/ivm.py
    added the time() and iter() accessors

  python/noePotTools.py
    splitTable: 
      -fixed selection of short range restraints (changed < to <=) 
      -fixed bug where an ambiguous restraint was also classified as
       short range.

  python/posDiffPotTools.py
    fixed setup for EnsembleSimulations

  python/protocol.py
    matchInexactAtomEntry: 
      -leading/trailling segid whitespace is not significant  
      -added missing simulation argument from an AtomSel- atoms were
       not matched in noncurrent Simulations.   
    initCoords: fix for deleted bfactors, occupancies if
      deleteUnknown=True and loading from a noncurrent Simulation.  

  python/psfGen.py
    pdbToPSF: 
      -improved documentation. 
      -now pdbRecord arg is optional 
    addDisulfideBond:
      added option to treat a disulfide as a distance restraint 
    pdbToSeq:
      -now raises custom exception if seqs is empty before returning 
      -now strip leading/trailing whitespace from segid
    cisPeptide: 
      updated to deal automatically w/ multiple segids

  python/rdcPotTools.py
    added chi2 function, ExtraStat

  python/regularize.py
    fixupCovalentGeom: always set mass>0, even if not doing dynamics 

  python/relaxData.i
    broke out the RelaxData into a separate relaxData module

  python/relaxRatioPotTools.py
    analyze:
      now print out per-restraint information

  python/sansPotTools.py
  python/solnScatPotTools.py
  python/solnXRayPotTools.py
    create_ helpers:
      added minQ parameter/argument

  python/sardcPotTools.py
    added chi^2, rmsd functions
    Rfactor: add support for sub-selection

  python/selectTools.py
    correctSymmetricSidechains: 
      -better handle missing atoms
      -now checks angle is inside range *after* correction and reverts
       it if farther away  

  python/torsionDBPotTools.py
    torsionDBPotTools module: updated torsion angle database potential
    currently for proteins only.

  python/varTensorTools.py
    saupeToVarTensor: now return ensemble VarTensor - to support
                      ensembles of Saupe matrices.

  python/varTensorTools.py
    added pairwise averaging to RDCPot. 

  vmd/publicVMDInter
  vmd/vmdInter
    added the reap method to clean up thread environment

  vmd/thread.cc
    wait: now reset tp member to 0 so pthread_join does not get called twice


Fortran Interface

  source/comand.fcm
  source/symbol.fcm
    increased maximum line length to 512 characters

Common Low Level Libraries

  CDSlib/fixedSymMatrix
    added operator*(mat,symmat) operator*(mat,symmat) and test

  CDSlib/symMatrix
    added operator+/-(SymMatrix,SymMatrix) and tests

  common/atomSelLang
    -atomSelLang: added support for ranges for index and id properties
    -made attr >=/<= actually work


  common/ensembleSimulation.cc
    added getEnsembleSimulation static function

  common/pdbTool.cc
    write(): added TER after final structure if writeChainID==True

  nmrPot/utils.hh
    moved outerProd to utils.hh

 many files:

   various changes to silent gcc -Wall
   the most important being changing 
     Simulation::type and Simulation::name from char* to String
     UNUSED was added to sthead.hh to demark (sometimes) unused
   functions.

TCL Interface

  tcl/import_nmrstar.tcl
    formatting (whitespace) changes 

  tcl/findTCL
    updated to deal with system Darwin installations

Helper Scripts/Programs

  bin/calcSAXS.in
    added minQ parameter/argument

  bin/calcTensor.in
    -added pairwise averaging to RDCPot. 
    -added chi^2 to output

  bin/getBest
    added the -members command-line option 

  bin/xplor.in
    add quotes around $USER in case it is not set. 


Architecture-specific changes

  arch/Darwin_10_x86_64/source/Makefile
    Intel compiler updates - thanks to P. Mercier

  arch/Darwin_10_x86_64/Makefile.defs
    updated omitted lib list

  arch/symlinks
    updated for Darwin 11

  arch/Linux_x86_64/Makefile.defs
    -OMITTED_SHARED_LIBS: removed libresolv - problems on Ubuntu
    -updated for old versions of gnu make

		     Changes from 2.29 to 2.30

-->  2.30 released 2012/01/26

Example Scripts

  eginput/PSF_generation/genLigand.py
    added proper masses

  eginput/assignFit/02refine.py
    changed the random seed... so that subsequent 03assignFit succeeds


Fortran Interface

  source/fxrefin.f
    catch overruns in bessel function lookup array

  source/fxmap.f
  source/xmap.f
    fix old(?) bug: not enough args in wrtitl

  source/comand.fcm
  source/parser.f
  source/xplorFunc.f
    fixed memory growth problem caused by repeated calls to
    xplor_parse() from xplor.command().
    
    The command buffers grew without bound. 
    
    Now, there are two buffers, one used if the qsubshell argument is true
    and the other if it is false. This safely allows XPLOR --> Python -->
    XPLOR calls. Also, if qsubshell is true, the buffer indices are reset
    to 1, so memory use no longer grows without bound.
    
    The BUFSTK variable has been removed- this is a vestige from the
    ``rotating'' command buffer.


TCL Interface

  tcl/aeneas_tools.tcl
    standardJointFilter: added -primarySequenceDistanceFilter flag to
    (optionally) filter out all other assignments if an intra-residue
    assignment is a possibility.  

  tcl/import_pipp.tcl
    process2dPippPeakTable: added the -intensityThreshold option

Python Interface

  python/cdsVector
    added __radd__ __rsub__ __rmul__ __rdiv__

  nmrPot/distSymmPot.cc
    allow atoms to be missing in some ensemble members

  common/ensemblePot
    added the ensWeights() read accessor
    ensWeight() read accessor: added a default memberIndex value

  common/ensembleSimulation.cc
    fixed invalid reference to sim pointer

  python/ivm.py
    ivm fixup for translate + torsion topology

  python/planeDistTools.py
    added a call to protocol.updatePseudoAtoms()

  python/regularize.py
    covalentMinimize: the meaning of the selection argument had been reversed! 

  nmrPot/sardcPot
    -fixed bad ensemble weighting booboo
    -fixup to consistently use pot->ensWeight instead of member->weight
    -added the Dmax() accessor
    -added PAIRWISE averaging, test

  python/sardcPotTools.py
   -saupeMatrix: this now returns something, but needs testing. 
   -added useSign arg default val
   -fix to deal w/ ! comments and properly deal w/ nonmatch condition

  python/simulationTools.py
    StructureLoop: added the structInfo member 

  python/trace.py
    class Trace: added method run()

  python/xplorInit.py
    fixes s.t. cwd is last in the Python load path
      (also changes in bin/xplor.in for this)

  python/varTensorTools.py
    -saupeToVarTensor: updated to take optional Dmax argument so that 
     proper (not scaled by Dmax) Saupe matrices can be input. 

Helper Scripts/Programs

  bin/calcTensor.in
   added -plot option, facility to plot calculated vs. observed correlations 
   including error bars representing spread in calculated values 

  bin/ens2pdb.in
    initCoords: disable maxUnreadEntries check
    -missing atoms are now deleted, so that invalid coords aren't printed
    -the -delete command-line option has been added

  bin/xplor.in
   -quiet output of ipcrm - so no program or people get confused. 
   -fixups for case when num_threads > number of cores on a numa node. 
   -added smarts for better dealing with the case of the number of
    processors on a numa node is not an even multiple of
    NUM_THREADS. Previously, numa nodes would be under/oversubscribed in
    this circumstance.  
   -fixes for mixed localhost remote.host localhost specifications of
    machines: to get process id correct.  

  bin/calcSAXS.in
    add an EnsembleSimulation.sync() after deleting atoms- otherwise
    confusion ensues if atoms are really deleted and Ne>1.

  bin/getBest
    fixed -all to work with ensembles with more than 10 members 

  bin/pbsxplor.in
    now generate a default output (log) file from the input script filename


Documentation

  helplib/nih-py-csaPot
  python/csaPotTools.py
    update concerning units 

Low Level Libraries

  CDSlib/cdsSStream
    fixed IStringStream str() members

  common/mmapMalloc.cc
  alloc
   -reworked MMapMalloc to use alloc from Rusty Russell. Previously,
    fixed-address mmaps were used, and ensemble simulations would
    sometimes crash, particularly for heterogeneous ensembles.


  nmrPot/ Potentials:
    make error message (when reading restraints) less confusing and
    deterministic:
      fix behavior of hitting nonfatal error when reading restraints:
        the remainder of the restraints would not be read. 
      fixed by clear() ing the input stream.

  added another supported swig version

  Added support for python2.7 

  arch/Makefile.common
    add: if DEBUG==1, add FFLAGS_NOOPT to FFLAGS

Architecture-specific

  arch/Darwin_10_x86_64/surfD/Makefile
    updated optimization reduction
  arch/Darwin_10_x86_64/source/Makefile
    updated gfortran-4.6 options - thanks to J. Howarth
  arch/Darwin_10_x86_64/Makefile.defs
    added optimization flag
  arch/Darwin_10_x86_64/fortlib/pppack/Makefile
    reduce optimization level for ppvalu (segfaults w/ -O2 or -O3)

  arch/IRIX64_6.5/Makefile.defs
    now use c99 C compiler

  arch/equivList
    updates for 64 bit Darwin

  arch/Linux_x86_64/intVar/Makefile
  arch/Linux_x86_64/source/Makefile
    reduced optimization levels to avoid optimizer-induced regressions

  arch/Linux_x86_64/Makefile.defs
    updated optimization flags - thanks to P. Mercier

  arch/Darwin_10_x86_64/Makefile.defs
    updates from P. Mercier for intel compilers

  arch/getDarwinCPU
    added the i3 processor 


		     Changes from 2.28 to 2.29

-->  2.29 released 2011/09/20

Example Scripts

  eginput/assignFit
    added assignFit example, for assignment using rdcs, csas

  eginput/pre
    rearranged and added a second example contributed by N. Anthis

  eginput/PSF_generation/pdbTest
    mod for pdb update of entry 2lhb

  eginput/relaxRatio
    added example of use for ubiquitin structure determination

  eginput/sardc/refine.py
    updated

Fortran Interface

  source/genic.f
  source/initia.f
  source/intcor.f
  source/intcr.fcm
    removed the MAXLIC fixed parameter

TCL Interface

  tcl/import_nmrstar.tcl
    readNMRSTARShiftTable: updated to read single character residue names 


Python Interface

  common/atomSel.cc
    comparisons between Simulations now based on modifiedID, not pointer val

  common/atomSelAction
    Fit: added the transDiff accessor

  python/csaPotTools.py
    makeTable function: fixed so it actually works

  nmrPot/noePot:
    -various fixes to better support EnsembleSimulations, including
     heterogeneous ensembles.
    -now, sum weighting and per-term weighting should be supported

  nmrPot/relaxRatioPot
    updates
    implemented cut_off leveling of Chi^2

  nmrPot/posSymmPot.cc
     addEquiv... : throw exception if given an EnsembleSimulation

  nmrPot/sardcPot
    -gradient fixes
      added gradient wrt alignment tensor,
      added gradient contribution due to alignment tensor rescaling
    -changed get_avector_scale() to avectorScale()
    -removed avectorLimit fudge factor
    -code reworked to make it readable.
    -added domainSel member
    -fixed definition of variance
    -showViolations: now print out restraint err 
    -added the err restraint accessor
    -added the irredTensor accessor
    -avectorScale is now allowed to be negative
    -changed diff(): now it is no longer predivided by deltaObsErr
      This changes the reported rmsd.
    -returned chisq value was corrected: now it is divided through by the 
     number of restraints.
    -Restraint:
     renaming and now expose useSign and distance members with accessors.
    -added freeDist member to change distance parameter
    -removed spherical_sampling_init from the public interface

  python/cdsList_template.i
    added remove method

  python/distSymmTools.py
    -added genPolyRestraints

  python/ensembleSimulation.i
    rewritten destructor: now disown after calling deleteSimulation

  python/monteCarlo.py
    randomizeTorsions: added range.

  python/parseTools.py
    -new module with custom tools for parsing strings as input streams
    -moved findNested, readFloat to this file.

  python/potProxy.py
    fixed up potProxy s.t. AvePot(PotList) are now iterable

  python/protocol.py
    initStruct: optionally suppress output of XPLOR commands. Only
    required for XplorWrapProcs (from non-default XplorSimulations).

  python/psfGen.py
    fixes biomt case with ssbonds
    seqToPSF: allow comments preceeded by # character

  python/rdcPotTools.py
    Rfactor_infinite: updates for special cases

  python/restraintStats.py
    now use simulationTools.potType instead of potName to id type 

  python/ringGeom.py
    -ringGeom: pucker function modified to additionally accept a list
     of torsion values as input 
    -ringGeom: pucker function: changed order of angles and buffed up
     docstring 

  python/sardcPotTools.py
    -convertFromXplor: fix for assignment regular expression
    -readRestraint: fix: now use XPLOR restraint err value
    -added R-factor to analysis
    -readRestraint: fixed value of useSign for DIPO-style restraints 
    -added chi2 to extraStats 
    - create_SARDCPot: will now read DIPO-style XPLOR rdc table,
      deducing the value of distance. Added the useSign argument.

  python/simulationTools.py
    -StructureLoop.makeFilename: fixed so optional structNum is really
     used
    -genAveStats: increased initial barrier timeout to 1 week (was off by 24) 

  python/torsionTools.py
    torsionTools: setTorsions function: changed first dir to -1

  python/varTensorTools.py
    calcTensorOrientation: fix for axis atom resid overlap with other resids

  python/waterRefineTools.py
    documentation update

  python/xplorPotTools.py
    added VEAN support

  surfD/surfInternal.hh
    increased constants

Helper Scripts/Programs

  bin/calcDaRh.in
    added the -segid and -startResid cmdline options 

  bin/calcETensor.in
    now use loadPDB s.t. heterogeneous ensemble members can be
    read. (but calcTensor_ensemble does not yet support this)  

  bin/calcTensor.in
    -fixed bug which scrambled order of output when multiple tables
     were specified.
    -added -getTags to give verbose, parsable tensor info.

  bin/getBest
    added the -quoted option

  bin/targetRMSD.in
    -added the -psf2 cmdline option s.t. two different psfs can be specified.
    -fixed bug in which -diffSeq was required for different selections,
     even when the sequences were identical
    -now report Fit.transDiff instead of Fit.translate: this is the
     distance between centers of mass.
    -added the -showRigid cmd-line flag to print out transDiff, and
     rotation for each rigid body fit.

  bin/xplor.in
    -changes to parallel processing s.t. XPLOR_RSH is called once for
     each remote host and then one process is run (via -smp) for each
     time the host is listed. This conserves networking resources and may
     speed startup time. It is essential to be able to use rsh with a
     large (> ~100 cores). For it to work, like node names must be grouped
     together. If the node names are not grouped (e.g. -machines node1
     node2 node1 node2), then this optimization will not be used.  
    -changes to better support Solaris (grep --> $GREP, etc) 
    -THREAD_FILENAME hack to deal w/problems with multiple processes
     writing to /dev/null and corrupting mmap-allocated memory 
     on Darwin x86 and ppc platforms
    -fix logfile naming for case when a single job is running on a
     remote host. 
    -Change: .0 is not added for process 0 log file 

Documentation

  doc/python/tut.tex
    updates to MultRamp docs

  helplib/faq/node0150.txt
    added ACPYPE link

  helplib/nih-py-csaPot
    added bit about DaScale, reference

  helplib/nih-py-xplorWrap
    added docs on disableOutput, enableOutput

  doc/xplor/manual_ypress.tex
    fixup in nonbonded description 

Low Level Libraries

  common/dlmalloc.c
    new upstream version

  common/ensemblePot.cc
    calcEnergyAndDerivs: now call modified.clear()

  common/ensembleSimulation
  common/simulation
    SharedAlloc:
      no longer initialize the esim member to the current EnsembleSimulation:
      this must now be manually initialized
      (this is so that SizeOneSimulations are used when appropriate -
       in the future it's also possible that sub-EnsembleSimulations will be
       allowed)
    
      As a result all CDSVector objects which use SharedAlloc must
      initialize the alloc member
    
     SharedAlloc now has an EnsembleSimulation* member 

      EnsembleSimulation now has a SharedAlloc member
     these used so that multiple EnsembleSimulations can be active at once
     (in particular, Ne=1 allocations should work correctly when Ne>1 
      EnsembleSimulations are current)

    constructor:
      change for size one ensembleSimulations: id is no longer reset to
      the subSim's id. This is so that Simulation::deleteSimulation works
      properly for size one ensembleSimulations (and doesn't cause a later
      crash). 
    
    deleteAtoms:
      now call Simulation::syncAllSimulations so that everything is
      properly sized, etc. Otherwise AtomSels return bogus values.

    Simulation: 
      added the rawID() method, and made id() method overridable.
     
     id() is overridden by size=1 EnsembleSimulations to return the id of the 
     subSim. This is to maintain behavior that size=1 EnsembleSimulations are 
     identical to their subSims, but still retain a unique rawID which can be
     used (for instance) to delete them.
   EnsembleSimulation::SharedAlloc members now explicitly constructed
       - to specify EnsembleSimulation 

  CDSlib/cdsVector.hh
    -added setAlloc method
    -Rep: no longer call allocator for zero size allocations

  CDSlib/spline
    spline: added getderiv member funct.
    fixed end value of slope in periodic case
    fixed type in operator
    added periodic case to derivs
    spline 1D: added getsecondderiv member function

Architecture-specific

  -add amd64 architecture package for Mac

  -now used simpler Linux ARCH setttings.

  -no longer compile IPO for AMD64 Linux package




		     Changes from 2.27 to 2.28


Example Scripts

  eginput/saxs_EI
    added EI-free SAXS+RDC example
    includes mutation script 

  eginput/PSF_generation/genLigand.py
    now also generates a .top file
    new behavior:
      typenames are now truncated to 4 characters w/ leading "G" -
        if there is a clash- those atoms will have the same typename.

Documentation

    corrected switching function definition (eq. 4.9 in the XPLOR manual)

Databases

  databases/chemShiftTens
    additional and updated tables from Ben Wylie


Helper Scripts/Programs

  bin/calcTensor.in
    added R-factor, and R-inf to default output. updated documentation 

  bin/pyXplor.in
    properly protect single/double quotes in arguments 

  bin/xplor.in
    added mechanism to propagate INT or TERM signals to remote jobs.
    fixup for SCYLD misbehavior for num_threads<2 


Python Interface

  python/atomSel
    AtomSel: get constructor from list of atom indices working in Python

  python/bigraphMatching.py
    Tools to perform bipartite graph matching.

  common/bondAngle
  python/bondAngle.i
    added BondAngle class

  python/cdsVector_template.i
    fixed fromList (previous only worked if size did not change)

  python/diffPotTools.py

  python/ensembleSimulation.i
    added the Comm wrapper class 

  python/h3JNC.py
  python/h3JNCPot.py
    new H3JNC potential term

  nmrPot/sardcPot
    avector_real: removed two-layercontainer of container with SharedAlloc
    merge from xplor-mmap (no change merge)

  nmrPot/planeDistPot
    added weight member to Restraint class 
      along with WEIGHT statement in input tables
    added GAUSSIAN and SIGMOID potential types

  nmrPot/prePot
    PREPot::showViolations: improved output for SUM restraints
    PREPot: added mkSumRestraints
    fixed bug: some arrays were never sized for stereo mode 

  python/prePotTools.py
    create_PREPot: added optional paraCenter, sumWeights args to facilitate
                   creating SUM restraints

  python/protocol.py
    genExtendedStructure: 
      added support for maxFixupIters=0
    initCoords: 
      changed erase implementation from using XPLOR interface
    initDihedrals: 
      default dihedral restraints: now only add them if
      the atom farthest from the backbone is present.   

  python/psfGen.py
    pdbToSeq: better deal with misformatted ATOM records seqToPSF:
         added ntermPatch, ctermPatch arguments to customize protein
         termination   
    seqToPSF: 
      -bugfix for ctermPatch
      -added the "custom" seqType 
      -now treat seq arg as file if its length is > 4 characters 
      -add singleChar argument to interpret sequence as
       a single-character residue names

  python/pyConvert
    Vec3s are no longer converted to tuples

  python/relaxRatioPotTools.py
    updates

  python/restraintStats.py
     RestraintStats:
       -added collect method for parallel communication of
        per-structure stats. Now collect stats on all structures and
        then subsample based on structNums argument.
       -added s.structNums member for to simply store seen structures
         members summarize* structNums is now optional.  
     summarizeViolations: 
        now sort by name instead of index: index is meaningless in the
        vdw term. 

  python/regularize.py
    fixupCovalenGeom.fixupLoop_xplor: now catch unknown coordinate
    (and other) errors in XPLOR minimization and dynamics.

  nmrPot/sardcPot.cc
    added missing initializations

  python/selectTools.py
    renameResidues 1->3 protein sequence mapping.

  python/simulationTools.py
    StructureLoop:
      docs for averageRestrain: clarify meaning of inconsistentAveStruct.
      writeStructure: 
          added exception type encountered if pwd.getpwuid fails
          changes made while unbound 
      genAveStats: 
        -reworked to collect per structure energy/violation info and
         communicate it back to the proc 0. 
        -now do not try to do any fitting in the case of
         ensembles waitForProcesses: now commented-out.  
      filename, makeFilename: now take an optional structNum argument
      run(): now use ensembleSimulation.Comm for ensembleSimulations
    minimizeRefine(): 
      reworked s.t. flattened PotList is not used in minimization 
    analyze(): 
      remove extra comment listing cross-validated terms which is
      printed only if the terms contain sublists. 

  python/solnScatPot.i
    pairDistribution: now initialize count field

  python/solnScatPotTools.py
      bugfix

  python/torsionDBTools.py
    tools for updated torsion database potential

  python/torsionTools.py
   setTorsions: bug fix: 
    if angle specification was in opposite direction of tree def., the
    rotation would be incorrect.  

  python/varTensorTools.py
    added configIVM_fixAxis function
    topologySetup: added fixAxis keyword
    added eulerAngles function and test
    changed current_axisResid to 5000

C++ Interface

  common/atom.hh
    isValid: now return false for default-constructed Atoms

  common/atomSelLang
    AtomSelLang: added the recall keyword
    added the dollar sign to characters allowed within strings
    new atomSelLang.setRecallSelection() function

  common/dihedral.hh
    added derivs(pref,derivList) convenience function

  common/ensemblePot
  common/ensembleSimulation
  common/xplorWrapProc
    re-enabled MMapMalloc for better ScaleMP performance
    now use fflush(NULL) before fork.

  CDSlib/cdsMap
    added clear() method, test
    changed visibility of methods getAtom, getAtomConst, and add to private.
    operator[], getAtom: optimization removing multiple map passes.

  CDSlib/cdsMatrix
    added operator*(vector,matrix) - more efficient for column-major
      matrices 
    added operator*=(matrix)
  
  CDSlib/cdsSStream
    added second str() method which takes an argument

  CDSlib/cdsString.hh
    added synonym for gsub method: replace
    added find methods
    added count method

  CDSlib/cdsVector
    added append method/test

  CDSlib/fixedVector.hh
    added scale method

  CDSlib/pair.hh
    simplified the default constructor

  CDSlib/spline.hh
    Spline (1D): 
      added constructor from two vectors
      added deriv(), secondDeriv() methods

  CDSlib/vec3.hh
    default constructor: 
      Added initialization (0,0,0) - to make sparta derivs earier .

  intVar/publicIVM.hh
    PublicIVM::step: 
      now check for error when catching Finish, return val changed.

TCL interface:

  marvin/MarvinNOEPotential
  marvin/Peak
    fixed inappropriate use of non-public CDSMap methods



Architecture-specific

  arch/Darwin_8_x86/Makefile.defs
    FLD_FLAGS cleanup
    createF77SharedLibrary: now use $(CC) instead of hard-coded gcc
    new element for OMITTED_SHARED_LIBS



		     Changes from 2.26 to 2.27


Helper Programs

  bin/calcSAXS.in
    -added -exptPointsSpline cmd line option removed debug print message 
    -fixed difference calculation (5th column of output) 
    -change to output residual instead of calcd/expt difference
    -now check that input pdb files exist missing protons warning now
     goes to stderr  

  bin/calcTensor.in
     added the -subSel option

  bin/testDist.in
       applied A. Bornstein's patch to make path independent

  bin/xplor.in
     -added A. Bornstein patches to
        1) get --help-script output when --help is given
        2) properly propagate binary xplor's return value
     -updated fortran i/o buffering settings from Jack Howarth 
     -will now consider the CINGSH env var to locate cing startup script

Example Scripts

  eginput/PSF_generation/addAtoms.py
  eginput/PSF_generation/addAtoms2.py
      updated to use high level PDB reader/writer from protocol module

  eginput/dna_refi/refine_full.py
      added comments re: use of old parameters

  eginput/saxsref
      added example of use of SAXS data in protein structure determination

Python Interface

  nmrPot/csaPot.cc
  nmrPot/cstMagPot.cc
  nmrPot/jCoupPot.cc
  nmrPot/nbTargetPot.cc
  nmrPot/orderPot.cc
  nmrPot/planeDistPot.cc
  nmrPot/posRMSDPot.cc
  nmrPot/prePot.cc
  nmrPot/psolPot.cc
  nmrPot/rdcPot1.cc
  nmrPot/sardcPot.cc
      merge A. Bornstein patch for better treatment of spaces in
      restraint tables 

  nmrPot/atomDensity
    DensityGrid: 
      added readCCP4 (for maps) + tests, docs
      changed signature of writeEDM: now takes filename argument
      added default constructor
      getData: added swig range checking for arguments 

  nmrPot/prePot.cc
     -fix: added nissing allocations
     -PREPot::showViolations:
        updated output along lines of suggestions from N. Anthis
     -calcGamma:
        fixed bug in stereo calc for slow interconversion
     -PRERestraint::energy(): now truncate the value of diff to
      10,000. This to avoid crashes due to very large energies when
      the atoms get unphysically close.  
     -Restraint::energy: remove truncation of diff_


  nmrPot/posSymmPot.cc
      fixup for error message

  nmrPot/sardcPot.cc
      fix: added missing allocations

  nmrPot/torsionDBPot
      Added torsionDBPot module with TorsionDBPot2D and
      TorsionDBPot3D.

  python/cdsMatrix.i
      added __iadd__ (performance improvement for large matrices)

  python/protocol.py
     -initParams: added the use_dihe optional argument
     -initRamaDatabase: change nres to a number proportional to the
      number of residues in the appropriate simulation. Required for
      use with very large systems.

  python/pyInterp.cc
      PyInterp::command: change to get correct return value

  python/selectTools.py
    rigidProteinSelections: added entries for the CED residue

  python/simulationTools.py
     -StaticRamp constructor: added stride parameter; plus new test
     -saRefine: fixes to topology, parameter setup

  python/solnScatPotTools.py
      fitParams: inner loop optimizations

  python/spline.i
    -Spline: added 2nd constructor (taking 2 arguments) 
    -added typecheck
    -typemap: use of overloaded functions w/ typemapped args requires
     typecheck typemaps.  

   python/spline3D.i
    -new 3D spline class with gradient.

  python/torsionTools.py
    deleted rotomericStats.py after moving RotomericStats class to
    torsionTools.py 

  python/varTensorTools.py
    calcTensor: 
     added the optional selection argument to specify a subset of
      restraints to use for the SVD fit.  

  python/rdcPotTools.py
    Rfactor_infinite: added selection argument 


TCL Interface

  tcl/aeneas_tools.tcl
      match2d: reversed the order of range in warning messages about
      from/toProtonShifts being out-of-range. createShiftAssignments:
      now check for empty (missing) shift values and simply print a
      warning message (instead of crashing).  

  tcl/import_pipp.tcl
      added process2dPippPeakTable (after verifying it works) 

  tcl/marvinNOEpotential.i
      added sorted versions for some PASD output quantities
      and updated output for new order of output
      prompted by CDSMap reimplementation

  tcl/tclXplor.cc
      now override built-in tcl exit command so that proper Xplor-NIH 
      cleanup takes place. 
      Output changed because now final messages (and times) are
      printed.

XPLOR Interface

  source/fenergy.f
  source/setor.f
      added missing parameter to SEDIHE. This likely has no affect on
      the results 

  source/hbdb.f
     bugfixes: hbdbpatt: 
       -initialize all of hbfiltmap, hbprop elements
       -now more careful about going out of range
       -removed multiple infinite loops

  source/slink.f
    bugfix: subroutine slink: logical flags for dihedral and improper
    terms were incorrectly set. This resulted in slinked dihedrals and
    impropers getting zeroed out.  



Low Level Libraries

  CDSlib/fixedArray3D.hh
      New container class for statically-allocated 3D data.

  CDSlib/cdsExcept.hh
      added A. Bornstein patch: additional constructor taking String arg

  CDSlib/cdsIterator.hh
      members now protected to allow class derivation

  python/cdsMatrix
     -fixed constructor w/ initializer for CDSMatrix<int>
     -New cdsVector.CDSVector*cdsMatrix.CDSMatrix operation
     -(cdsVector.CDSVector=v, cdsMatrix.CDSMatrix=m) Faster m*v.

  CDSlib/cdsMap
  CDSlib/redBlackTree
  CDSlib/templateStack.hh
      modified patch from A. Bornstein:
        converted CDSMap to use red black tree

  CDSlib/cdsString
     -merge A. Bornstein patches:
        added cast to int
        change argument of constaints(string)
        fixed justification of operator<<
     -readline: fix for reading long (>1024 char) lines, added test of
      this functionality  

  CDSlib/spline.cc
      merged periodic 2D fixes (gradient estimation in constructor)
      from Guille.

  CDSlib/spline3D
      New 3D spline template class with gradient.

  common/atomSelLang.cc
      added the index keyword

  common/mmapAlloc
     -alloc: added (optional) 4th addr argument - used by mmapMalloc
     -alloc: do not subtract from addr unless it is !=0

  common/dlmalloc
  common/mmapMalloc
     -initial version of malloc-on-mmap for shared memory allocation
      This motivated by poor performance on the ScaleMP architecture and
      suggested by their personnel.
     -added mutex protection for alloc and free
     -cleanup: add explicit call to MMapMallocData destructor to
      prevent resource (semaphore) leakage  

  common/ensemblePot
  common/xplorSimulation
     -sharedPID now calls MMapMalloc::alloc (and it is now cleared)
     -added support for prepending pid to C++ cout output by setting
      the PREPENDPID env var. This should be expanded to include stdout
      from the C library.  

  common/ensembleSimulation.cc
  common/ensembleSimulation.hh
      updated to use MMapMalloc instead of MMapAlloc
      bug fix for SharedString: no longer return raw char* ( so binary
        strings can be better handled, and so string length is properly set )

  common/semaphore.cc
     -added query method for SVSV semaphore implementation
     -added extraData member. It is used by the SysV implementation to hold the
      pid of the Semaphor creator. The destructor only allows the
      creator to call IPC_RMID.

  common/xplorWrapProc.cc
     -added calls to MMapMalloc:incr/decrNumThreads before fork/after waitpid
     -slave no longer deletes sharedData- that is done by the master
      (who created it - this is necessary to delete the Semaphore (SysV)
      now slave does call SimulationWorld::finalize() - to clean up its
      SysV semaphores new debug output added  

  surfD/compute
  surfD/surf
    bugfixes
      Surf class temp_cons member: change type and initialize
      Surf::quick_sort_planes: replace use of memcpy w/ memmove because of
        known memory overlap.

Documentation Updates

  doc/python/rdc-expt.pdf
    added fig needed for tutorial

  helplib/nih-py-pdbTool
    update read() docs regarding negative model 

Platform Specific
  arch/equivList
    fixed mac (Darwin) ppc lines
    updated for 64-bit version of Intel/Darwin 

  arch/getDarwinCPU
      added full path for system_profiler command (in case /usr/sbin is
      not in path).  

  arch/Linux_2.2_i686/Makefile.defs
      GNU C/C++:
        reduced optimization from -O3 to -O2

  arch/Darwin_10_x86_64/Makefile.defs
  arch/Darwin_10_x86_64/fortlib/Makefile
  arch/Darwin_10_x86_64/python/Makefile
  arch/Darwin_10_x86_64/source/Makefile
  source/darwin64time.f
  source/osx_x86_64.f
      untested contributions from J. Howarth

  arch/Linux_2.4_x86_64/Makefile.defs
    Intel V11 compilers: add the -ipo flag - improves C++ performance,
    makes linking take longer.

  arch/Linux_2.2_i686/Makefile.defs
      now default to gfortran if LOCAL_F77 is not specified in Makefile.loc


		     Changes from 2.25 to 2.26


Helper Scripts

  bin/aveStruct
    script to compute average (unregularized) structure
    moved and updated from previous location eginput/gb1_rdc/aveStruct.py

  bin/calcSAXS
   - widen numeric output fields for increased precision 
   - added -exptPoints cmdline option verbose output changed 
   - added command-line options to fully control fitting parameter range

  bin/ens2pdb
    generates pdb entry from ensemble of structures 
    (and does SEGID -> ChainID conversion)

  bin/xplor
    -change to allow middle entries in equivList to be recognized
    -added -rsh cmdline option. 
    -no longer append .0 to outFile if numProcs=1

  bin/pbsxplor
    - added support to propagate the -rsh option or the value of XPLOR_RSH 
      on the submitting machine to the batch job. 
    - fix: output of qsub is to be printed, not returned 
    - added the -N cmdline arg to set pbs name
    - added -nomail option

  bin/targetRMSD
    changed selection of atoms which are moved in the fit to all known

Python Interface

  fixed missing exception handling: this means more errors are catchable.

  python/cminpack
    added cminpack + python interface for nonlinear least squares

  python/cdsList_template.i
    -added append method
    -added removeAll method

  nmrPot/cstMagPot.cc
    Fixed verbose output of cstMagPot.CSTMagPot.addrestraints()

  python/diffPotTools.py
    added call to protocol.updatePseudoAtoms after adding clock atoms

  python/ivm.py
    breakBonds: now can optionally take two arguments (to specify two atoms)

  nmrPot/nbTargetPot.cc
    added nbTargetPot - can target various functions of atom-atom distance

  nmrPot/noePot.cc
      addRestraints: properly clean up partially-built restraints 
      (avoid memory leak)

  python/potProxy.py
    Python proxy class used in fixing python potential term reference 
    counting, avoiding reference cycles: 
     ->potential terms can now be freed after they're created.
    Potential terms are wrapped in a PotProxy which decrements the
    rc_ptr refcnt when __del__ is called.  

  python/prePotTools.py
    create_PREPot: fixups for fixTau=False
    registerTerm: 
      fix to avoid reference cycle 
      now unset thisown for each term to avoid shutdown errors

  nmrPot/prePot
    -updates to support fast/slow ensInterconvert
    -showViolations output improvements

  python/protocol.py
   -matchInexactAtomEntry:
     *updates to better read cyana-generated iupac files: 
      -will now match name H to HT1. 
      -for rule swapping leading digit with trailing: 
       now the entire non-digit portions of the names must match. 
     *added more code for nucleic customRename=True (HN)
     *now handle malformed coordinate fields
   -initDihedrals: 
     fixes to work properly with reloading.
   -initCoords: changed message printed if unreadEntries to add warning
   -initCoords: return value now also has an entry for PDB remarks 
   -writePDB: now takes remarks argument 
   -cartesianTopology: added updatePseudoAtoms call

  nmrPot/relaxRatioPot.cc
    resetTesselationFlags: added resize of omega2 to avoid array overrun 

  python/restraintStats.py
    -in concert w/ that in XplorPotTools: 
          treat VDW restraints in standard way
    -getViolations: added method to signal that restraints is unsupported

  python/psfGen.py
    seqToPSF: for proteins, now support aria peptide linkages 
        (more link statements) for aria topology files. 

  python/regularize.py
    -covalentMinimize, fixupCovalentGeom, 
    -fixupCovalentGeomIVM, addUnknownAtoms: 
       now reset the constraints interaction settings before return 
    -addUnknownAtoms_new: fixed selection of which unknown atoms to add. 

  nmrPot/sardcPot
  python/sardcPotTools.py
    added SARDCPot contributed by Jie-rong Huang and S. Grzesiek

  python/selectTools.py
    added IVM_breakIsopeptides

  python/simulationTools.py
    minimizeRefine: added translateRegions argument 

  python/simulationTools.py
    -StructureLoop.writeStructure: deal gracefully with failures of 
      pwd.getpwuid (seen on scyld systems). 
    -StructureLoop.filename: fixed old string exception 
    -saRefine: added numSteps, htFinalTime, htNumSteps arguments, 
               added high-temp dynamics phase. 
    -testGradient: made exception type more explicit
    -fixed exception type encountered if pwd.getpwuid fails

  python/sansPotTools.py
  python/solnXRayPotTools.py
    added genFormFactors functions- called by the create_ functions, and 
    also called externally to regenerate form factors w/ new values of q.

  python/solnScatPotTools.py
    -solnScatPotTools:
      added readData func- used for sans and saxs data
    -fitParams: 
       *initialize bg s.t. this function can be called more than once
       *fitParams: now rhobNum, r0Num and V0Num treat values <1 as 1. 

  nmrPot/solnScatPot
    -added setExpt accessor
    -modified:
      calcI_N- to include boundary contribution
      setQValues: to allow the number of q values to change
    -no longer a C++ template

  python/torsionTools.py
    setTorsions: added optional ivm and verbose arguments. 

  python/varTensorTools.py
    added varTensorTools.registerExptToVarTensor for expts handling

  python/waterRefineTools.py
    tools used in explicit solvent refinement.

  python/xplorInit.py
    changed socketComm startup timeout to depend on numProcs

  python/xplorPotTools.py
    -now add restraints method for class, instead of per instance 
      -> this to prevent a reference cycle. also added VDW ``restraint list''
    -violations now returns PY_Restraints

XPLOR Interface 

  source/fxparse.f
  source/fxrefin.f
    added default value, input checking of TURNS fiber parameter.

  source/hbdb.f
    fixes from Alex (via Justin Lorieau) to properly recognize 
    N-terminal protons. 

  source/linuxtime.f
  source/x86_64time.f
    frehp: rearrange s.t. verbose mesg prints before abort

  source/genic.f
    fixed ancient bug in genic.f wherein subroutine patch didn't check for out
    of bounds natom count. This bug only struck with structures having
    residues numbers of special size. A test case has been added for this.

  source/sup2.fcm
  source/supccr.fcm
    patch to reorder COMMON elements - contributed by Jack Howarth 

Platform Specific:

  arch/Darwin_8/Makefile.defs
  arch/Darwin_8_x86/Makefile.defs
  arch/getDarwinCPU
    -Darwin findSharedLibs mods s.t. Frameworks are also searched
    -merged contribution from Pascal Mercier to support 64-bit Darwin.
     involves renaming PPC platform to Darwin_8_ppc.

Examples

  eginput/gb1_rdc/anneal.py
    -add HBDB term

  eginput/gb1_rdc/wrefine.py
     new water refinement example

  eginput/pasd/mth1743
    added the mth1743 pasd example

  eginput/pre/newRefine.py
    now write out a .bumps file which lists close contacts obeying 
    constr inter

  eginput/PSF_generation/addAtoms2.py
      fixed selection syntax error

  eginput/PSF_generation/isopeptide.py
    added isopeptide example

  eginput/PSF_generation/PROT2.seq
    added example of N-terminal acylation

  eginput/sardc/
      New example of use of SARDCPot contributed by Jie-rong Huang and 
      S. Grzesiek

Common Code

  common/atom.cc
    increased value of INVALID_COORD to be consistent with XPLOR value- 
    important for atomSelLang atom selection. 

  common/atomSel.cc
     containsIndex: fixed bug in which index range was not checked

  common/atomSelLang.hh
      added getNamedSelection (and it checks that the selection is up-to-date)
      the pseudo keyword now uses this new function.
      differences from the XPLOR atom selection language:
         removed two bugs:
	   1) previously HB# would match HB (in addition to HB1, HB2, etc)
           2) previously, an extra trailing ) produced no error

  common/ensembleSimulation.cc
    finalizer: now shutdown ensemble threads 

  common/pdbTool.cc
    -read(): 
      *added check for short lines
      *now use special rule for (molmol created?) files which lack segid 
         columns
      *remarks start in column 7 (previously included space in col 6)
    -writePDBAtom: now write a TER record between segs if writeChainID set

  common/potList.cc
    PotList::add now print warning mesg if checks that ensemble sizes 
    do not match 

  common/simulation.cc
    deleteSimulation: changed simulationList delete from direct 
      ref count decr to assignment. 
     This fixes a nasty bad pointer dereference. 

  common/simulationWorld.cc
    init: reworked putenv use s.t. arg is char* (not const char*) 

  common/xplorSimulation.cc
    select: changed from XPLOR to AtomSelLang selection language 

  common/xplorWrap.cc
    deleteAtoms: now do syncTo at start

  common/xplorWrapProc.cc
    before forking: call XplorSimultion::syncTo to get XPLOR atom data in
    state consistent with that in Simulation.


Low-Level Libraries

  CDSlib/cdsComplex
    added abs2 method; test of norm/abs2

  CDSlib/cdsList.cc
    -fixed memory leak in resize: for case when cnt>1
    -added uniq helper function

  CDSlib/cdsVector.hh
    removed unneeded/unused destructor

  CDSlib/matrixTools.cc
    callEigen: changed call signature to pass by ref instead of val

  CDSlib/rc_ptr.hh
    -fixed destructor memory leak: the CountHolder (counter) was 
     never deleted. 
    -destructor: now, if refcnt gets to zero, delete the ref cnt holder 
      (previously, it was never deleted) 
    -added forceDelete method for manually deleting reference counter object
    -changed ~CountHolder s.t. it no longer explicitly deletes the 
        pointed-to object - this left to operator-- (this s.t. 
        forceDelete can be used).
    -added test of forceDelete use.
    -added release method

  CDSlib/spline.cc
    Spline2D: constructor from vector: fixed to read row-major

  fortlib/blas
  fortlib/lapack
     resynced lapack and blas from netlib source

TCL Interface 

  tcl/aeneas_tools.tcl
    protect against divide-by-zero range errors

Topology/Parameters

  toppar/waterRef/
     inputs for explicit solvent refinement.

  toppar/protein-1.0.top
  toppar/protein-1.0.par
    added isopeptide linkage patch - contributed by Olivier Serve 



		     Changes from 2.24 to 2.25

Platform Specific Changes:

  now works with Mac OS X 10.6 for Intel platforms

  Mac OS X build now uses frameworks for Python and tcl.

Helper Scripts:

  bin/calcSAXS
    -change behavior for calcSAXS: no longer delete missing protons
    -added -sans cmdline option: for calculation/fitting of SANS curves
    -added -rhobStart, -rhobEnd cmdline options
    -now add appropriately scaled bg back to calcd (and expt) on output
     doc updates.
    -added -altDeuteratedSel cmdline option
    -can now fit or specify value of isotropic background contribution
     using the new command-line options -bg, -bgNum, -bgStart, -bgEnd.
    -now place info in header of output
    -added -fractionDeuterated cmd-line argument
    -added -maxQ command-line option + functionality
    -added warning if very few protons found
    -bug fix! - previously always reset rhob to zero after the fit
    -now print vacuum radius of gyration

  bin/calcTensor
    -bugfix for case (not ensembleMode) and multiple pdbs: 
     only a single pdb was considered in the fit
    -fix for multiple rdc tables: treated potList as list- could
     generate errors.

  bin/findClusters
    added -noFit, -fitSelection cmdline parameters

  bin/getBest
    -fixed order of presentation of usage string
    -can now specify multiple .stats files on the command line

  bin/pbsxplor
    -limit length of -N (job name) argument to 15 characters
    -look for the resources_available.cores resource (if available) to
     determine ncpus (thanks to Steve Fellini)

  bin/targetRMSD
   bug fix: fixed fitSel so it works added calculation of rigid body 
   rotation, translation amounts. Also chaned default setting for fitSel2.

  bin/torsionReport
     now actually generate psf and read coordinates if -psf option is omitted.

  bin/xplor
    -command-line args -csh-env, -sh-env: no longer export PYTHONHOME
    -added -cinsh, CING environment support
    -numabind: now use multiple numa nodes, if a single node hasn't 
     enough cores

Example Scripts

  eginput/dna_refi/refine_full.inp
  eginput/dna_refi/refine_full.py
  eginput/dna_refi/refine_full_lj_elec.inp
    fix nucleic parameter file used to version 1.0

  eginput/dna_refi/ensemble.py
    changed name of average structure file

  eginput/PSF_generation/genCircPep.py
    added simpler example of generation of cyclic peptide. The
    previous example is now named genModCircPep.py

  eginput/PSF_generation/addAtoms2.py
    now use faster addUnknownAtoms_new

  eginput/diffTens:
    examples using the diffusion tensor as a structural restraint.

  eginput/gb1_rdc/aveStruct.py
    now use loadPDB/initCoords/writePDB instead of pdbToPSF/PDBTool

  eginput/gb1_rdc/analyze_ProbDistPot.py
      - allow all dof for alignment tensors (for ave. struct calc)
      - no longer treat StructureLoop.inconsistentAveStruct as an error

  eginput/gb1_rdc/pairRMSD.py
    change: now read all coordinates into memory once

  eginput/pasd/cvn/makeContactMap.py
    helper to generate residue contact maps like those in
    J. Biomol. NMR 41, 221-239 (2008).

Fortran Interface:

  source/linuxtime.f
  source/util.f
    -hacks/workarounds for treating /dev/null (corresponding to filename
     off or none) when running -smp on binaries compiled w/
     gcc/gfortran-4.4.3:
       VINQRE: always treat file w/ unit 5 and name /dev/null as unopened.
       ASSFIL: retry VOPEN w/ different unit # if there is a failure opening
               /dev/null

  source/enbond.f
  source/parmio.f
    -expanded use of vdwoff to all VDW potential types
    -reversed (internal) vdwoff meaning

Python Interface

  enabled SWIG-generated keyword support.

  common/xplorWrapProc.cc
  common/xplorSimulation.cc
    XplorWrapProc: change the behavior of simulation.Simulation(clone=True)
    If the current XplorSimulation is not the default Simulation, it is
    now properly cloned if that flag is set (previously the default
    XplorSimulation was always cloned). This required:
    -arranging for the correct slave to fork/wait at creation/de
    -saving a ref the XplorWrapProc associated with the cloned XplorSimulation 
    -keeping track of whether the slave is a direct child.
  
  nmrPot/jCoupPot.cc
    calcContrib: now throw exception if atoms are too close

  nmrPot/solnScatPot.cc
    -calcBoundaryPoints: fix computation of triangle center points
    -added bg accessor, support for isotropic background correction
    -changed boundary layer calc to simply place a sphere at the
     center of each boundary voxel- no more random generation of points.
    -boundary volume calculation improvements:
       now bounded by outter surface generated by increasing atom
       radius by 3 angstroms and inner surface compsed of triangles
       from the outter surface dropped along the normals.

  python/atomAction.py
    PrintPos: change to print SEGID instead of index

  python/cdsMatrix.i
  CDSlib/matrixTools.cc
    added fix, test for determinant of size 1,1 matrices

  python/checkWrap.py
    fixed to find memory leaks in wrapped constructors

  python/csaPotTools.py
    added GLY-specific NCA-style auto-parameter assignment

  python/diffPotTools.py
  python/planeDistTools.py
  python/prePotTools.py
    create_*Pot: added call to updatePseudoAtoms()

  python/distSymmTools.py
    genDimerRestraints:
      added resids2 arg so that different residue ranges can be specified,
      and the segids argument can be set to None to disable segid
      specification. 

  python/ensembleSimulation
    added collect method to EnsembleSimulation, and added coverage test

  python/ensembleSharedObj.py
    added collect helper function

  python/pasd.py
  tcl/aeneas_tools.tcl
  tcl/sa_protocols.tcl
    in anticipation of more some transition to Python, added pasd.py, 
    currently holding default values of some parameters.
    updated sa_protocols, aeneas_tools to use these parameters.

  python/pdfEstimation.py
    tools for probability density function generation.

  python/posDiffPotTools.py
    loadPDB now called with deleteUnknownAtoms=True; docs updated

  python/protocol.py
    -no longer refer to deprecated Exception.message
    -syncArrayBeforeDelete:
      (used to synchronize bfactor, occupancy fields if atoms are deleted)
      now returns a cdsList instead of a Python list.
    -matchInexactAtom: change matching rule from 1st char to all but last
    -added writePDB helper function. PDB contents are returned.
    -initCoords, loadPDB:
      *added optional loadOccupanciesBfactors argument to load these fields
       in to an XplorSimulation.
      *added processBiomt argument. If set to True, BIOMT PDB will be
       read, and PSF+PDB entries will be added.
    -loadPDB:   added optional processSSBonds argument

  python/psfGen.py
    -changed default value of failIfInsertion
    -psfGen.pdbToSeq() now raises an InsertionExceptionexception when
     a nonblank iCode entry is found. This can be disabled if
     psfGen.failIfInsertion is set to False. 
    -pdbToPSF, pdbToSeq:
     *added support for reading, understanding BIOMT PDB records
     *added optional processSSBonds argument
    -addDisulfideBond: fix to deal more gracefully with missing
     entries specified by an SSBOND record.

  python/regularize.py
    -fixupCovalentGeom optimization:
      now only loop over those residues included in sel arg.
    -no longer refer to deprecated Exception.message
    -addUnknownAtoms_fast:
      now always catch CovalentViolation exceptions from fixupCovalentGeom
    -added addUnknownAtoms_new:
      uses algorithm to iteratively add atoms using addUnknownAtoms_fast.
    -fixupCovalentGeom: print more info for verbose>4

  python/sansPotTools.py
    -added SANS support for Mg
    -added fractionDeuterated argument - describes the deuteration of
     non-exchangable protons.
    -create_SANSPot: 
      *added arg to deal w/ alternatively deuterated selections
      *added maxQ, cmptType arguments

  python/simulationTools.py
    StructureLoop: 
      -added averageFixed/RigidRegions arguments passed down to
       minimizeRefine. 
      -writeStructure: now add username/time/date to pdb REMARKs
      -genAveStats: now print out sorted loops
    -calcAverageStruct:
      -now recalc alignment tensors after computation of ave. struct
      -fix up tensor pseudoatoms for case where regularization is not done,
     -minimizeRefine:
        -clean up minc: no need to have two ivm objects
        -switch to use cartesianTopology helper
        -rigidRegions, fixedRegions again obeyed.
        -removed varTensor stuff.
         ->initial, final tensor values will not be set by calcTensor.
            - this now needs to explicitly done after averaging coords
         ->tensor freedom setting should be obeyed.

  python/solnScatPot
    calcIfromF: barriers added to prevent races for Ne>1, num_threads>1

  python/solnScatPotTools.py
    -fitParams:
      will now optionally fit isotropic background scattering
      optimized parameter search loop.
    -normalize(): fixed for normalizeIndex=-2,-1

  python/solnXRayPotTools.py
    create_solXRayPot: added maxQ argument

  python/torsionPMFTools.py
    tools for generation of database torsion-angle potential surfaces.

  python/varTensorTools.py
    -added function getRegisteredTerms()
    -now use this in massSetup() and topologySetup()

  python/xplorPotTools.py
    improved nonbonded violations printout

TCL Interface

  tcl/import_xeasy.tcl
    added process2dXeasyPeakTable

  tcl/aeneas_tools.tcl
    added standard2dInitMatch


Databases

  databases/torsions_raw
    replaced all remaining instances of rama w/ xrama so that raw
    torsions work correctly.

Low Level

  CDSlib/array3D.hh
    added Array3D template with reference counting and resizing; 
    and unit tests

  CDSlib/cdsMatrix
    added operator+=(T)/operator-=(T) 

  CDSlib/cdsVector
    added operator+/i(T)
    added operator+=(T)/operator-=(T) 

  CDSlib/fixedMatrix
    added rawCopy method

  CDSlib/spline.cc
     Spline2D constructor from zVec:
       fixed so that the zVec data is read correctly.

  common/atomSelAction
    added minDistance function

  common/derivList
    operator[]: add check that derivList for sim was allocated

  common/atomSelLang
    added the AROUnd selection keyword

  python/cdsVector
    -added __iadd__ and __isub__
    -added __add__(T) and __sub__(T)

Build/Test Process
  arch/Darwin_8_x86/Makefile.defs
    findSharedLibs: updated to deal w/ otool results lacking leading /
  eginput/gb1_rdc/testTargetRMSD
    improved coverage of targetRMSD
  arch/Linux_2.4_x86_64/Makefile.defs
    intel v9 compiler: added intlc lib for forwards compatbility
  arch/Darwin_8/Makefile.defs
  arch/Darwin_8_x86/Makefile.defs
  arch/Linux_2.4_x86_64/Makefile.defs
  arch/Linux_2.2_i686/Makefile.defs
    fixed XLIBPATH
  arch/Linux_2.4_x86_64/vmd-xplor/Makefile
    no longer try to statically linnk libstdc++
  bin/findSwig
    validated swig version 1.3.40
  python/Makefile
    added link to libpy for all wrapper .so objs- to provide direct
    symbol linkage.


		     Changes from 2.23 to 2.24

Example Scripts:

  eginput/gb1_rdc/analyze_ProbDistPot.py
  eginput/gb1_rdc/analyze_anneal.py
  eginput/gb1_rdc/analyze_refine.py
  eginput/gb1_rdc/anneal.py
  eginput/gb1_rdc/dihed_g_all.tbl
  eginput/gb1_rdc/refine.py
    modified TYR/PHE chi2 torsion angle restraints to be used with
    useDefaults set in protocol.initDihedral

  eginput/gb1_rdc/anneal2.py
    added alternate faster version of anneal.py

  eginput/protG/anneal.inp
    updated XPLOR script s.t. .pdb files are always written

Help System:

  online tutorial updates

  rdcPot docs
    clarified useSign meaning

  New FAQ entry
    entry regarding powell irregular exit messages

  added google search on some web help index pages

    web-dist: now copy INSTALL instructions to WEBDIR

Helper Programs/Scripts

  bin/xplor.in
    -now use numactl to get better memory affinity, particularly
     important for Ensemble calculations.
    -will now better handle spaces and single quotes in arguments
    -removed Darwin env vars which, while once necessary, now mess things up
    -now allow (option, argument) pairs to be separated by =, for
     consistency with Python cmdline args

  bin/pbsxplor.in
    -add warning message if node isn't found in psbnodes output
    -added error message and quit if input file can't be found.
    -fixes for job shell, and not hardcoding rsh use

  bin/pyXplor.in
    -reworked special character protection again

  bin/torsionReport.in
    -now use circular statistics for more reliable computation of
     average rotomer angle values.

  bin/idleXplor
    idle for Xplor-NIH- available only w/ srcdist. This is a GUI for
    Xplor-NIH Python development.

  bin/getBest
    added -index cmd-line option

  bin/calcSAXS.in
    -now support resampling experimental data using -numQ argument
    -add -rhob, -volumeScale command-line options- these override the fit
         parameters.
    -updates for hetereo Ensembles
    -now can set ensemble weights

  bin/targetRMSD.in
    -added -write flag for writing out fit structures
    -fix so that fitSel is actually used.

  bin/calcETensor.in
    -fix for -weights option when space is used for separator

Python Interface

  python/protocol.py
    loadPDB: 
      added correctSymmetricSidechains argument - passed to initCoords
    initDihedrals:
      changed TYR/PHE default restraints to be consistent with
      selectTools.correctSymmetricSidechains
    loadPDB: 
      added maxUnreadEntries arg, passed to initCoords.
    initDihedrals:
      -added reload argument
      -now print out # restraints read
      -changed counting to use (perhaps faster) numRestraints() instead of
       len(restraints())
  
    RDCPot:
      added support for ASSIgn ... OR assignment table syntax for precise
      ambiguous assignment.
      RDCRestraint::bondVectors method has been removed.
      added test, and updated docs
      showViolations: fixed atoms printed for when both selections have wildcards
      made useSign a per-restraint variable - motivated by ssNMR
    RDCPotTools: 
      comment-out unused calcTensorSize function
      removed CC prefactor definition
      getRDCType: 
        added methyl type (only for THY for now); updated examples

  python/csaPotTools.py
    -added alternate NH CSA parameters contributed by D.A. Marvin and 
     S.K. Straus. Doesn't use the HN atom for def. of tensor orientation.
    -added note on sigma units
    -doc/python/csa-methods-marvin.pdf

  python/solnScatPotTools.py
  python/sansPotTools.py
  python/solnXRayPotTools.py
    -added analyze_chi2 function - added chi^2 analysis to .stats file
    -lifted the restriction that q values must start at q=0 for using
     the efficient uniform-q algorithm. This slows down gradient
     calculations a little bit. 
    -getF accessor: now calls modified.update()
    -normalize: fixup for problem uncovered by use of chi2 function in
        analyze_chi2- for case normalizeIndex>=0.
    -switched to linear interpolation for sampling saxs/sans curves, errors
    -fix for (non-1) vol/rad scale setting.
    -change parameter range argument processing to make easier to specify
      default value
    -fixes for ensemble calculations:
      calcIfromF:
        fixed to work properly with ensembles
    -changed return type of SolnScatPot::qValues(), others to const&.
        This results in a huge speedup, because it's called in inner loops in
        calcI_uniform, and calcDerivs_uniform.

  NOEPot
   showViolations: fixed distance report output. Now print distance range.

  python/selectTools.py
    -convertToAtom: 
        change behavior for Atom arguments when there is a Simulation mismatch.
    -convertToAtomSel: 
        allow input sel's simulation val to be used
    -rigidProteinSelections: 
        fixed longstanding selection error for GLU entry
    -updated helper functions to recognize swig 1.3.36 wrapped objects

  python/simulationTools.py
    -RampedParameter.runAction:
       changed representation of substituted VALUE literal to avoid underflows
    -added a new function named saRefine() which does performs a
     simplified simualed annealing protocol.
    -minimizeRefine/ensembleAvePos: 
      don't try to compute ens. ave. struct for heterogenous 
      EnsembleSimulations.
    -minimizeRefine:  
       added initial cartesian minimization to fix the bond and angle
       terms before the main minimization with minPots.
     -testGradient: 
         cap absolute error threshold at the value tolerance

  python/torsionTools.py
    -new tools for analyzing/manipulating torsion angles

  rotomericStats.py
    -new tools for rotomeric state analysis w/ circular statistics

  python/cdsList_template.i
    __getsplice__: change return type to simple CDSList (from CDSList_out)
      This so that resulting slice template is instantiated.

  python/cdsVector_template.i
     -added support for element-by-element vector division

  python/ivm.py
      removed unused method

  python/trace.py
    -added hack to search XPLORNIH distribution if filename not found and
     it's a relative path

  python/pyXplor.cc
    -pythonStartup:
      now properly call Py_SetProgramName()
    -python_interp:
      now handle the Python -c cmdline argument

  common/pot.hh
  python/pot.i
  python/potList.i
  python/publicIVM.i
  python/pyConvert.cc
    reference counting cleanups for Pot (and PotList) objects
      common/pot.hh
        clear instanceData_ member on initialization s.t. we can properly 
        tell if it's never been initialized by a Python object
      python/pot.i
        added decrRefCount method
        destructor: no longer delete self. This may cause new reference cycles
      python/potList.i
        remapped remove method so that associated Pot's ref count is decremented
        added an unref typemap to decrement all Pot's ref counts before deleting
          a PotList
      python/publicIVM.i
        added an unref typemap to decrement the PotList's ref count before 
          deleting the PublicIVM obj. This unref typemap is necessary for all
          objects which contain an PotList member.
      python/pyConvert.cc
        fromPy(PotList): increment PotList's reference count if the arg is a 
          PotList. If it's a plain Python sequence, then create a Python
          PotList first - so that all pots have their reference counts 
          incremented- and then decremented when the PotList is destroyed.

  common/pdbTool.cc
  common/pdbTool.hh
  python/atom.i
  python/pdbTool.i
    -Added a new method called writeAltLoc() that can write the altLoc
     field.

  python/diffPotTools.py
  python/protocol.py
    -some small fixups for relaxation data read in subroutine in
     DiffPotTools.py and for setting pseudo atoms topology in
     protocol.py 

  python/protocol.py
  python/psfGen.py
    -changes so that Ensembles can be loaded w/ different numbers of
     atoms, and different numbers of sequences. i.e. so that loadPDB
     works for this circumstance. 
    -Converted xplor.command uses to xplor.fastCommand to avoid sync/syncFrom
      added new sync arg to seqToPSF, mods to pdbToPSF to sync after
      complete psf is generated.
    -added topology/parameter support for metal ion atoms

  nmrPot/orderPot
    -initialize Restraint a/bSel using esim instead of its subSim

  python/orderPotTools.py
    -updated orderPotTools.analyze to print ave, min, max order parameters

  nmrPot/relaxRatioPot.cc
  nmrPot/relaxRatioPot.hh
  python/relaxRatioPotTools.py
    -initial support for refining directly against NMR relaxation
     data.

  nmrPot/distSymmPot
    -changed constructor to take two Simulation* args.
    -addRestraint: carefully set current EnsembleSimulation to obtain
     the correct shared memory allocation behavior for 
     EnsembleMemberSimulations.

  python/distSymmTools.py
   -create_DistSymmPot: added optional sim, sim2 arguments

  python/varTensorTools.py
    -mods so that a VarTensor can exist in only a single
     EnsembleMemberSimulation 
    -copyTensor:
        fix so that it actually works.
    -addAxisAtoms:
        add sim argument
        update so that ANI residue number can be 4 digits
    -configIVM_fixRhToOther: 
        bugfix.
    -cleanups so that hetero EnsembleSimulations work properly.
    -create_VarTensor: added simulation arg to updatePseudoAtoms call

  nmrPot/varTensor
    -fixes for EnsembleSimulation tensor parameter atoms :
        introduced local-copies of orientation atoms used for case
        ensembleAxis()==False, ensembleDa/Rh()==True
    -setEnsembleDa/Rh(): 
        fix so that Da, Rh have same values when going from False --> True
    -updates to work with hetero EnsembleSimulations
    -set default value for the freedom member

  python/atom.i
    -Python Atom object pos/vel accessors now return new Vec3 objects
     instead of references. This should have minimal performance impact.

  python/socketComm.py
    added extra communication at client startup to try to shake out Darwin bug

  python/xplorSimulation.i
    fromSimulation: now supports EnsembleMemberSimulations

  python/pyConvert.cc
    fromPython(AtomSel): now allow argument to be an Atom obj

  common/atomSelLang
  common/atomSelLangLex.lex
  common/atomSelLangYacc.y
  common/testClass.cc
    supports subset of XPLOR atom selection language
    now used by EnsembleSimulations, but not by XplorSimulations

  python/atomAction.py
    randomizeDomainPos: now use convertToAtomSel

  common/potList.cc
    -fixed up energyReport values for EnsembleSimulation::AVETYPE_SUM
    -calcEnergyAndDerivs: fixup for ensemble aveType=SUM

  common/derivList
    -derivList: now have special treatment for
     EnsembleSimulations. See help file. 
    -expand Ensemble/MemberSimulation sharing to include the subSim

  nmrPot/posSymmPot
    added fix for case in which rotation matrix is singular

  common/ensembleSimulation
  common/simulation
  common/xplorSimulation
    -added read access to chemType array
    -added residueNum, residueName, segmentName atomNameArr array accessors
    -now allow heterogeneous ensembles of collections of species
    -updates for hetero EnsembleSimulations
      Simulation: changed def of char4 to use FixedVector
      EnsembleSimulation: now share all atom data (name, chemType, etc)
      EnsembleMemberSimulation: no longer use subSim's atomString
    -only potential term which may not handle hetero
      EnsembleSimulations: NOEPot

  python/atomSelLang.i
  python/protocol.py
    -added atomSelLang wrapper- for named selection registration. 
    -updated protocol.updatePseudoAtoms to use this new interface, and
     to treat EnsembleSimulations specially: update pseudo atom
     selection for all member simulations. 

  common/ensembleSimulation.hh
    -EnsembleSimulation: added makeCurrent static method-
    -EnsembleMemberSimulation: added appropriate type() return value
    -now use subsim's select() if size==1

  common/ensemblePot
    -EnsemblePot:
      changed name of set-accessor setWeights to setEnsWeights

  nmrPot/atomDensity
    -Fixed bugs in atomProb based density to atomDensity based grid
     conversion 
    -WriteEDM fixed with the data output. Data would not get divided
     by dmax if data is 0. This avoids NaN in edm output.

  nmrPot/atomProb
      WriteEDM()-> if the data value is zero, data value is not
      divided by dmax. This avoids NaN in edm output

  nmrPot/probDistPot
  python/probDistPotTools.py
  python/simulationTools.py
      -Added new energy function based on cross correlation
      -Redefined rms() value.
      -Scaling depends on number of atoms in selection.  
      -probDistPotTools.py forms the frond end for creating probDistPot class
      -"prob" object is created using probDistPotTools.py now in
        simulationTools.py 

TCL Interface

  tcl/startxplornih.tcl
    -now clear errorInfo so that previous (ignorable) errors don't cause
     spurious printouts in the tcl tests.

XPLOR Fortran interface

  source/cstran.f
    fixes in treatment of CICP abd WCICP arrays. This fixes a major bug 
    introduced on 2009-09-04, where CDIH energy evaluation would be
    nondeterminant.
  source/cstran.f
   finally rationalized use of CICP/WCICP arrays- now allocated by NATOM,
   their use w/ MCMPHI has been removed.

  source/hbdb.f
    setpottype: fix to handle case nij=-2 (i.e. so it doesn't crash)
    hbdbpatt: moved large 2D arrays from stack to heap to avoid segfaults
              when running 32 bit code on amd64 (on scalar)

  databases/torsions_raw/setup_new_shortrange.tbl
    -updated to call xrama instead of rama

Topology and Parameters

Low Level C++ routines

  CDSlib/cdsRegex.hh
    findIndex(): added default offset value

  CDSlib/fixedVector.hh
    added pointer() accessors

  common/semaphore.cc
    wait: now protect sem_wait from EINTR. This so that e.g. strace
    doesn't crash the program.

  common/xplorWrapProc.cc
    remove atomRadius array manipulations

  bin/findSwig
      added version 1.3.36, changed various files so it works.

  common/xplorSimulation.cc
    syncTo: moved assertion into if clauses where it's really required

  common/simulation.cc
  common/simulation.hh
  python/simulation.i
    Simulation: added syncAllSimulations helper static method

  common/xplorWrap.cc
  common/xplorWrapProc.cc
    now use Simulation::syncAllSimulations where appropriate

  common/ensembleSimulation.cc
    enable line-buffering for stderr. Without this, output is lost when
    the children are killed.

  common/semaphore.cc
    unified the Sys V and posix semaphore code in semaphore.cc. This 
    simplifies make dependecies and the compilation of nmrPot/test

  common/xplorWrapProc.cc
    generating random seed: now use rand num from SimulationWorld

Architecture Specific Notes

  arch/Darwin_8_x86
    updates for gfortran 4.4. Still some problems, so distributed
    binary still compiled w/ gcc-4.2

  arch/equivList
    update such that AMD64 platforms use the ia32 build if running a 2.4
    kernel (this because 2.4 doesn't properly support posix semaphores)

  arch/Linux_2.6_x86_64 (amd64)
    switch to posix semaphores - simpler and more robust

		     Changes from 2.22 to 2.23


Example Scripts:
  new eginput/pre example of using PRE distance restraints with the
  improved/simpler PRE interface.

  new eginput/diffTens example set including scripts for relaxation
  data processing, docking and structure refinement using rotational
  diffusion tensor-based restraints.

  eginput/gb1_rdc/refine.py
    now perform SVD during simulated annealing

  eginput/gb1_rdc/analyze_ProbDistPot.py
    New analysis script which includes ProbDistPot to restrain the
    average structure to the calcualted input structure ensemble.
      Analyze the structural file produced by running anneal.py. Check for the 
      violations in energy, rmsd and stereochemical violations between average 
      structure calculated with and without using probDistPot.

  eginput/PSF_generation/genLigand.py
    helper script to generate top/par info from a pdb
    file. Currently, CONECT records are ignored, so the molecule
    should be grouped as a rigid body.

  eginput/dna_refi/validate.py
      added validation script

  eginput/dna_refi/ensemble.py
      now support -quick flag
      noeNH force constant reduced from 200 to 1
      xray scattering terms now have radiusType specified

  eginput/PSF_generation/testHBDB.py
    added test of Python interface helpers for HBDB

  eginput/PSF_generation/pdbTest
    updated to reflect change in pdb entry 2ycc (mutation from lys to M3L

  eginput/runAll
    now can use the runDirPrefix env variable to specify alternate
      location for the runDir
    now set the return status appropriately

  eginput/PSF_generation/genCircPep.py
    now initialize random seed (by time) and decrease MD stepsize

  eginput/PSF_generation/gen-edta-dna.py
  eginput/PSF_generation/gen-edta-k28c.py
    added generation examples for CED and TED residues

Help System:
  updated pyXplor -py -pydoc -k so that keyword search works better.

Atom Selection Language

  added the PSEUdo token- used to select pseudoatoms.


Python Interface

  python/diffPotTools.py
  nmrPot/diffPot
        added support for relaxation data processing.
        added support for optimization of diffusion tensor
        temperature.

  python/prePotTools.py
    create_PREPot:
      added clockResid, clockSegid arguments
    addClockAtoms:
      rearranged argument order
      rework so that preexisting clock atoms can be used.
    renamed T?X/Y atoms to T?A/B
    topologySetup: will now fix or free appropriate atoms


  python/atomAction.py
    centerOfMass: return (0,0,0) if selection empty, mass=0 or unknown atoms

XPLOR Fortran interface

  source/rama_gaussians.f
    ALLOCRAMAS: add shortcut return if oldsize==newsize

  source/hbdb.f
    fixup for if-clause which assumed logical short circuit (not-Fortran)

  source/nbonds.f
    fix possible memory leaks where heap pointer was assumed to be >0


  source/x86_64time.f
    increased heap debugging messages

Topology and Parameters

  toppar/nucleic-1.1.par
  toppar/protein-1.0.par
    be more careful about restoring previous echo/message state

  toppar/edta.par
    added include protection ; now include ion.par for MN params
  toppar/ion.par
  toppar/ion.top
    added include protection (to prevent loading more than once)
  toppar/nucleic-1.1.par
  toppar/protein-1.0.par
    moved edta.par include protection into that file


  toppar/axes-1.0.par
    removed dependency on protein.par: 
        kbond is now hardcoded to a value of 1000

  toppar/edta.par
  toppar/nucleic-1.1.par
  toppar/nucleic-1.1.top
  toppar/protein-1.0.par
    added TED nucleic residue - modified from Junji Iwahara's files.
    Parameters for the portion of the conjugated EDTA tag shared with CED
    is now in edta.par- it is only loaded once. protocol.py was updated
    such that erasing these parameters is possible.

  toppar/protein-1.0.par
  toppar/protein-1.0.top
    CYSP: added missing methyls impropers
    added CYSP and CED spin-labelled residues to the topar files

Helper Programs/Scripts

  bin/targetRMSD.in
    fix for case selection != selection2 and diffSeq==True
    fix so that running with -diffSeq works again
    changed doFit variable name to be less confusing


  bin/pbsxplor.in
    try to get pbs output to a single file in the current directory

  bin/pyXplor
  bin/xplor
    allow the # character in command-line arguments
    fixup for SMP process startup
    for localhost-spawned jobs, make separate TMPDIR for each process
    update TMPDIR to be unique for localhost MACHINES
    TMPDIR setting: now use /dev/shm if it's writable. Can be overridden
    by XPLOR_TMPDIR.
  bin/xplor.in
    now set TMPDIR to a subdirectory which is created (and destroyed at
    the end of this script). For this to work, the execs were removed (so
    that removal would happen after execution of bin.$ARCH/xplor.
    
    This change will help reduce spew in /var/tmp and more importantly,
    will avoid mmapAlloc crashes due to the presence of old mmaped files
    left when a jobs was aborted.

  bin/testDist.in
    set ECHO to /bin/echo on Darwin (thanks to Ben Eisenbraun)

  bin/findXcookie
    fixed to deal with case that xauth returns more than one match


  bin/compareTensors.in
   new helper used to compare two alignment tensors

  bin/calcSAXS.in
      changed default normalizationIndex to -3
      increased the precision of the output

      added -fit option now calls solnScatPotTools.fitParams, and includes the
      solvent boundary layer.

  bin/testDist.in
    added tests in eginput
    add infrastructure for running quick tests in eginput


build setup:
  modify Makefiles s.t. lapack/blas are autobuilt if LAPACK/BLAS_LIB isn't
  set.

Python Interface

  python/varTensorTools.py
    calcTensor: remove rdcs, csas from calc if their scale val is 0
    VarTensor_analyze:
      fix logic for syncAxisAtoms
    added helper function saupeToVarTensor
    calcTensor, calcTensor_ensemble:
      now make alignment tensor orientation right-handed
    added function unRegisterTerm; added info to ivm topo config function


  nmrPot/varTensor.cc
    Rh: protect against returning (slightly) negative values
    energyMaybeDerivs1:
      enabled derivative calcs for the case ensembleAxis==True

  python/protocol.py
    ion.par/top: added reset support in initParams/Topolgy
    initCoords: now allow file or string to be specified
    initCoords: use new bfactors, occupancies pdbTool accessors for speed
    initCoords: now pass sim to correctSymmetricSidechains
    matchInexactEntry: logic to read H2 and H3 (HT1 and HT2) atoms
    loadPDB:
      now return the InitCoordsResult from initCoords
    initHBDB:
      fix to work with multiple segments
    cartesian/torsionTopology:
      updated so that rdcPot, prePot and planeDist pseudo atoms get topology
      autoconfigured

  python/simulationTools.py
     1. Added two new passing arguments to structureLoop(averageRestrainSel &
        averageRestrain) 
     2. minimizeRefine: 
          added a straight gradient minimization before calling AnnealIVM()
          added new code to reflect the changes made in atomDensity & 
  	    probDist class.
   StructureLoop:
      Added argument named averageRestrain in to control the inclusion
        of probDistPot energy term in average structure calculation.
      New member named "inconsistentAveStruct" which 
        is set to 1 if the average structure calculated have an 
        energy or violation greater than the calculated structures.
        In addition, warning will be written on to the ave-structure 
        pdb file

  common/atomSel.hh
    AtomSel:
      removed the non-const version of the indices() method

  nmrPot/solnScatPot
      fixed gradient for case useGlobs==TRUE and normalizeIndex>-2
        added volumeScale, radiusType
        added boundary-layer solvent contribution to SAXS calculation.
        Also- now allow atom radii and excluded volumes used in excluded
        solvent calculation to float independently
         (as done in Svergun et al. J. Appl. Cryst. 28, 768 (1995).)
        Some changes commented-out to allow all tests to pass.
    optimization:
      converted F (scattering amplitudes at all angle values) from vector of
      vectors to matrix.
    change to meaning of glob entries - now assume weight is normalized
    energyMaybeDerivs2: various optimizations

  python/sansPotTools.py
  python/solnXRayPotTools.py
  python/solnScatPotTools.py
      svergun volume/radius params: correct to reverse-engineered values
      create_SolnXRayPot: added rho0 argument
      create_SansPot, create_SolnXRayPot:
        added volumeScale argument
    analyze: changed floating format of output  saxs data
    added fitParams helper function used to fit solvent parameters of the
    scattering curve.

  nmrPot/csaPot.cc
  nmrPot/cstMagPot.cc
  nmrPot/jCoupPot.cc
  nmrPot/noePot.cc
  nmrPot/orderPot.cc
  nmrPot/planeDistPot.cc
  nmrPot/posRMSDPot.cc
  nmrPot/prePot.cc
  nmrPot/psolPot.cc
  nmrPot/rdcPot1.cc
    added better checking for restraint table input errors

  python/selectTools.py
    correctSymmetricSidechains: 
      speed optimizations
      performance improvement by restricting initial atom selection


  common/pdbTool
    added occupancies, bfactors accessors

  nmrPot/atomProb
    Added a new ScaleType in atomProb class called normalize. 
    added getGrid accessor

  python/symmetry.py
    testC2: now use mat3.rotationAmount

  python/mat3
    added functions:
      det, rotationAmount
    added method:
      scale
    rotVector: added code for special case (from intVar/dint-node.cc

  python/cdsMatrix.i
    SymMatrix: added scale method

  python/cdsVector_template.i
    added element-wise operator*
    added numpy-style (element-wise) vector multiplication
    added pow, removed duplicate __mul__

  python/minimize.py
    added a simplex optimization routine (from scipy) and test

  python/potList
    added the keys() method

  nmrPot/atomDensity
  python/atomDensityTools.py
    -added variable to control the atomRadius of the generated 
    -Updated the atomDensity to incorporate grid rotation & translation
    -map / added new code for picking Map rotation & 
     translation that gives energy less than the 
     given percent of the max energy. 


  nmrPot/probDistPot.cc
    New energy term which restrains a structure to a target map
    (computed from an ensemble, EM map, SAXS curve, etc)

  nmrPot/atomDensity.cc
  nmrPot/atomProb.cc
  nmrPot/probDistPot.cc
      Done optimization on the files to reduce the computational time.


  nmrPot/atomDensity.cc
  nmrPot/atomDensity.hh
  nmrPot/probDistPot.cc
  python/tests/probDistTest.py
      Added rotation and translation to the grid class.

  nmrPot/atomDensity.cc
  nmrPot/atomDensity.hh
  nmrPot/probDistPot.cc
  nmrPot/probDistPot.hh
  python/atomDensity.i
  python/probDistPot.i
  python/tests/probDistTest.py
      atomDensity.cc & atomDensity.hh-> class which calculates the 
      reweighted atom densities.
      probDistPot.hh & probDisPot.cc ->  energy term based on reweighted 
      atom density.
      probDistTest.py-> test files for the energy term mentioned above.

  common/ensemblePot
  common/ensembleSimulation
  intVar/publicIVM
      implemented sum aveType in EnsembleSimulation
      signal_childDied:
        only abort if one of the ensemble processes has exited.
      EnsemblePot:
        added a local set of ensemble weights. Updated all appropriate 
	pot terms to use the accessor to get the correct set of weights

  common/xplorPot
  common/xplorSimulation
    added some nonfunctional stubs for XplorPot ganging

  python/pot
    all potential terms:
      removed a built-in reference cycle which prevented Python and C++
      Pot objects from being deleted.

  python/avePot1
  common/avePot.cc
    violations: now do proper rounding in float->int conversion 
    avePot:
      now save a copy of the averaged pot. term so that it doesn't get deleted.

  python/xplorPotTools.py
    fixed HBDB analysis

  nmrPot/selNBPot.cc
    NeighborBin::findXYZBin: make sure return result is in range.


  python/atomSel.i
      fixed __eq__ method
  python/atom.i
      added __eq__ method: can now compare Atom objects
  python/posDiffPotTools.py
      now crash if no atoms are selected

  common/xplorWrap.cc
      XplorWrap::select: now add linebreaks to lines longer than 125 char

  common/xplorWrapProc.cc
    better randomization of MMapAlloc uid

  nmrPot/planeDistPot
    showViolations: now print range rather than single target distance

  python/psfGen.py
    pdbToSeq: optimizations by reordering and use of elif
    pdbToSeq: now recognize water
    residueTypes entries are now autofilled from the registered (in
      protocol) topology files - when deduceSeqType is first called

  python/regularize.py
    fixupCovalentGeomIVM: output formatting fixup
    fixupCovalentGeomIVM: added translateRegions argument

  python/ivm.py
     - fixed problem of run exiting during minimization if temperature=0:
          do bathTemp=0 check only for integration.
     added constrainBond method
     hinge: replaced '==' w/ 'is' when comparing AtomSel

  python/atomSel
    fixed __eq__ s.t. AtomSels can be compared w/None; added test


TCL Interface

  tcl/noe_reporting.tcl
    replaced ln --symbolic with ln -s

Internal Variable Module

  intVar/dint-node.cc
    HNodeTorsion(): properly treat speecial case where |rotDir| almost 1
    removed dubious conditional for bend-type nodes


Low Level C++ routines

  CDSlib/cdsComplex
    added / operator for noncomplex arguments
    complex multiplication by float fixed. Test added

  CDSlib/cdsMatrix
    added setCol/Row and tests
    optimization: use memcpy instead of for loop


		     Changes from 2.21 to 2.22


Helper Scripts

  bin/calcSAXS.in
    fixed so that the -psf flag is actually used
    added the -expt command-line option for better comparison w/ experiment
    added -selection and -normalizeIndex cmdline options
    add support for normalizeIndex=-3
    added -nostderr option so that runAll tests pass
    added the -fit and -verbose flags
    now print out chi2 value

  bin/pbsxplor.in
    added pbsxplor convenience command - to launch Xplor-NIH jobs without
    writing a PBS script

  bin/calcTensor.in
    added -ensemble flag/capability to properly treat a structural ensemble

  bin/targetRMSD.in
    now support selection2, fitSelection2 cmd-line arguments

  bin/findClusters.in
    new script use to find clusters of similar structures

  bin/getBest
    now support absolute paths

------------------------------------------

Example scripts

  eginput/gb1_rdc/analyze.py
    averageFilename: now include SCRIPT

  eginput/gb1_rdc/aveStruct.py
    added -psf flag

  eginput/gb1_rdc/anneal.py
  eginput/gb1_rdc/refine.py
    reduce high-temp nonbonded force constant
    updated to use new massSetup, torsion/cartesianTopology capabilities

  eginput/PSF_generation/pdbTest
    added example with resid=0

  eginput/dna_refi/ensemble.py
    fixups to remove parameter errors
    moved initCoords/covalentMinimize to avoid ANI atom warnings
    fixed up xray setup for compatibility with new defaults

  eginput/EIN_HPr_diffTens
    new example illustrating the use of diffusion tensor-based restraints
    in protein-protein docking

  eginput/dna/axis.pdb
    changed axis atom coords s.t. bond lengths are 1A

------------------------------------------

Topology and Parameter file changes

  toppar/protein-1.0.par
  toppar/protein-1.0.top
  toppar/protein-2.0.par
     added setting of toppar version variable

  toppar/protein-2.0.top
     fixed ALA HB methyl def; added version variable

  toppar/axes-1.0.par
    updated to include parameter pseudo atoms used for RDC Da and Rh

------------------------------------------

Changes to low-level libraries

  CDSlib/cdsString
    added strip() method

  CDSlib/cdsMath.hh
    added cube() inline function

  CDSlib/cdsList
    added 2nd DEFAULT_ASIZE template parameter
    added qsort method

    fixed array allocation s.t. memory is not wasted
      (was array of void*, now array of char)
    fixed to that DEFAULT_ASIZE is applied to the copy constructor
    added letterObj() method for debugging.

    template arg mods s.t. g++ 4.2, 4.3 will compile

  CDSlib/cdsString.cc
    const fix

------------------------------------------

TCL interface

  tcl/import_pipp.tcl
  tcl/import_xeasy.tcl
    increased verbosity of read functions

  tcl/aeneas_tools.tcl
    defaultJointFilter: added options -passNetFrac and -minExpectedNetScore
    capitalization fix

------------------------------------------

Common C++ Interface

  common/ensembleSimulation.cc
  common/ensembleSimulation.hh
    fixup const method declarations:
      members of the MemberData struct *can* change for const objects

  common/coordComparer
    added CoordComparer class- to measure differences from one step to the 
      next

  common/pot.hh
  common/potList
    Pot: added empty updateDelta method
    PotList: created implementation which calls updateDelta for each 
             contained potential

  common/pdbTool.cc
     pdbTool read optimization.
        major bottleneck was the use (primarily construction) of the old 
	pdbHash table used to map (segid resid atomName) to id. Replaced this 
	data structure with something faster and more balanced.
        Other optimizations include less use of StringStream and subString 
        functions which have some overhead.
      
        The code includes a fix: previously, the least significant digits of 
	the floating point numbers were filled with garbage. During to 
	rounding differences, this changes the test output slightly.

      created AtomToIndex class to formalize interaction with the
      num/name/segid -> index map
      Also, fix bug encountered for minresids<1.

    writePDBAtom:
      clamp values of bfactor and occupancy fields such that pdb format is
      preserved in the face of invalid values


------------------------------------------

Python Interface

  python/nbond.i
  python/nonBondTools.py
    readXplorRadii:
      optimization and fixup of functionality for 1-3 and 1-4 contact 
      exclusion generation (by using a C++ routine). This will speed up the 
      first invocation of vdwViolations.

  nmrPot/planeDistPot.cc
    addRestraints: print warning if no restraints read
    addPlaneAtoms: left justify segment name
    added simulation() accessor

  python/solnScatPotTools.py
    analyze changed output format for calcd/exptScale values
    changed default cmpType to plain

  python/regularize.py
    fixupCovalentGeom: don't process residues not in selection

  python/ivm.py
    now call updateDelta before each step
    run: added check for zero temperature

  nmrPot/solnScatPot
      mods so that globCorrect can be called in the middle of a 
      dynamics/minimization run if a threshold # of steps have been taken, 
      or if an atom has moved too much.
      auto glob correct fixes
      verbose: changed from bool to an int
      setGlobCorrectReference: now also set globCorrectCalcType
      info: output auto glob correct info
      added new normalization type: minimizing chi^2 (normalizeIndex=-3)
      normalizeIndex=-2 gradient fixed
      moved calc of excluded solvent scatt contribution from python to 
        C++ layer
      add read-accessor for radii member

  python/derivList.i
  python/pyPot.i
      update DerivList python interface to work with 
         PyPot::calcEnergyAndDerivs
      added tests to exercise this
      updated pyPot docs accordingly.

  python/simulationTools.py
      now include summarizeExtraQuantities output in .stats output
        use registerExtraStats function
      get extraStats reporting and output working, including for potLists of
        terms which have extraStat
      testGradient: added the eTolerance argument

  python/rdcPotTools.py
    added R factor, Da and Rh to extraStats
    removed unused psf_template
    create_RDCPot:
      file argument can now be a sequence of filenames
    now support CAHA measurements

  python/varTensorTools.py
    calcTensor:
      now set oAtom to the origin, if its coordinates are invalid.
    addAxisAtoms: left justify segment name

  python/protocol.py
    added support for versioning of topology and parameter files
    initCoords:
      move call correctSymmetricSidechains to after matchInexactAtomEntry call
    initHBDB:
      added restraintFile argument for specifying fixed HB restraints.
    cartesianTopology:
      fixed breakAllBondsIn statement to work with non-trivial nonstring
        selections
    torsionTopology and cartesianTopology now configure the appropriate 
      topology for pseudoatoms associated with VarTensor, PREPot and 
      PlaneDistPot pot. terms
    massSetup:
      sets mass and friction settings for pseudoatoms associated with 
      VarTensor, PREPot and PlaneDistPot pot. terms

  python/planeDistTools.py
  python/prePotTools.py
  python/protocol.py
  python/varTensorTools.py
    moved initialization of parameters for axis pseudo atoms from *Tools.py
    to protocol.py. Now use axes.par.

  python/selectTools.py
    correctSymmetricSidechains:
      -added backwards-compatibility hack for incorrect ARG sidechain chi5
       torsion definition, and corrected it for future toppar versions
      -changed allowed range of chi2 for TYR, PHE to 0..180 degrees

  nmrPot/planeDistPot
       added useSign method - now allow signed atom-plane distance

  python/prePotTools.py
     new set of helper tools for PREPot
     now properly supports EnsembleSimulation

  nmrPot/prePot
    regularize txmin/max accessor cases
    info:
      print out much more state information
    added clock atom read-accessors with rationalized names
    showViolations: updated to support showAllRestraints

  python/xplorPotTools.py
    for HBDB term, now place output of HBDB print in the .viols files


  python/residueAffPotTools.py
    create_ResidueAffPot: added intradomainContacts argument

  surfD
    new algorithm for numerical representation of a molecular surface.

  nmrPot/diffPot
    new potential term for encoding a rotational diffusion tensor restraint

  python/psfGen.py
    pdbToSeq: fixes so residue number=0 works

  python/cdsTypeMaps.i
    now fail gracefully if None argument is specified

  python/checkWrap.py
    fixups to get minimally working again
      in particular findNested was completely broken...
    fix to catch variable names with surrounding () in NewPointerObj
    added -v flag

------------------------------------------

Documentation Updates

  helplib/nih-py-planeDistPot
    corrections from J. Ellena

  helplib/nih-py-prePot
    regularized txmin/max accessor cases

  helplib/nih-py-ensembleSimulation
    now document identical nature of each ensemble member

  test/fiber.inp
    added example of writing out diffration data

  online tutorial:
     conversion to pdflatex and replaced large bitmaps with pngs
     updates from Jan. 2009 Xplor-NIH class

------------------------------------------

Platform Specific

  arch/Linux_2.4_x86_64/Makefile.defs
    PROFILE=1
      -no longer try to get gprof working. It doesn't work with shared libs, 
       so it's hopeless.
      -now try to get stack callback info from oprofile using
       -fno-omit-frame-pointer
    added support for version 11 of the Intel Compilers


------------------------------------------

XPLOR Interface:

  source/fxmap.f
    FXBFT2: fixed argument list for BSLTBL call



---------------------------------------------------------------------------

		     Changes from 2.20 to 2.21

XPLOR Interface

  source/parser.f
    set print:
      now attempt to close a file before reopening for write. This may be 
      dangerous, but it fixes use of the -smp flag under Darwin.

  source/darwintime.f
    now allow closing of unit 5 (stdin). Dangerous?

  source/ncs.f
  source/rotlsq.f
    changed output from unit 6 to PUNIT

  source/xplorFunc.f
    fixups flagged by g77. In particular:
      it doesn't like initialization of file-static data (initialized in
      XPLOR_INIT). Hopefully, this will always by initialized to zero and
      that corresponds to .FALSE.

Python Interface

  DistSymmPot: new Python/C++ potential term:
    DistSymmPot - for distance symmetry restraints
    supports both ensemble-averaged symmetry and strict symmetry of each 
    ensemble member

  intVar/dinternal.cc
    resetCM: handle the case in which all atoms are fixed

  python/maxLikelyFit.py
    -Added a new method in maxLikelyFit.py for calculating the Average
     RMSD and made necessary changes in mleFit to reflect this. 
    -Fixed the methods in maxLikelyFit.py that is used to write the
     variance of selected atoms and rotation & translation matrix
     obtained from maximum likelihood fitting. 
    -Added a new method for writing out the PDB files of the fitted
     structures along with the mean structure in maxLikelyFit.py 

  noePot:
   fixed bug in which spaces were required between selection parentheses

  python/noePotTools.py
    create_NOEPot: now allow file arg to be list

  python/nonBondTools.py
    changed defaultRadiusScale from 0.9 to 0.8

  common/pdbTool.cc
      Changed default value of b factor in pdbTool.cc from 1.0 to 0.0.
      This matches the default value given by the XPLOR interface.  The
      default occupancy value remains at 1.0, since that matches
      classic xplor.   
      
  python/posDiffPotTools.py
    -analyze: added more info output
    -set a default threshold value (used to det. # of violations)

  nmrPot/posSymmPot.cc
    fixed the definition of violations() to use threshold()

  common/potList.cc
    rms():
      change calculation method for the case of same type of restraint, 
      but numRestraints=-1.

  python/protocol.py
    loadPDB: 
      -added deleteUnknownAtoms argument
      -added optional model argument
      -now catch exception in initCoords so that currentSimulation is
       properly reset.
    initCoords:
      -allow maxUnreadEntries to be None to disable the check
      -fix so that erase option only affects atoms in selection.
      -add call to selectTools.correctSymmetricSidechains
      -properly handle 2nd maxUnreadEntries (fractional) component
      -now returns an object with two lists--one of the b factors of
       every atom in the simulation, and one of the occupancies of
       every atom in the simulation.  
    initNBond:
      changed default rcon and repel values to the final values used in
      refinement scripts

  python/pyInterp.i
    added pyInterp python interface

  python/psfGen.py
    -fixup for DNA generation: better way of getting resid range
    -Added code to automatically parse PDB SSBOND header lines.  It's
     called by pdbToPSF after reading in the sequence, and
     automatically calls addDisulfideBond for each SSBOND line.   

  nmrPot/rdcPot1.cc
    -addRestraints: now print warning if no restraints read
    -added support for varying axis atoms separately in different
     ensemble members 

  python/regularize.py
    -fixupCovalentGeomIVM: covalentViols:
    -added fixupCovalentGeomIVM:
      -the old version of fixupCovalentGeom, which has grouping features
       not present in the new version
      -deal with terms which return violations==-1
      -in case multiple structures are found w/ same # of violations, 
       set the return structure to that w/ the lowest energy.
    -addUnknownAtoms: added optional maxFixupIters arg

  python/selectTools.py
    convertToAtom:
      fixed exception error
    added correctSymmetricSidechains - to swap atoms to conform to
      Xplor-NIH conventions: Valid range for phe, tyr, and asp
      chi2 and glu chi3 is -89.99..90 degrees.  Beyond that, the names are
    getSegsResidues:
      -changed invocation so that it now accepts AtomSels
      -Bugfix.  Old code was returning a list of
       residue numbers & names with an entry for each selected atom,
       resulting in many repeats.

  python/simulationTools.py
    fixed b-factor calc in aveStruct.py and in StructureLoop.genAveStats
  python/simulationTools.py
    minimizeRefine:
      added arguments rigidRegions, fixedRegions
      fixed bug in which only one potential term was scaled

  nmrPot/solnScatPot.cc
    weights member:
      changed accessor from MODACCESSOR to explicit, because
      setting it can change exptScale, so it must be recalculated.
    calcGlobCorrect: 
      -fixes so it doesn't have side effects. It should now properly work
       to correct for small numAngles, even if useGlobs=False.
      -overriden so that corrected I(q) can be explicitly specified
    -fixes to normalization - introduce ave. normalization (index=-2)
    -now throw exception if calcing derivs when using non-uniform calcType
    -fixed rms definition to better reflect energy

  python/solnScatPotTools.py
    analyze:
      updated calculation of deviation and chi^2 
      now always scale calcd/expt by the proper normalization

  python/sansPotTools.py
  python/solnXRayPotTools.py
    no longer pre-normalize weights for chi^2 calculation: 
      this is now handled by the potential
    create_*Pot: now throw exception if no datapoints are defined.
    moved globRules to common solnScatPotTools location
    create_solnXRayPot:
      -fix up treatment of chi^2 weighting for normalizeINdex>=0
      -fixup handling of weights and normalizeIndex
       aSelection now excludes ANI atoms
       added normalizeIndex and preweighted arguments
    getCombinedAtoms:
      optimization to remove creation of AtomSels in an inner loop.
      This changes output because the atom selection used the hydro
      keyword, while 
      now all atoms whose name starts with "H" are chosen (the correct
      behavior). 
    useGlobs:
      -optimization: remove use of AtomSels inside inner loop of glob 
       determination
      -fixed so that it handles multiple segments

  python/varTensorTools.py
    configIVM:
      now enable topo setup for case of ensembleAxis

  python/xplorPotTools.py
    add some support for the NCS term

  common/xplorSimulation.cc
    -fixed setAtomMassArr so that XPLOR-side values would get updated by 
     implementing an overloaded version in XplorSimulation

Example Scripts

  eginput/runAll
    Removed the -f option

  renamed 
    eginput/marvin => eginput/pasd

  eginput/protG/protG_mkpsf.inp
    actually make peptide bonds...

  eginput/pasd/cvn/.runAll
    add example of using mleFit


  eginput/PSF_generation/genDNA24bp.py
    added genDNA24bp.py example (using fixupCovalentGeomIVM)

  eginput/gb1_rdc/anneal.py
    fix so that commented-out rdc code will work (if uncommented)

  eginput/gb1_rdc/pairRMSD.py
    Added a command line option called -noFit. If specified, the
    structures are not fitted together before the RMSD
    calculation.

  eginput/gb3_ensemble/order.py
    update NOE setup to use Python/C++ NOE term with explanatory comment.

Helper commands

  bin/xplor
    -The -smp command-line option now works correctly for Intel Macs.
     It now works on all platforms except for ppc Macs.
    -fixup for -scyld when num_threads<2 and SCYLD_PROCESSES>#nodes
    -fixed: changed  == to =

  moved eginput/protG/tang.py to the helper script bin/torsionReport
    fixed up for degrees --> radians change in Dihedral::value

  added getBest helper to toplevel bin directory. This helper grabs
    the structures in a .stats file - it is useful for command-line
    manipulation. 

  renamed:
    eginput/dna_refi/plotIrange.py => bin/calcSAXS
    added -psf and -help-script options

  bin/pdb2psf
    -Added a command line option to delete the unknown atoms from the PDB file 
     before the PSF file is been written. 
    -Bugfix.  If pdb2psf is called on a file that doesn't contain any
     periods (eg., 'temp'), the resulting PSF file is named '.psf'.   
     Changed to check for PDB filenames that don't contain periods, and
     to produce PSF files with appropriate names (eg., 'temp' -->
     'temp.psf') 

  bin/calcDaRh.in
    fix so that rdc scaling actually works.


  bin/targetRMSD
    Added a command line option called -noFit. If specified, the
    structures are not fitted together before the RMSD
    calculation.

Parameters / Topology

  toppar/protein-2.0.top
    ARG: swapped chi5 definition to match IUPAC

  toppar/nucleic-2.0.par
    added base angle corrections from the 1.1 file


Low-level modifications

  CDSlib/cdsVector.hh
    added sum() function

  The gfortran compiler (as of version 4.3) now works for AMD64.


		     Changes from 2.19 to 2.20

XPLOR Interface

 merged FX-plor functionality. Special thanks to
  Wen Bian, Gerald Stubbs and Don Marvin for making this possible.
  See documentation at
    http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/
  ------------------------------------------------------------
  added fortlib/specfun/ribesl.f
  ------------------------------------------------------------
   hbdb
      allow zero value of hbprnfrq to disable facility
    ------------------------------------------------------------
      source/genic.f
      source/prototypes.hh
        replaced the DELTI2 subroutine with deleteAtoms, which has
        been modified so that it can be easily callable from the C++
        interface. 
------------------------------------------------------------
  source/xplorFunc.f
    xplor_init: added flag so its not executed twice

------------------------------------------------------------
  arch/Linux_2.2_i686/Makefile.defs
  common/simulation.cc
  source/linuxtime.f
    mods to support gcc/gfortran 4.3 on ia32
------------------------------------------------------------
  source/carb.f
    printcshifts:
      define RMSD as a weighted average of CA and CB shifts
      define NUMBER ans the sum of CA and CB violations
      DECLAR RMSD   --> $RESULT
      DECLAR NUMBER --> $NUMBER
------------------------------------------------------------
  source/etor.f
    added a tolerance parameter dihed_colin_tol:
      the value of cosine of the angle between two bonds above which the bonds 
      are considered colinear. Previously, it was a hard-coded constant.
    it can be set via the command set TOLTorsion <val> end
    the current value can be accessed via the $DIHED_TOL variable.
------------------------------------------------------------
  source/x86_64time.f
  mods to allow compilation using gfortran
------------------------------------------------------------

PASD/Marvin 

  Example Scripts
    eginput/marvin/cvn/refine.py
      Added a final refinement stage.  Refine.py is based on
      eginput/gb1_rdc/refine.py, with filenames changed and only NOE
      and TALOS restraints enabled.   
      
    eginput/marvin/cvn/talos2cdih.tcl
      Also added a short TCL routine to convert TALOS restraints into
      a XPLOR CDIH file, using the rules worked out for Marvin.
      Marvin reads the TALOS files directly, so it doesn't need this,
      but refine.py needs an XPLOR constraints dihedral file.  

    eginput/marvin/cvn/talos/pred/
      Now shipping the individual-residue TALOS output for the CVN
      example, since we're using it in the example structure
      determination. 

    eginput/marvin/cvn/check_talos_predictions.tcl
      Converted CVN eginput scripts to those used for structure
      calculations in paper.   
  
  TCL Interface

    tcl/aeneas_tools.tcl
      -Made writing of .peaks, .shiftAssignments, and .exceptions files
       optional.
      -Added stereopartner recording to standard3d and 4d initMatch
           procs to support stripe routines  
      -Added support in standardJointFilter for applying netfilter
           contact map to different pots than those used to generate it 
      -Bugfixes to correctShiftOffset proc.  In determining output
       report, was comparing calculated offset to minOffsetToApply,
       rather than comparing their absolute values.   
      -Changed flag name in solvent line proc from shiftTolerance to
          just tolerance, to match all the other procs' flags.   
      -correctShiftOffset: minOffsetToApply argument:
          changed default value from 0.02 ppm -> 0.015 ppm
          bugfixes
      -Eliminated calls to initializeLikelihoodsFromFilters in
          standardJointFilter.  These were overwriting the previous
          likelihoods generated from each peak assignment's network
          score.   
      -Added -verboseOutsideSpectrum flags to match*d procs.  Lets
          me control whether complaints about peaks being outside of
          the spectrum are added to the remarks. 
      -Removed symmetryFilter proc
      -Removed primarySequenceDistance proc
      -Removed generateShiftAssignmentPeakPositionLikelihood proc,
          which was never used.   
      -Removed markCrowdedPeaks, which is no longer used
      -Removed stripeCorrection proc, which is replaced by code in
          newstripe.tcl 
      -Removed netfilter proc: functionality moved to netfilter.tcl
      -Removed secStructFilter proc - never used.
      -Updated correctShiftOffset proc, to agree with my old
          codebase.  Now includes flags for minimum number of
          symmetric peaks,  below which no offset will be calculated,
          and minimum offset to apply, below which I judge that it's
          just noise and not worth applying.  Finally,
          correctShiftOffset now throws an error if it does find an
          offset worth correcting, so that the standard*match proc can
          know that it needs to re-match the peaks.   
          This routine might be worth getting rid of entirely, since
          it appears to be relevant for IL-4 only.  My initMatch
          scripts for IL-4 now apply Dan Garrett's hand-determined
          offset corrections to the peak locations before matching, so
          correctShiftOffset isn't even used in that case. 
      -Removed netFilterMini: replaced by code in netfilter.tcl
      -Updated standard3dInitMatch in a few ways:  
           A.  Can now define solvent ranges here, so that solvent
               peaks are removed consistently with any hand-solvent range
               determination 
           B.  Now drops shift assignments whose proton shifts are
               outside of the from and to spectral ranges.  This replicates
               what Dan Garrett does in STAPP, whose parameters don't
               allow folding or aliasing along proton dimensions.   
           C.  Can now define the size of the broad tolerance (in ppm)
           D.  Changed call to correctShiftOffset to handle the
               possibility of an error being thrown (described above). 
           E.  Added -allWeakPeaks flag, which causes all peaks to get
               distance ranges for weak peaks.  Needed because some
               datasets don't have peak intensities available.
           F.  Added -writeEachStage flag, which forces shift assigns,
               peaks, and exceptions to be written at several places during  
               initialMatch, to support statistics gathering on prefilters
           G.  Changed to call new stripe filter code
           H.  Changed standard tight tolerance from 0.03 ppm to 0.02
               ppm, which is what my 2.1.19 code used.   
      -Made corresponding changed to standard4dInitMatch
    tcl/deprecated.tcl
      includes symmetryFilter and primarySequenceDistanceFilter procs- 
      used in old scripts.
    tcl/netfilter.tcl
      -moved the network filter code out into a separate file
      -temporary? change to rollback likelihood
          calc change.  I now just give previous likelihood = 1 for PAs that
          pass, and 0 for PAs that don't.  Was what I had for 1/24/08 marvin
          runs, which seemed to be more accurate. 
      -Changed behavior when raw intrares scores are low.  Was
          previously setting low scores to be equal to the floor
          value.  But that leaves suspicious residues easily able to
          make contacts.  Changed so that low scoring residues get
          their intrares score reset to 1.0, which makes it harder
          (but not impossible) for them to create contacts.  Seems to
          be an improvement, judging by contact maps 
      -Changed netfilter proc to allow it to calculate a contact
          map on the basis of one set of spectra, and to apply it to a
          different set.  This is because 3dN and 4dNC spectra rarely have
          any long-range contacts, and therefore add nothing but noise to
          the contact map calculation. 
      -Bugfix to code that deals with to-from partners.  If a given
          SA has a recorded name for its to-from partner, make sure an
          actual SA with that name exists, because it could have been
          deleted (which leaves the name string describing a non-existent
          SA) 
    tcl/noe_reporting.tcl
      -added completenessSummarizeMarvinResults
         proc, which generates PA likelihoods from the best 10% of
         structures as measured by their local NOE completeness--ie., NOE
         completeness of just the from and to SAs that go into a
         particular PA.  Uses different structures for each PA.  Seems to
         work better in noisy situations, like ThTP pass2. 
      -Fixed overall NOE completeness calculation used in selecting
          converged structures.  Was using mean of each spectrum's
          completeness, which is clearly wrong.  Now I count numbers
          of neighbors and accounted neighbors for each spectrum, sum
          them up, and calcualte overall completeness correctly. 
      -Added new summarizeMarvinResults proc, which ranks structs by #
          peaks nonviolated. Doesn't use completeness.
      -Added nunNonviolatedPeaks proc to support above.
      -Modified chooseBestFraction to support above.
      -Bugfix to old summarizeMarvinResults--was using -inverseBound
          flag to set inverse methyl correction.  Doh, but I don't use
          that proc any more. 
      - Added support for not writing avg PDB, .peaks,
          .shiftAssignments files to newSummarizeMarvinResults and
          completenessSummarizeMarvinResults. 
      - Bugfix to newSummarizeMarvinResults:  Before I create a
          symlink to a converged PDB file with the "converged" tag in its
          name, I now check to make sure it doesn't already exist. 
      - Change to completenessSummarizeMarvinResults.  I now
          activate peakAssigns (for calculating individual SAs' NOE
          completeness) based solely on whether or not they're violated in a
          given structure.  There's no stochastic element to it at all,
          which is appropriate.  I should perhaps eliminate this entire proc
          as a clever idea that didn't pan out, but I'll make that decision
          later. 
    tcl/noe_stats.tcl
      -Changed settings used for updating activation during NOE stats
          calc to prevent SA inactivation, and to explicitly set
          inverse bound 
      -Added new tcl file noe_stats, which contains procs to handle
          activation-sensitive calculation of NOE statistics.   
      -Added procs to calculate 
        number of high likelihood peaks
        number of good high likelihood peaks
        number of high likelihood long range peaks
        number of good high likelihood long range peaks
        number of shift assignments with no high likelihood peak assignments
      -added calls to print those stats as part of the standard newStats report.
    tcl/pdb_support.tcl
      -Changed readPDBremarks proc to require a -fileName flag, for consistency
        with readPDB, which also uses the -fileName flag
      -Added support for writing to the occupancy and b-factor columns
       of PDB files, using names "aux1" and "aux2".
    tcl/import_pipp.tcl
      - Modified to make experiment-specific import routines (eg.,
          read3dCPippPeakTable) optional, and to allow nmrDraw import
          routines to receive and pass on remarks correctly.  All of
          this comes down to running the low-level procs inside of
          eval statements, with the remarks variable names being
          passed along correctly.   
      - Better handling of errors that I catch involving unassigned
          peaks during process3dAssignedPippPeakTable.  I now reset
          errorInfo appropriately, so spurious errors don't appear in
          top-level calls to puts $errorInfo. 
      - I now set the previousLikelihood of peakAssigns in
          process3dAssignedPippPeakTable to 1.0 
      - Added process4dAssignedPippPeakTable, which is entirely
          analagous to process3dAssignedPippPeakTable  
    marvin/ShiftAssignment
      -Eliminated references to EquivPeakAssignmentSet.
      -Bug fix to support removing shift assignments correctly. 
    marvin/MarvinNOEPotential
      - Added functionality to remove all peakAssigns and explicit
          exceptions involving a given shift assignment.  This is
          automatically called when actually removing a shiftAssignment,
          but is exposed to the user as well.  Makes removing shift
          assigns much easier, since it eliminates a lot of TCL-side
          code. 
      - Bug fix involving neighbor list regeneration.  I wasn't
          forcing a neighbor list regeneration when I added or removed
          shiftAssignments or when the inverse caches need updating.   
      - Bug fix in updateInverseCaches.  When I delete a
          shiftAssignment, I clear its toFromPartner's pointer to the
          removed SA.  But I don't clear its toFromPartner SA's
          toFromPartnerName slot.  Now I check whether that name is the
          name of a valid shiftAssign before trying to set the pointer.   
    tcl/shiftassign_tools.tcl
      -Added a proc--dropShiftAssignsInShiftRange, which is used in the
          standardNDinitMatch procs.
      -Bugfix to recordStereoPartnersForShiftAssignments.
      -Added support for recording a shiftAssignment's stereo partner
       in a table.
    marvin/Peak
      Changed chooseAnAssignment method to calc overall likelihood of
      each peakAssignment just as it's done during
      PeakAssignment::updateActivation, and then to normalize them.
      If total likelihood is very low (<0.001), it gives up and makes
      all of that peak's peakAssignments equally likely.   
    tcl/sa_protocols.tcl
      pass2 proc was missing calls to use the original MC scoring
          function and to prevent SAs from being inactivated.  Fixed. 
    tcl/sa_protocols.tcl
      Temporary? change to support changing the values of krama and
          ktalos during pass2 and origPass- 
    tcl/primarySequenceExceptions.tcl
      Code to create inverse exceptions for every SA pair that's
          within a particular number of residues in primary sequence. 
	  Helps ensure that TALOS alone can set the backbone angles, and
          deals with problems caused by few observed NOE contacts  
	  between residues close in primary sequence leading to missed
          contacts.  Primary sequence neighbors often have very  
          limited sidechain-sidechain contacts because of restrictions
          placed by secondary structure. 
    tcl/newstripe.tcl
      New stripe analysis method that avoids using the same peaks as
          targets for multiple shift assignments 
      - Moved code for counting SAs w/ zero targets into its own
          routine, so it can be called either after recording all
          possible targets, or after they've been filtered. 
      - Reorg of prefiltering code (targetIsReasonable).  
      - Now iterates calls to targetIsReasonable during
          filterTargetsForInitialReasonability, to promote convergence.
          Note that this doesn't guarantee identical results each time,
          since it depends on the order in which SAs' targets are
          filtered. 
      - No longer force from SAs to choose targets before the to
          SAs.  Now just choose targets for all SAs, in random order 
      - Changed scoring function from fraction of intrares + bbnseq
          partner SAs that are covered by compatible targets to fraction
          of intrares + bbnseq possible targets that are compatible.   
      - Added optional proc that deletes SAs which have zero targets
    tcl/import_nmrdraw.tcl
    tcl/marvin_lowlevel.tcl
      Change to the flagVal proc, to allow it to match several
          different targets. 
      For example, 
        flagVal $args [list -pot -potList] 
        will match both -pot and -potList calls in an argument list.  
        Needed by several procs in the new stripe filter,
        standardInitMatch, etc. 
    tcl/selection_tools.tcl
      -stereopartnerList proc:  added asn HD21/22 and gln HE21/22 as
       stereopartners.
      -Changed behavior of previousResidue and nextResidue procs to
       always return a single residue string, and throw an error if >1
       next- or previous residue is found.
    tcl/sa_tools.tcl
      -Bugfix to structPrecision.  Was allowing (optional) grabPDBfiles
       call to overwrite main coordinate set before it was copied to
       the comparison set.   
      -Added automatic generation of symbolic links to converged
          structures, so they can be grabbed easily by other scripts
          without having to refer to the avg pdb file's remarks lines.
          Probably useful 
      -Added createViewScript proc, for VMD inspection of converged structures 
      -Changed standard method for generating mean coords to allow vdw
       minimization during cleanCovalentGeom.
    tcl/talos_tools.tcl
      -Folded in individual-residue TALOS input/output from my old codebase.  
       This creates restraints more conservatively, direct from TALOS's
       res_*.tab files for each residue.  The acceptable range is set
       to the observed range of database hits, plus a padding (default
       5 degrees).  There's also a minimum range (default 20 degrees)
       to prevent over-restriction from cases where you  
       have very tightly grouped database hits.  
      
      -This also adds the ability to write out the resulting TALOS
       restraints as XPLOR dihedral restraints.  
      
      -This code also has a bugfix relative to my old codebase.
       Situations where the database hits wrap around +/- 180 degrees
       are handled gracefully.  This was causing surprisingly large
       numbers of bad (or extremely broad) TALOS restraints  
       in my old codebase.  
    ------------------------------------------------------------

------------------------------------------------------------
Python
    changed default Python version for output from 2.4 to 2.5
    ------------------------------------------------------------
    new:  python/symmetry.py
        contains test for dimer C2 symmetry
    ------------------------------------------------------------
    added distance symmetry potential: 
      same as the XPLOR NOE distance symmetry restraints for normal
      Simulations, but enforces symmetry between EnsembleSimulation
      members.
    ------------------------------------------------------------
    atomSel module
      added asUnion/union function
    nmrPot/posSymmPot.cc
       -fixed bug in gradient
       -now throw an exception if there are fewer than 3 equivalent atom sets
       -changes to PosSymmPot mostly to expose internals so that the 
        translate/rotate operations could be repeated externally
        rationalized return type of equivAtomSelPairs and equivAtomPairs
       -added rotMat, centroid and translatedCoords accessors
    nonBonTools.py
       vdwViolations now takes extra arguments to optionally determine
       violations involving only selected atoms.
    python/xplorPotTools.py
      PotData.__init__:
        added try...except clause for getting violation info
          motivated by distance symmetry NOE restraints for which the noe
          print statement doesn't work.
      now print out XplorPot::scale in analysis (.viols file)
      now get, print rmsd, violation info from the CARB term
    ------------------------------------------------------------

    rdcPot
      added gyroA/B output to info()
  
    atomSelAction:
      RMSD: constructor can also take an AtomSel argument
      Fit.translation now returns a Vec3, not a tuple.
    ------------------------------------------------------------
    python/simulationTools.py
      StructureLoop:
        -rmsd to average structure is now calculated
         correctly. Previously, rmsd was calculated to unregularized structure.
        -constructor: added averageRegularize flag to allow disabling
                     regularization. 
        -added the structureNum method
        -averageFilename now supports the SCRIPT replacement of pdbTemplate.
        -fixups for EnsembleSimulation calcs:
           -now call barrier in constructor to clean up list of
            running processes early 
           -run(): made cpuTime calc EnsembleSimulation-safe
      StructureLoop.genAveStats: allow for missing files when
         generating statistics (instead of crashing) 
      StructureLoop.run() now sets a number of members to the instance
         (self) object, including cpu time, calculated structure precision and
         restraint statistics. Also, it now returns the instance object.
      StructureLoop.writeStructure:
        set the default potList and altPotList arguments from
        StructureLoop's averagePotList and averageCrossTerms, respectively
      calcAverageStruct:
        now takes new arguments potList and regularizeSteps, used for optional
          regularization by minimizeRefine
      minimizeRefine:
          fixed typo in clause which ensures covalent energy terms are present.
      testGradient:
          -added a text header for EnsembleSimulation gradient tests
          -fixes for when dealing with EnsembleSimulations: it should
           now actually work correctly and now supports xyz components
      convertToPotList: can now take a bare potential object
    ------------------------------------------------------------
    python/solnScatPotTools.py
    python/solnXRayPotTools.py
      added Xiaobing Zuo's nucleic acid volume values- can optionally 
        activate these values.
      added Mn,Zn to supported metal atoms
      create_solnXRayPot: changed the default selection from not hydro
    ------------------------------------------------------------
    ivm
      -added untested rotate2 node type
      -fixes s.t. IVM.hinge() actually works with previous argument types
      -optimization of breakAllBondsIn method- moved loops to a
        C++ extension defined in the .i file.
      -added simulation() accessor
      step():
        now check if newTimeStep is smaller than minStepSize and throw an
        exception if so.
      -additional optimizations
    ------------------------------------------------------------
    python/residueAffPotTools.py
      added 1999 Mizagawa/Jernigan contact potential 
      create_ResidueAffPot: 
        added optional argument interdomainContacts.
        fix justification (to left) of segname
        now has optional potentialName argument to switch
          between different potentials
    ------------------------------------------------------------
    python/selectTools.py
      numResidues:
        fixed default argument (so a null selection correctly selects
        zero atoms) 
      added getSegids() helper
      added convertToAtomSel() helper
    ------------------------------------------------------------
    avePot:
      fixed gradient error which sometimes would double the gradient
    ------------------------------------------------------------
    python/psfGen.py
      seqToPSF: 
        right justify space-padded segid
        the length of segName is now handled correctly.
      deduceSeqType:
        will now throw an exception if a residue name is longer than
        four characters 
      pdbToSeq:
        added helper code to catch the case of truncated ATOM records:
        short lines such that the segid has fewer than 4 characters.
    ------------------------------------------------------------
      python/regularize.py
        fixupCovalentGeom:
          -now catch and ignore small timestep errors from the IVM
          -new algorithm which works residue-by-residue
           and uses fast SetProperty and new AtomSel helper functions.
          -vdw fixup
          -added fixupLoop_xplor: now do residue-by-residue fixup in XPLOR
        addUnknownAtoms:
          now just exit if there are no unknown atoms
        fixupCovalentGeom: tighten XPLOR TOLT parameter for this routine
        simple fixes to covalentMinimize
    ------------------------------------------------------------
      python/protocol.py
        added initHBDB helper function
        matchInexactEntry:
          added new name transposition rule.
          matchInexactAtomEntry:
        import regularize.CovalentViolation
        initCoords matchInexactAtomEntry: 
          add strictResNames flag argument
        moved covalentMinimize and fixupCovalentGeom to regularize.py
          genExtendedStructure: now use fast atomSelAction.SetProperty
      genExtendedStructure:
        changed the default atom selection to exclude RDC axis atoms. This
        so it will now do the right thing when called after the RDC terms
        are set up.
      pdbLocation:
         switched to new .gz ftp location
      downloadPDB:
         now use urllib2
      loadPDB:
        fixup resetting of current simulation
      added addUnknownAtoms_fast, and call to it from addUnknownAtoms if the
        missing atoms are separated by a single bond from a known atom
    ------------------------------------------------------------
      pdbTool
        added strictResNames flag and ability to require strict residue naming
        changed exception type returned by PDBTool::read to IOError
    ------------------------------------------------------------
      atomSel
          added helper functions intersection(), notSelection() and union()
          which create pseudo selections
    ------------------------------------------------------------
      common/xplorWrap.cc
        deleteAtoms:
          added call to XplorSimulation::syncFrom after deletion
    ------------------------------------------------------------
      simulation
        all Simulation objects are now reference counted
        Simulation::deleteAtoms:
          the argument is now a list of atom indices instead of a
          selection string.
          the Python .i files added an indirection to keep the
          previous behavior. 
        added atomMassArr/setAtomMassArr accessors
    ------------------------------------------------------------
      common/atomSelAction.cc
      python/atomAction.py
        moved SetProperty from atomAction to atomSelAction for optimization. 
        Renamed previous definition to SetPropertyArr
    ------------------------------------------------------------
      common/xplorWrapProc.cc
        freeAtomData: bug fix:
          now use dynamic_cast and check result when down-casting to obtain a 
          XplorWrapProc.
    ------------------------------------------------------------
      python/socketComm.py
        collect: added diagnostics in case of readData failure
    ------------------------------------------------------------
      added posDiffPotTools
       a potential term to help evaluate structural RMSD
    ------------------------------------------------------------
      selNBPot
        added CENTER aveType to selNBPot
    ------------------------------------------------------------
      restraintStats
       TermEntry now has methods to calculate mean, dev of energy,
       rmsd and viols 
    ------------------------------------------------------------
      added python/maxLikelyFit.py
       module for molecular fitting based on maximum likelihood estimate.
       written by Robin Thottungal
    ------------------------------------------------------------
      jCoupPot
        better diagnostics if bad selections are encountered

------------------------------------------------------------

Low Level Libraries
    ------------------------------------------------------------
      CDSlib/cdsList.hh
        sort method: try to make a default comparer argument
    ------------------------------------------------------------
      CDSlib/rc_ptr.hh
        allow proper cleanup of pointee.
        no longer set counter member to zero.
        copy constructor: made safe for null counter members
        added methods for manual reference count manipulation:
          incr, decr count
        added methods for casting up/down TYPE class heirarchy:
           cast, dyn_cast
        mods so that destructor zeros counter member

Helper Scripts
------------------------------------------------------------
  calcTensor, calcETensor, calcDaRh have been moved into the bin directory
  added mleFit and domainDecompose helper programs
  seq2psf:
    added the -cisPeptide option and usage test
  targetRMSD:
    add check that all atoms used for fitting are known
  calcTensor:
    fix crossTabs initialization type
    added -crossValidate option

  bin/xplor
    -handle the case in which the machines list starts with localhost, but
     also contains nonlocal machines.
    -formalize and document arch/equivList format
  tcl/findTCL
    support for recent versions where TCL_INC_SEPC is replaced by
        TCL_INCLUDE_SPEC 

Example Scripts

  -added validation scripts
     these check that the calculated results are of suffient quality.
     These can take a long time to run. Run with 
       eginput/validate
 
   -eginput/runAll
       added -keep command-line option

    ------------------------------------------------------------
   eginput/gb1_rdc/
    * added analyze_anneal.py, analyze_refine.py for analysis, validation
    *refine.py
      -added SCRIPT to averageFilename
      -accept function:
         loosened tolerance on rdc rmsd
      -properly ramp the Vgyr scale factor
      - added a cross-validated PosDiffPot term to compute rmsd to the crystal
        structure.
      - bumped the number of calculated/analyzed structures to 20, and added a
        -quick flag to reduce it back to 3

    *anneal.py
      -now start from randomized torsion angles instead of extended structure
      - anneal:
       - initialize coords from model.pdb - these coords are not used in calcs
       - remove initial calcTensorOrientation- but add it after extended 
         structure is generated
       - set averageContext in StructureLoop
    *analyze.py
      - allow for missing structure files (instead of crashing)
   ------------------------------------------------------------
     eginput/dna_refi/ensemble.py
        fixup selections: hydro --> name H*
   ------------------------------------------------------------
      eginput/PSF_generation
      *testNAG.py
        increased maxFixupIters
      * added addAtoms2.py
      * added writeChainID.py example


		     Changes from 2.18 to 2.19

new helper script:
  bin/targetRMSD - to compute rmsd to a known structure

arch/equivList - Mac platform
      updated to run Darwin_9, confirmed by user feedback

added parallel.txt
      write-up describing parallel structure calculation capabilities

configure script
      improve error message for case appropriate xplor binary is not present.

XPLOR interface:
      removed the BUFMAX parameter from comand.fcm
      a consequence is that the rotating command buffer no longer rotates:
        it just gets larger
      added two array helpers:
        assign_char_2d and get_char_2d
      removed the NDSMAX parameter - associated arrays are now on the heap
      removed the MXRTP parameter
      removed the MXRTI parameter
      removed the NHBMAX constant parameter
      fixed ASSIgn docs for xdipo/dipo potential
      added xadc XPLOR term contributed by G. Bermejo (reference ???)
 
  source/parser.f
      changes to sizes of heap-allocated strings. Probably not needed.

   XPLOR angle, bond, dihedral and improper violations:
      added NUMBER declar'd variable

Python Interface

  gyrPotTools:
       updated Vgyr ranges to match those in the paper
        added Rg targetType - needs gradient, testing of Rg targetType
  
  pdbTool:
      added ability to write to the ChainID field (by setting the 
      writeChainID flag).
      PDBTool::read():
        better support for a subset selection- these atoms are no
        longer added to the unplaced list. 
  
  protocol:
      loadPDB: added simulation argument
      addDisulfideBond: fixed to make working, plus docstring
      initDynamics:
        fix so that eTolerance isn't specified as negative if bathTemp argument
        is omitted.
      initCoords: now allows selection to be a plain string
      fixupCovalentGeom:
        changed default angle and dihedral tolerances from 5 to 2
        degrees. This picked up some problems in less-used parameters.
      matchInexactAtomEntry:
        handle case when occupancy or Bfactor are invalid numbers

  xplorPotTools:
      now get number of XPLOR restraint terms from XPLOR NUMBER variable
      added restraints class support for the ANGL XplorPot term

  python/psfGen.py
      moved addDisulfideBond from protocol to psfGen w/ compatibility call

  spline:
      added support for periodic splines
      added Spline2D - bicubic interpolation, w/ gradient

  vec3:
      __neg__: fixed so that it doesn't have side effects

  dihedral:
      overhaul of Dihedral class
      changed return units from degrees to radians
      added derivs method
      changed constructor (old constructor is emulated by Atom typemap)

  densPotTools:
      create_DensPot:
        fixed location of an import statement

  added cstMag potential for refinement against chemical sheilding 
     tensor magnitudes. Reference forthcoming.

  nonBondTools:
      allow atom names to contain the +'' character

  simulation:
      added Simulation::deleteAtoms

  ivm:
      ivm.hinge: change arguments to be more sane.
                 backward compatibility maintained.


  added support for Python2.5

Example scripts

  eginput/PSF_generation/testDiS.py
      added disulfide test/example

  eginput/gb1_rdc/bicelles_new_hnc.tbl
      removed one rdc due to consistent violations
  eginput/gb1_rdc/refine.py
      accept: loosened required rdc tolerance

  updated eginput examples in eginput/gb1_rdc/


  eginput/protG/calcDaRh.py
      small fixes 
        CH normtype should now work
        modePowder should now be correct
        noise argument should be better handled
      documentation fixes

  eginput/protG/calcTensor.py
        - added normType option for RDC scaling
        - fixes to correctly handle multiple rdc experiments
        - added rdcWeights option to correctly weight multiple experiments
        - added the following command-line flags:
           -psf, -useDistance, -maxDa
        - fixed bug in which tensor atoms were improperly reset before
          calculating rmsd.

  eginput/PSF_generation/addAtoms.py
      added call to fixupCovalentGeom

Parameter/Topology Changes

  toppar/ion.par and toppar/ion.top:
      changes to avoid conflicts with protein.top/par

  toppar/nucleic-1.1.par
      nucleic base proton angle parameters:
        adjust angles proton+heavy atom angles so that they add up to
	360 degrees. Previously, there were always violations of >2 degrees.


Internal Variable module:
    fixed handling of diatomic molecules

    resetCM():
          now perform reset if fixed atoms are present - previously it just
        exited if there were any fixed atoms.

    corrected center of mass calculation:
      this improves algorithm stability for the case of nonuniform masses.


Marvin/PASD 

  tcl/noe_selecting.tcl
      Changed definitions in isShortRange and isLongRange to do
      exactly what the C++ code in PeakAssignment.cc does, in order to
      eliminate confusion. 

  eginput/marvin/cvn/convert_restraints_to_xplor.tcl
      removeLowLikelihoodPeakAssignments:
        fixed name of the -cutoff flag

LICENSE
      added government rights clause from A. Hubbs

switched from cvs to bzr version control software.

documentation fixes, additions


		     Changes from 2.17 to 2.18

Helper scripts

  -bin/seq2psf
        added the -protonateHIS flag
  -added bin/targetRMSD


C++ infrastructure

  CDSlib/cdsComplex.hh 
        fixed up pow(complex,pow)
        added functions operator*(int,complex) and pow(complex,exponent)

  CDSlib/cdsMatrix.cc 
        now support multiplication with GenMatrix; SymMatrix*vector now works
        added rawCopy method

  CDSlib/cdsVector.hh 
        splitRep: made this method public

  CDSlib/fft.cc 
        disambiguate ::pow call for Irix
        fixed call to ::pow
        added wrapper class for FFTPACK

  CDSlib/fft.hh 
        added wrapper class for FFTPACK

  CDSlib/fftpack.hh 
        removed redundant consts
        int --> long conversion: needed for 64 bit arches
        added wrapper class for FFTPACK

  CDSlib/matrixTools.cc 
        determinant:
          reworked to have saveData- for optimization
          explicitly coded size 2 and 3 expressions - much faster than lapack calls.
        added function determinant (from PLU decomposition) and tests
  CDSlib/symMatrix.cc 
        now support multiplication with GenMatrix; SymMatrix*vector now works
        added missing #include
  CDSlib/vec3.hh 
        crossMat: reworked to use only constructor

  intVar/publicIVM.hh 
        added recenterLargeDispl to PublicIVM: used in
        syncPos. Disabled by default.

  common/atom.cc 
        atom:
          pos, mass, vel, fric read accessors have been inlined.
          This required #including simulation
        simulation:
          which required un-inlining Simulation::atomByID and rearrangement of
          #includes
        made usual constructors inline

  common/atomSel.cc 
        AtomSel: moved binary methods out to stand-alone functions
          intersects --> intersect
          isMonomericallyEqualTo --> monomericallyEqual
          primarySequenceDistanceTo --> minResidDiff
        Added primarySequenceDistanceTo <anotherAtomSel> function.  This is broadly
        useful, so it belongs here.  Need to add a test for it.

  common/atomSelAction.cc 
        updated Fit and RMSD to use AtomSels for fitting, comparison

  common/mmapAlloc.cc 
        added the deleteFile function
          so that the mmapped file can be deleted regardless of order called.

  common/pdbTool.cc 
        better treatment of altloc and icode entries:
          nonblank icodes are now ignored
          altloc enties in allowAltLoc are read, otherwise entry is ignored.
        added commented-out check of residue name
        write: check if atom coordinates are within range (valid). Warn if not.

  common/pot.hh:
        calcEnergy() now returns float_type instead of EnergyReport

  common/simulationWorld.cc 
        added memoryUsed function

  common/xplorSimulation.hh 
        added clone argument to constructor - if True, the new
        XplorSimulation will be a copy of the current one. If False,
        if will be a brand new XplorSimulation, with no atoms, etc.

  common/xplorWrap.cc 
        fixed bug: SELRPN messages were printed when XplorWrap->select called
        added the qatmchk argument to the XPLOR energy() subroutine.
        This defaults to .TRUE. for all XPLOR use. Within the C++ interface it is
        .FALSE.
        This is for performance in addition to provide proper (not crash)
        behavior, particularly when gradient minimizing.

  common/xplorWrapProc.cc 
        XplorWrapProc::freeAtomData:
          make sure pointers are correctly mmap or free - deallocated
        exec'ed children are now started -quiet -- banner is not printed
        disable master_exit_handler:
          it kills the slaves, and they don't get a chance to clean up.
        two bugs fixed:
          the master process now has a xplorDerivs instance variable - it had
          been using the static variable, leading to problem when multiple
          XplorWrapProcs were used.
        shutdown/cleanup change:
          now only the slave deletes sharedData. It seems to be cleaned up
          anyway when the slave exits- causing semaphore errors when the
          master had tried to clean up.
        added the clone argument to the constructor:
          if false (old behavior) a new xplor process is exec'd, if true
          the existing forked process info is used.
        static variable firstCall in function allocSharedData replaced by
          a variable in the instance-specific sharedData structure -
          this so that calls to XplorSimulation after the first one would be
          successfull.
        xplorwrapproc_slave:
          added a wait loop so that the slave process waits for the master at
          startup
        fixed bug: SELRPN messages were printed when XplorWrap->select called
        added the qatmchk argument to the XPLOR energy() subroutine.
        This defaults to .TRUE. for all XPLOR use. Within the C++
        interface it is .FALSE.
        This is for performance in addition to provide proper (not crash)
        behavior, particularly when gradient minimizing.

  common/xplorWrapProc.hh 
        two bugs fixed:
          the master process now has a xplorDerivs instance variable - it had
          been using the static variable, leading to problem when multiple
          XplorWrapProcs were used.
        shutdown/cleanup change:
          now only the slave deletes sharedData. It seems to be cleaned up
          anyway when the slave exits- causing semaphore errors when the
          master had tried to clean up.
        see the commit message for xplroWrapProc.cc

Example scripts:

  eginput/PSF_generation/testPDB2PSF 
        mods for disuse of seqres, accompanying psf fixes

  eginput/gb1_rdc/README 
        added targetRMSD.py script, test

  eginput/gb1_rdc/analyze.py 
        updated to split NOE restraints and turn off ANI VdW interactions
        now report a proper VdW energy

  eginput/gb1_rdc/anneal.py 
        updates:
          note proper # structs
          now generate new extended structure for each structure calculated
        added missing (optional) cart_cool definition
        fixed typo

  eginput/marvin/cvn/cvn_n15noe.shifts 
        Corrected some typos in 15N shift table:
        1.  Several residues had two lines of, eg., HA1|HA2 instead of
            HA1|HA2 and HA2|HA1.  Fixed. 
               Residues affected:  2 5 6 15 27 28 45 65 78 96
        2.  Also changed selections for phe/tyr deltas & epsilons from
            CD1|CD2 to CD*, since they're almost certainly averaged.
               Residues affected: 4 9 29 54 80 100
        3.  Finally, note that previous version had a typo in
            definition of Y29 epsilon carbon: 
            Was CE1 | CD2.  Changed to CE#, which fixed the problem.
        
        Note that this shift table should be the input for TALOS, not
        the 13C one (which lacks entries for backbone carbonyls, for
        some reason). 

  eginput/marvin/cvn/initMatch3dC.tcl 
  eginput/marvin/cvn/initMatch3dN.tcl 
        Updated to reflect name change of correctShiftReferencing proc to
        correctShiftOffset

  eginput/protG/README 
        added calcDaRh.py - determine Da, Rh in absence of structure info

  eginput/protG/anneal.inp 
        rework parallel startup logic again - for case of num_procs>numStructs
        fixes to avoid non-integer structure count

  eginput/protG/calcDaRh.py 
        added calcDaRh.py - determine Da, Rh in absence of structure info

  eginput/protG/calcTensor.py 
        will now (optionally) print out back-calculated RDCs
        fitSel can also now be specified on the command-line
        updated to support command-line options


  nmrPot/Makefile 
        added gyration tensor volume potential term
        added selNBPot/ residueAffPot--
          empirical potential to capture hydrophobic forces.
          Current potential based on a K. Dill contact map.
        added planeDistPot
        approximate molecular volume calculation from analytical surface area

  nmrPot/gyrPot.cc 
        added square well potential
        gyration tensor volume potential term

  nmrPot/gyrPot.hh 
        added square well potential
        gyration tensor volume potential term

  nmrPot/neighborBin.hh 
    deal with case where too many bins would be created - atoms are very far 
    apart 
    changed template parameter from pointer-to-atom to atom instance.
    also added an ATOMLIST template parameter.
    no longer refer to an atom radius member- instead just pass a simple
    spacing argument.

  nmrPot/noePot.cc 
    added support for ASSIgn ... OR restraint syntax
    initial changes to support the TO keyword in the ASSIgn statement:
      in the restraint class, replaced sel1, sel2 members with selPairs()
      accessor
    
      The python layer includes a compatibility layer such that sel1 and sel2
      continue to function.
    now throw an error if the ASSIGN .. OR syntax is detected

  added planeDistPot distance-to-plane restraint potential term

  nmrPot/selNBPot.hh 
        added dSwitch
        bug fixes in neighbor determination
        added selNBPot/ residueAffPot--
          empirical potential to capture hydrophobic forces.
          Current potential based on a K. Dill contact map.

  nmrPot/surfaceArea.cc 
    added null destructors
    optimizations
      changed many instances of rc_Neighbor to SA_Neighbor*
       removing this indirection lead to a large speed-up
     did same with rc_Vertex:
       no big gain from that.
    comment-out updateNeighbors: not used for moveTol==0
    re-added neighborBin for optimization
    overlap: added moveTol argument
    tried to make nonzero moveTol work. No luck yet.
    replaced code with transpose with left-vector multiply
    now derivs from ModifiedBase
    removed TouchingList::init
    
    various optimizations, using const where possible,
      using raw pointers instead of ref counted pointers
    
    bug fix: now initialize sim member
    
    cache neighbor list in new neighbor member
    
    singleAtomDerivs:
      add optional scale parameter
      avoid divide-by-zero error by adding small value to Omega
    
    getOverlappingAtoms:
      use touchingList if cRadius allows it
    
    added A member- previously determined surface area. Used to avoid 
    unnecessary (possibly dangerous) derivative calculation.
    
    optimization (?) to outerProd
    Vertex constructor: added initializers
    now expose more info: Omega angle

  nmrPot/volume.cc 
        added null destructors
        cache atom.pos()
        coded derivatives of tetrahedra in nonlazy fashion
        changed deriv support from VecVec3 to DerivList
        added sa_saveData member
        added derivative info
        approximate molecular volume calculation from analytical surface area

  nmrPot/volume.hh 
        added null destructors
        changed deriv support from VecVec3 to DerivList
        added sa_saveData member
        added derivative info
        approximate molecular volume calculation from analytical surface area

Python Interface

  python/atomAction.py 
        SetProperty:
          can now specify array of values.
        added getProperty function.
        added function: centerOfMass
        randomizeDomainPos: fixed error in CoM calc

  python/cdsMatrix.i 
        support inter-symMatrix/matrix multiplication
        added much SymMatrix support -
          multiplication by matrix, vector, svd, inverse
        added space before trailing template > for later swig versions
        SymMatrix:
          fixed constructor, so that size-only can be specified.
          removed get method
          changed set method to use underlying method.
        moved cdsComplex stuff to cdsComplex.i

  python/cdsTypeMaps.i 
    removed unused variable from DEFAULT_REF_TYPEMAP
    DEFAULT_REF_TYPEMAP - Python-to-C++:
      add attempt to directly copy any underlying C++ object to the target
      C++ object without going through the fromPy machinery - this is an
      optimization.

  python/cdsVector.i 
        now references the correct documentation
        added CDSVector<DComplex>

  python/cdsVector_template.i 
        added space before trailing template > for later swig versions
        added __str__, __mul__, __div__

  python/csaPot.i 
        allow positive values of Da, and changed sign convention
        added inline functions for computing CSA powder patterns

  python/csaPotTools.py 

  python/densPotTools.py 
        fixup to correctly count the mass
        added explicit destructor, call to base class destructor
        create_SurfaceArea:
          added radiusType argument, support for heavyatom radius parameters
        
        support for XplorWrapProc XplorSimulations
        create_DensPot: don't crash if number of attached protons is unexpected
        create_DensPot:
        
          now disable convex hull by default
          explicitly set moveTol to zero (will crash with any other value)
        replaced calcEnergyAndDerivs with calcEnergyAndDerivList
        changed default atom selection
        corrected capitalization of createDensPot
        corrected default target value
        fixup for atom radius setup.
        make timing info optional
        density potential and test

  python/derivList.i 
        added __get/setitem__ methods
        get method return val is no longer const - impt. for Python pot terms

  python/fft.i 
        added fft module

  python/findPython 

  python/findSwig 

  python/gyrPot.i 
        gyration tensor volume potential term

  python/gyrPotTools.py 
        create_GyrPot:
          added softScale, hardScale arguments
        updated documentation
        now create two terms - hard and soft.
        change default lower hard range from 14.5 to 14
        replaced tag atom selection with selectTools.numResidues
        added square well potential
        create_GyrPot:
          added resScaleFactor argument, changed default value
          reduced default scale factor to 1
        analyze:
          output format fixups
        gyration tensor volume potential term

  python/hybridMC.py 
        use getXplorSimulation instead of xplor.simulation

  python/ivm.py 
        cleanup
        run:
          now checks for atoms with large displacements before dynamics.

  python/mat3.i 
        added inverse

  python/minimize.py 
        conmin:
          added stepsize argument
  python/noePot.i 
        initial changes to support the TO keyword in the ASSIgn statement:
          in the restraint class, replaced sel1, sel2 members with selPairs()
          accessor
        
          The python layer includes a compatibility layer such that
          sel1 and sel2 continue to function.

  python/noePotTools.py 
        create_NOEPot:
          added splitRestraints, deltaResidLR arguments, functionality

  python/noeTest.py 

  python/noeTest.py.out 

  python/nonBondTools.py 
        update to work with XplorWrapProc
        now allow chemical types to contain underscores
        readXplorRadii:
          updated to correctly use 1-4 list
          now read nonbonded exclusion list from the PSF and use that too
        vdwViolations:
          change default value of radiusScale from 1 to defaultRadiusScale=0.8
  python/planeDistPot.i 
        distance-to-plane restraint

  python/planeDistTools.py 
        update to work with XplorWrapProc
        helper functions for distance-to-plane restraint

  python/protocol.py 
    fixes to xplor manual URLs
    added helper function:
      initCarb13
    loadPDB:
      added optional string argument
    matchInexactAtomEntry:
      added check for residue name mismatch
    loadPBD: added verbose argument
    added pseudoResNames:
      residue names to ignore when counting unreadable pdb ATOM entries
    initCoords:
      maxUnreadEntries is now a tuple, and value increased.
    downloadPDB:
      now remove temporary .pdb file
    initCoords:
      overload maxUnreadEntries to allow number to be specified as
      fraction of the number of residues.
    readPDB renamed to downloadPDB
    loadPDB: now has two arguments, to load from file or url
    matchInexactAtomEntry:
      now bomb if a nonnumeric resid is encountered
      altloc- now treat with PDBTool.allowedAltLoc
    initCoords:
      added maxUnreadEntries argument - to bomb on psf/pdb mismatches
    added loadPDB, readPDB helpers, to aid in reading PDB entries from the net
    reverted to previous version of genExtendedStructure
    genExtendedStructure:
      added genWithoutProtons argument to trigger an alternate algorithm
      in which a sub-XplorSimulation was created without protons and first
      fixed-up. Then protons were added with hbuild. The idea was that
      this would be a faster algorithm. Unfortunately, it turned out to
      not be the case.
    fixupCovalentGeom:
      now check that the same pot combination is never used twice in a row.
      added an additional verbose level.
    genExtendedStructure:
      added maxFixupIters argument

  python/psfGen.py 
    pdbToSeq: new arguments:
      useSeqres: defaults to false, better to read sequence from ATOM
                 records
      useChainID: useChainID - overrides segment name by default
    also: now terminate sequence determination when an ENDMDL record is found
    seq2PSF: added support for n-terminal ACE residue
    fixes so that a nondefault XplorSimulation can be used
    residueTypes changed from tuples to lists

  python/residueAffPotTools.py 
        included simulation argument in AtomSel constructor
        create_ResidueAffPot:
          added sequentialCutoff argument
        analyze:
          fixed attractive reporting.
          added repulsive report
        SelNBPot/ ResidueAffPot documentation
        added selNBPot/ residueAffPot--
          empirical potential to capture hydrophobic forces.
          Current potential based on a K. Dill contact map.

  python/restraintStats.py 
        summarizeTerms:
          now break out terms in PotLists in a separate listing, s.t. the
          total energy is approximately the sum of all terms.
        added number of restraints column to the summary output.

  python/selectTools.py 
        numResidues:
          removed spurious print statement
        updates to rigidNucleicSelections
        added convertToAtom

  python/simulationTools.py 
        testGradient:
          added tolerance and epsilon arguments
          gradient difference is now scaled by gradient magnitude
        testGradient:
          added optional components argument
          now output is better formatted, and has a header.
        StructureLoop constructor:
          logic to better handle case where # procs > # structures. Avoid
          error message and print informational message.
        added comment concerning refactoring StructureLoop.genAveStruct
        testGradient: updated the docstring

  python/surfaceTools.py 
        create_SurfaceArea:
          added radiusType argument, support for heavyatom radius parameters
        
        support for XplorWrapProc XplorSimulations
        quiet XPLOR output
  python/varTensorTools.py 
        update to work with XplorWrapProc
        calcTensor_ensemble: added svdTolerange parameter; _analyze:
        fix problem with axes exactly alon xyz direction 
  python/xplorSimulation.i 
        getXplorSimulation: added default argument

Fortran source

  added the DIRS XPLOR term from N. Tjandra

  RAMA potential term:
    in files:
     databases/torsions_gaussians
     databases/torsions_quarts/
     databases/torsions_raw
           Changed delphic torsion setup scripts.  In code that selects
           free and disulfide bonded cysteines, I no longer use the
           existence of an HG atom as an indicator of whether or not a
           residue is in a disulfide.  Rather, I actually look for an SG
           atom that's bonded to the current residue's SG.  Thus,
           situations where the HG is missing, but no actual disulfide
           bond exists, will not be treated as if they were disulfides,
           eliminating a small source of errors.
           
           In cases where users have deleted the HGs and implemented the
           disulfide using NOEs, the DELPHIC torsion restraint will treat
           the cysteines as if they were not disulfide bonded.  Since
           NOE-based disulfides are not likely to have correct CB-SG-SG
           bond angles, there's no point in trying to have correct
           CB-SG-SG-CB torsion angles.
           
           This change to the setup scripts also eliminated a source of
           These corrections may result in minor changes to xplor output
           of various scripts!  Specifically, they will probably
           eliminate a few lines of "no atoms selected" style errors in
           the output of the DELPHIC torsion setup calls.
           
           MANY THANKS to Chun Tang from GMC's lab for catching this!
   

  source/darwintime.f 
        split out GETSYS into separate file for x86, ppc

  source/energy.f 
    added the qatmchk argument to the XPLOR energy() subroutine.
    This defaults to .TRUE. for all XPLOR use. Within the C++ interface it is
    .FALSE.
    This is for performance in addition to provide proper (not crash)
    behavior, particularly when gradient minimizing.

  source/nbonds.f 
        upinb: suppress normal printing of 'Ran out of space' message

  source/update.f 
        suppress SCRATC-warning: message if WRNLEV==0

  source/noe.f 
        Eliminated weird status message.  Whenever R-6 averaging was
        selected, xplor would print "R-6 averaging.", for no apparent
        reason.  Wouldn't do that for any other averaging type.

        Updated documentation of the help message for the
        NOE ASSIgn statement to reflect the existence of the 
        ASSIgn ... OR syntax. 
        

Marvin/PASD updates

  marvin/MarvinNOEPotential.cc 
        Added hasExplicitInverseException routine, and added == operator to
        ExplicitInverseException

  marvin/Peak.hh 
        Added isCrowded flag to Peak class

  marvin/PeakAssignment.cc 
        Added isBackbone flag, isBackboneSequential function.
        Moved primarySequenceDistance routine to ShiftAssignment class
        to make it available in more cases.

  marvin/ShiftAssignment.cc 
        Moved primarySequenceDistance calcualtion from PeakAssignment to here

  tcl/aeneas_tools.tcl 
    change set A
      1.  Bug fix to reportUnassignedAtoms:  No longer complains about
          missing proline Ns 
      2.  Added -bbn-seq flag to PSD filter
      3.  Added markCrowdedPeaks proc, for use by stripeCorrection
      4.  Updated stripeCorrection for markCrowdedPeaks
      5.  Updated stripeCorrection to handle cases where no target is
          expected (eg., in 3dN with only intraresidue peaks used as targets)
      6.  added netFilterMini, the poorly-named residue-pair version of
          the network filter 
      7.  Added convenience routines for processing:
              standard3dInitMatch
              standard4dInitMatch
              standardJointFilter
      8.  Added passSummaryJointFilter, which I'll probably remove

    change set B
      1.  Made match*d tolerant of shiftAssigns that don't have
          chemical shift values. 
      2.  Gave match*d ability to not use shiftAssigns with low
          previousLikelihoods. 
      3.  Improved reporting of peaks outside of the spectrum in match*d.
      4.  Gave recordUnfoldedPositions the ability to work with a
          subset of a pot's shiftAssignments.
      5.  Corrected a not-yet-tickled bug in removeDiagonalPeaks.  If
          you're enforcing heavyatom positions being near the diagonal
          as well (only occurs in 4dCC spectra), then I forgot to
          multiply by 1/sqrt(2). 
      6.  Explicitly set previousLikelihood of newly created
          ShiftAssigns to 1.0. This doesn't actually change behavior,
          since the C++ default was 1.0.
      7.  Changed networkFilter to not count pairs of SAs that are
          to-from partners by default, since they don't generally have
          peaks or peakAssignments corresponding to them. 

  tcl/atomSel.i 
    AtomSel tcl wrapper code:
      extend TCL wrapped class with intersects method to minimize code change. 

  tcl/import_nmrstar.tcl 
    Added two features:
      1.  Can handle cases where shift entries have an author_residue_id code.
      2.  Expanded automatic mapping of nmr-star atom names to xplor
          atom names. There should be very little need for editing
          nmr-star shift tables by hand any more.
  tcl/marvin_lowlevel.tcl 
        reverted change: status messages go on stdout, not stderr
        Added binCenter routine, which is used by the correctShiftOffset proc.
        Also re- re- re- corrected the updateUser routine, which needs to spit
        its output to stderr, rather than stdout.  It does NOTHING if xplor
        isn't called with the -verb flag, so changing it to stdout BREAKS
        the expected output.  Please leave this as is, and flag any test
        or example scripts that use -verb as errors instead.
        changed verbose output from stderr to stdout
  tcl/noe_reporting.tcl 
    Greatly expanded statistics reported by the
    summarizeMarvinPass routine. 

  tcl/noe_selecting.tcl 
    Added likelihoodLessThanOrEqualTo and likelihoodGreaterThanOrEqualTo procs
  tcl/sa_protocols.tcl 
    Added cleanup of covalent geometry XplorPots, and made some minor changes
    to the "new" pass3 protocol, which includes inverse forces and is used
    with likelihoods direct from jointFilter.tcl, rather than from a pass
    of structure calculations

  tcl/sa_tools.tcl 
    Added flag to grabPDBfiles to allow user to specify a particular
    model number within the PDB file to read

  tcl/selection_tools.tcl 
        Fixed incorrect error message

  tcl/shiftassign_tools.tcl 
    Added ConsolidateIdenticalStereopartners proc, which handles some bad
    shift tables I found on the BioMagResBank.
    
    Also added some minor bugfixes, one of which was caught by the
    initMatchTest 

Topology and Parameter files

  toppar/ion.par 
        added ion.top/par from J. Howarth - probably cribbed from CNS

  toppar/ion.top 
        added ion.top/par from J. Howarth - probably cribbed from CNS

  toppar/nag.par 
        NAG topology and parameter files contributed by John Vakonakis

  toppar/protein-1.0.par 
        added missing IMPRoper for ACE methyl

VMD interface

  vmd/publicVMDInter.cc 
        added colorMeth argument to bond method

many documentation updates


		     Changes from 2.16 to 2.17


************** C++ Layer changes **************

	now use the supplied lapack, blas by default

  CDSlib/cdsVector.cc 
	added alloc member - so that instance information can be stored.
	added loadRawArray method - to load contents from a C-style array.

  CDSlib/rc_ptr.cc
	added reset method + test

  CDSlib/sthead.hh
	added global typedefs: MutexType SemaphoreType. These can be
	overridden by platform-specific includes

  common/avePot.hh
	scale no longer sets/uses subPot's value - now they're multiplicative

  common/derivList.hh
	changed argument names so that swig would supply default Simualtion*
	arguments.

  common/ensemblePot.cc
 	sharedPID member: added mechanism to detect intervening calls
        to fork(), and fail if detected 

  common/ensembleSimulation.cc
	barrier: re-enable exception thrown upon loss of member synchronization
	moved atom data arrays out of Simulation::SharedData into its parent.
	
	Lesson: never, never place pointers in shared memory.
	mods due to changes in Semaphore, Mutex:
	  now explicitly place Simulation::bThreadMutex and
	  EnsembleMemberSimulation::sem in shared (mmapped) memory,
	  and explicitly clean them up
	
	mods due to changes in Simulation

  common/mmapAlloc.cc
	added debug statement
	alloc: added optional uniqueID argument- overrides static value
	free: now correctly handles 0 pointers

  common/mutex-sem.cc
	semaphore:
	   changed sem type to SemaphoreType - this is currently
           defined in arch.hh  (in arch/$ARCH/include) - from a
           pointer type. This avoids one memory dereference, but more
           importantly, allows better control of where in memory the
           full Semaphore object resides. 
	   [ note that previously, sem was manually placed in mmaped memory for
	     shared usage. Now a shared Semaphore should be placed in
             shared memory explicitly. ]
	
	Mutex type is now explicitly MutexType, and not a void*. The current
	implementation is in terms of an underlying semaphore. This might be a
	template argument in the future. Again, memory localization is
	simplified.

  common/pdbTool.cc
	added useChainID flag
	chainID --> segname override; initial altLoc support

  common/simulation.cc
	resizeAtomArrays method removed, replaced with resizeAtomData.
	add/clearBondedPair methods removed
	changes to support XplorWrapProc:
	  all atom, and bond data now live in member data of type AtomData
	moved atom data arrays out of Simulation::SharedData into its parent.
	
  common/xplorPot.cc
	added simulation() method
	energy and derivs methods now call down to corresponding
        XplorWrap methods 

  common/xplorSimulation.cc
        renamed static method simulation() to defaultSimulation()
	mods to accomodate XplorWrapProc
	  wrap() method is no longer const.
	  added override of resizeAtomData
	constructur: now append child pid to simulation name for nonlocal
	  XplorSimulations
	syncTo: pass modified member to slave process

  common/xplorWrap.cc
	changes as in header
	added energy and derivs methods
	made public, virtual methods to support XplorWrapProc
	added local flag
	openFile: fixed removal of ASSFIL info message
	added en/disableOutput and fastCommand specializations to XplorWrapProc
	const changes; added energy/derivs methods; select changed to virtual

  common/xplorWrapProc.cc
	XplorWrapProc: wrapper to run XPLOR as separate process, w/
        shared memory communication. This allows one to set up
        multiple XPLOR simulations with different structures within
        one instance of Xplor-NIH.

  intVar/Makefile
	added -LEXEDIR

  intVar/dint-test.cc
	fixup for printCM --> printStepDetails change

  intVar/dinternal.cc
       -printCM renamed to printStepDetails and exported to PublicIVM
       -large timestep warning now doesn't print unless printStepInfo is 
        enabled

  intVar/publicIVM.cc
	syncPos: added (untested) recentering code

  intVar/publicIVM.hh
	printCM renamed to printStepDetails and exported to PublicIVM

  nmrPot/csaPot.cc nmrPot/rdcPot1.cc nmrPot/varTensor.cc
	VarTensor:
	  added initial support for ensembleAxis()
	  this to support varTensorTools.calcTensor_ensemble

  nmrPot/noePot.cc
	added *untested* log normal potType

  nmrPot/surfaceArea.cc
	mods for getting at internal deriv info
	mods to expose class details to SWIG - mostly meaning unnesting classes

************** Platform-specific changes **************

   Darwin/Intel
	updates so that LOCAL_CC, etc work ok
	now use -llapack -lblas for LAPACK_LIB
	createF77SharedLibrary:
	  remove FLD_FLAGS
	now supply default values of CC, CXX
	added default value for F77

  arch/Darwin_8_x86/python/Makefile
	removed DARWIN_LAPACK_LIB redirection

  arch/Darwin_8_x86/source/Makefile
	disable some optimization reductions
	reduced optimization level to avoid crash in orient tests:
	  orientations, parser

  Irix
  arch/IRIX64_6.5/Makefile.defs
	added explicit def. of BLAS_LIB (to libscs)

  Linux/x86
  arch/Linux_2.2_i686/Makefile.defs
	update for intel compilers version 9.1:
	  add -axP flag which allows generation of much faster Fortran code on
	   Core machines, with a slight penalty on althons.
	for pgi build, add -lpgsse2 for lapack
	added default values for CC, CXX

************** User-invoked scripts **************

  bin/pty-xplor (used by VMD-XPLOR)
	change from an indiscriminate wait to waitpid...

  bin/pyXplor.in
	whitespace protection: added missing quotes

  bin/seq2psf.in
	added the -custom_rename option - for nucleic acid naming

  bin/xplor.in
       -now export XPLOR_EXE to environment: so XplorWrapProc can
        spawn proper exe
       -updated behavior for finish-up when running parallel jobs:
	  now wait for only the first child job (process 0). That job has
	  already waited for the other active jobs in python/xplorFinal.py

************** Documentation updates **************

  online tutorial
	merged changes from class of 2006/12/08

  online Xplor reference manual
	added references for wildcards in the NOE syntax section.

  helplib/nih-py-avePot
	scale no longer sets/uses subPot's value - now they're multiplicative

  helplib/nih-py-ensembleSimulation
	updated w/ note about straddling potential terms

  helplib/nih-py-ivm
	updated hinge() method docs

  helplib/nih-py-noePot
	updated deviation docs a bit

  helplib/nih-py-varTensor
	nmrPot

  helplib/faq/node0950.txt
	updated hyperlinks into the XPLOR manual


************** Example script updates **************

  eginput/PSF_generation
	added pdbTest  
	  download and verify psf generation and coordinate reading
	added testPDB2PSF script and support files
	  validate PSF generation.

  eginput/PSF_generation/addAtoms.py
	updated dynamics stespsize

  eginput/cmdline
	added testParallel.py
          basic validation of parallel execution and communication capability

  eginput/dna_refi/
        added ensemble.py 
          - ennsemble refinement using RDCs, CSAs, solution scattering info
	added plotIrange.py
          - calculation solution X-ray scattering curve

  eginput/dna_refi/refine_full.py
	fixup to pdbToPSF by addition of customRename arg
	move covalentMinimize to before tensor atom creation

  eginput/gb1_rdc/
	added pairRMSD.py to calc pairwise positional rmsd

  eginput/gb1_rdc/refine.py
	changed CDIH threshold back to the default value

  eginput/gb1_rdc/sa_tmv_bice_rgyr.inp
	reworked to run properly when -parallel is specified

  eginput/marvin
	removed il4, protg example cases

	Disulfides are now treated with bonds, not NOEs.

	Scripts include support for running example in quick mode.
	 quick mode:
	   -only calculates 20 structures per pass.
	   -only calculates structure of the first 36 residues of CVN.
   	   -write_subset_*.tcl does the first matching of the complete
            set of peaks to the first 36 residues.  These scripts
            write out PIPP PCK tables of the assignable peaks that are
            then used by the initMatch*tcl scripts, which should speed
            them up considerably. 
  	   -subset_talos_pred.tab is just an edited version of
            talos_pred.tab, covering only the first 36 residues.
	

	initMatch scripts use shift referencing correction, stripe correction,
	network filtering, and primary sequence distance filtering.
	
	Replaced pass1 with pass2, since I now have good starting likelihoods
	from the network filtering.
	
	resByRes.tcl produces a report of the contacts to and from
        every residue.

  eginput/marvin/cvn/check_talos_predictions.tcl
	Eliminated direct readin of parameter file--now handled
        automatically by readParamPsfPdb

  eginput/marvin/cvn/cvn_c13noe.shifts
	Corrected a wrong residue name in shift table

  eginput/protG/.runAll
	fixed calcTensor line

  eginput/protG/anneal.inp
	cosmetic change

************** Python Interface Changes **************

  python/Makefile
	dist rule: copy .lines files over
	.so build rule: added LAPACK_LIB

  python/atomAction.py
	fixes for selections entered as strings
	randomizeDomainPos:
	  various fixups
	added methods:
	  copyAtomCoords
	  randomizeDomainPos
	
	removed global import of vec3 module contents

  python/cdsList.i
	added instantiation of CDSList_double

  python/cdsMatrix.i
	added constructor from list of lists
	changed int to float to get proper type deduction of sqrt
	added typemaps for DComplex
	added SymMatrix
	added eigen(SymMatrix/CDSMatrix) functions
	added trace, det functions

  python/derivList.i
	changed argument name

  python/ensembleSimulation.i
	added fromSimulation downconverter function

  python/ivm.py
	enabled printStepDetails
	minimizeEscape:
	  changed default numSteps
	added docstring
	setBaseAtoms:
	  fix to support multiple Simulations
	breakAllBondsIn:
	  optimization: not good enough- this must be placed in the C++ layer.
	fixed treatment of finalTime when minimization==True: ignore it

  python/nonBondTools.py
	updated to use new PRINT_FILE and PREV_PRINT_FILE xplor variables

  python/protocol.py
	updated hyperlinks into the XPLOR manual
	matchInexactAtomEntry:
	  added rules for strange nucleic base HN atom naming
	revived/rejuvinated covalentMinimize-
	  it is used by two scripts in eginput/dna_refi
	initCoorde: added useChainID flag
	matchInexact: handle chainID, altLoc
	fixupCovalentGeom:
	  handle increased levels of verbosity
	fixupCovalentGeom:
	 *constraints interaction statement now placed after initNBond, so it
	  doesn't get clobbered.
	 *nicer verbose printouts
	fixupCovalentGeom: added rigidRegions arg, xSim fixup
	fixupCovalentGeom:
	  added maxViols optional argument
	  for minimization, now step dEPred to current energy / 10. This to
	  avoid large step sizes when we start very close to the minimum.
	  now print out violations in extraTerms
	updated to support multiple XplorSimulations
	multiple methods now have optional simulation argument
	removed unused covalentMinimize function
	fixups for fixupCovalentGeom
	cartesianTopology:
	  fix to allow sel object to be an AtomSel instead of only a string
	fixupCovalentGeom:
	  mods to allow this to run on nonlocal XplorSimulations:
	  use the IVM instead of XPLOR's dynamics and minimization engines
	    (note that the runtime is longer, but the number of iterations is
	     about 10x smaller)
	updated to use new PRINT_FILE and PREV_PRINT_FILE xplor variables
	initDihedrals:
	  added optional string argument, for specifying restraint
  	  table as a string 
	fixupCovalentGeom:
	  added extraTerms argument - additional pot terms to be satisfied.
	fixupCovalentGeom:
	  updated to work when using EnsembleSimulations
	initNBon: added more docstring about cutnb/tolerance relationship

  python/psfGen.py
	pdbToSeq:
	  fixes so that the segment name gets read/set correctly.
	added ACE as a protein residue type
	seqres:
	  fix case of missing chainID in SEQRES field- now we really read the
	  SEGID from the first matching ATOM field
	deal properly with chainID (override segid)
	psfGen.seqToPSF:
	  Marius' custom nucleic atom renamings are no longer longer
  	  the default but still available via the customRename flag.
	deduceSeqType:
	  added URA to URI as residue name which will trigger identification
	  as RNA.

  python/pyConvert.cc
	fromPy(double):
	  fixed error checking to not crash when a complex is given

  python/pyInterp.cc
	constructor:
	  initialize exitStatus

  python/sansPotTools.py
	create_SANSPot: added weightByExpt toggle

  python/selectTools.py
	fixes to properly deal with multiple Simulations:
	sim arguments to functions removed

  python/simulationTools.py
	StructureLoop:
	  changed default value of averageCompSel to omit axis atoms.

  python/socketComm.py
	removed debug messages
	barrier:
	  added cookie info (calling frame's line number) to barrier message
	Connection constructor:
	  handle failure of gethostbyaddr: fall back to just using ip number
	  to identify the remote host.
	Comm: constructor: increased default timeout length to 1.6 days

  python/solnScatPotTools.py
	added Chi^2 to analyze output

  python/surfaceArea.i
	mods for getting at internal deriv info
	instantiate newly unnested classes

  python/varTensorTools.py
	added calcTensor_ensemble; added support for ensembleAxis to
	saupeMatrix and analyze 

  python/xplorFinal.py
	xplor.exitStatus is now treated differently:
	  any nonzero value will cause error message to be printed, and
	  final time stats to be skipped.

  python/xplorInit.py
	parseArguments:
	  support the case that argument ``options'' is a single string
	parseArguments:
	  formatting changes in error message.

  python/xplorPot.i
	added support for restriants() method for the CDIH term.
	the method is registered during XplorPot construction

  python/xplorPotTools.py
	updates to support multiple XplorSimulations
	updated to use new PRINT_FILE and PREV_PRINT_FILE xplor variables
	added support for restriants() method for the CDIH term.
	the method is registered during XplorPot construction
	PotData constructor:
	  added support for numRestraints - for CDIH term only.
	  motivated by Jurgen Doreleijers

  python/xplorSimulation.i
	getXplorSimulation:
	  fixup so that this works for size=1 ensembleSimulations.
	moved getXplorSimulation here from protocol.py
	added converter  (downcaster) from Simulation
	added helpers:
	  enable/disableOutput
	fixups for python shell and select wrapper methods
	added python convenience methods: shell, select, command, fastCommand

************** XPLOR code changes **************

  source/ccalls.c
	getusername: fix for case of failure in getpwuid

  source/energy.f  source/etor.f   source/pick.f   source/cstran.f
	fix nasty bug in etor: the check for bond colinearity would
	fire off at fairly large values of the dot product.

  source/funct.fcm   source/selrpn.f   source/string.f
	copyst subroutine:
	  now set new copyst_err logical if target string size is too small
	selrpn:
	  make use of copyst_err to set selerr appropriately.
	
	This allows C++ AtomSel object to throw an exception on such errors.

  source/hbuild.f
	format statement syntax fixup

  source/noe.f
	added log-normal potential type

  source/parmio.f
	fix for problem first noted in 1998:
	  http://www.bio.net/bionet/mm/x-plor/1998-August/001729.html
	
	vdw radii were incorrectly calculated from nbfix statements. This
	impacts the repel potential, and allows atoms to get too close.

  source/parser.f
  source/xplorFunc.f
	added DECLARed variables PRINT_FILE and PREV_PRINT_FILE
	involved increasing the length of CMDPMX in symbol.fcm
	getvar_asString:
	  now calls TRIMM on returned string

  source/prot.f
	Correction to the electric field part of proton shift
	calculation.  I wasn't summing up the effects of every heavy
	atom on each proton--rather, I was just returning the last
	heavyatom's effect on each proton.  David Wilton from 
	Mike Williamson's lab caught this.

  source/xplor.c
	added -sharedProc cmdline flag with call to C++ xplorwrapproc_slave
	changed new_argv initialization to ANSI C - for pgcc

  fortlib/lapack/Makefile
	no longer include routines which are already in blas

  fortlib/lapack/dsecnd.f
	commented out unnecessary external declaration for ETIME intrinsic

************** Changes to the Marvin/PASD facility  **************

  marvin/MarvinNOEPotential.cc
	-Eliminated generation of inverse exceptions for peaks expected
         to be near the diagonal, since that's handled by TCL.
	-Also eliminated a double-counting of accounted & unaccounted
         neighbors in updateNoeCompleteness.  The original code
         produced the same numbers as the current code, but spent twice
         as long doing it. 
	-Added method to reset the explicit inverse exceptions list

  tcl/aeneas_tools.tcl
	Added initializeLikelihoodsFromFilters
	Several changes:
	1.  match* routines now check whether a ShiftAssignment
            actually has a proton/heavyatom shift before trying to
            match it to a peak.  To support an (unused by default)
            option in stripe matching, which turns off SAs that don't
            have stripe targets. 
	2.  Eliminated recenterShiftAssignments.  Replaced with
            stripeCorrection. 
	3.  Eliminated origGenerateNetworkLikelihoods,
            try2GenerateNetworkLikelihoods, maxLinksInAgreement, and
            generateNetworkLikelihoods.  Replaced with networkFilter. 
	4.  NetworkFilter can accept multiple pots and analyze them together.
	5.  Eliminated stripeFilter and gatherTargetShiftValues.
            Replaced by stripeCorrection. 
	6.  Added correctShiftReferencing.  Detects any constant
            offset between the from and to proton dimensions and
            corrects peak positions to eliminate it. 
	7.  Added ability to create (with createExplicitExceptions)
            explicit exceptions for peaks expected to appear within solvent
            lines. 
	
	Note:  file also includes beginnings of secondary structure
         Hbond detection (with secStructFilter), but it doesn't work
         well yet, and is not used in released scripts. 

	addition in stripe filter--ability to update shiftAssignments' 
	shift values to the targets'.
	
	Lots of changes to the netFilter code, but mostly to the
        obsolete versions. 
	Modified enforceExpectedSymmetry proc into new symmetryFilter proc.
	
	match*d now uses improved mechanism for handling unfolded
	peak locations.  UnfoldPeakPosnToMatch is now the key proc,
        and it always returns two possible unfolded locations:  one
	with an even number of folds, and one with an odd number of
        folds.  match*d tries all combinations of those possibilities 
	in searching for peak position/unfolded SA posn matches.

  multiple files:
	Update to use atomSel class's == and intersects
        operators. Replaced occurrences of old TCL procs atomSelsEqual
        and atomSelsOverlap. 

  tcl/import_pipp.tcl
       -Added a proc to write PIPP PCK tables.  Doesn't yet handle PIPP-style
	assignments.  Also doesn't handle writing slice numbers.  Also missing
	ability to generate the DATA AXIS lines that are used to set spectral
	ranges.  Other than that, it's quite complete :-/
       -Improved comment-skipping in PIPP tables
       -Added rules in code for importing PIPP shift tables, ignoring
        lines beginning CUR_TYPE and ignoring lines commented out with
        a leading #, as Dan Garrett sometimes has.

  tcl/noe_reporting.tcl
	Changed format of one output line.
	Several additions:
	 1.  reportNOEaccuracy can now report on the accuracy of
	 peakAssigns above a certain likelihood, or those below a certain
	 likelihood.  Used to eval accuracy of accepted peakAssigns
	 and rejected peakAssigns, respectively. 
	 2.  reportNOEprecision now also reports on NOE
 	 discrimination, the fraction of peakAssigns that is either >
 	 a high likelihood cutoff or < a low likelihood cutoff.  High
 	 NOE discrimination correlates with convergence. 
	 3.  markGoodPeakAssignments reports number of unassigned
	 peaks, for convenience. 
	 4.  initialPeakAnalysis can now be set to report statistics
	 based on counting all peakAssigns, or only those whose
	 likelihoods are within a given range. 
	 Useful for evaluating performance of filters.

	-Added calculation of fbad-long using previousLikelihoods
	 arising from peakAssign filters 
	-Expanded residue-by-residue reporting function to combine
	 several pots' peaks into one report.
	-Modified summarizeMarvinResults proc.  Added separate flags
	 for violation and high-likelihood values to be used while
	 rescuing filtered PAs, so that the structures' accuracy need
	 not be too great to bring in filtered PAs. 
	-Added logic in PA rescuing, so that I don't add PAs to peaks
	 that already have high-likelihood PAs.  
	-Expanded reporting of the filtered-PA-rescuing stuff.

  tcl/noe_tools.tcl
       -Corrected wording of a thrown error--old version indicated
	wrong flag syntax 
       -A few Marvin peak reading & writing improvements:
       -Extended ability to parse both current marvin-formatted .peaks
        files and older marvin-formatted .restraints files.
       -Improved xplor-formatted output.  Added check for
	peakAssignments with intersecting to & from selections, so
	that they won't be written to xplor files--classic xplor can't
	deal with them.  
       -Also improved handling of bounds corrections--I now find the
        maximal upper and lower bounds corrections for all the
	peakAssignments of a given peak, and use those in generating
	the xplor ASSIgn's distance bounds. 
       -added support for Michael Nilges's extended-OR format for NOE
        ASSIgns.  If a given marvin peak has multiple peakAssignments
	to be written, the peak is written as an 
	ASSIgn (sel) (sel) d dmin dplus OR (sel) (sel) OR ... 
	restraint, which the current classic NOE code can parse correctly.
       -Two peak-reading bugfixes, plus I moved removeLowLikelihoodPAs from
	aeneas to here, and added removeFilteredPAs.  RemoveFilteredPAs is used
	at the end of initMatch scripts to clear out the filtered PAs.
       -RemoveLowLikelihoodPAs is used in convertToXplor, as a final
        cleanup before creating xplor-style NOE tables.
       -Added consolidateClosePeaks (from make_random_noes.tcl).  
       -added support for reading & writing the number of failed
        filters for each peakAssignment.  
       -Caught a few bugs in the xplor-format NOE reading routine.
       -now remove all explicit inverse exceptions before reading a
        new file of them 

  tcl/pdb_support.tcl
	Added support for reading specific models from a PDB file

  tcl/sa_protocols.tcl
	pass? protocols have been reworked.

  tcl/sa_tools.tcl
       -added code to print a Python traceback when an exception is encountered
       -Eliminated minor memory leak from non-cleaned-up atomSel.
       -Includes beginning of PDB cluster analysis.  Not used in
	released scripts. 
       -use appropriate env variables instead of paths relative to XPLOR_DIR

  tcl/selection_tools.tcl
       -Added a fairly complete test script for all the procs in
	selection tools.   
       -Some bugfixes to selection tools, engendered by the test.  
       -new code: previous and nextResidue procs
       -memory leak fixes in makeSelectionNonStereospecific and in
        stereopartnerForSelection. 

  tcl/shiftassign_tools.tcl
       -Added ability of initialShiftAssignmentAnalysis to make
	reports based on all peakAssignments, or only on those with
	likelihoods within a given range. Analagous to the changes in
	initialPeakAssignmentAnalysis. 
       -Corrected & expanded reporting of NOE completeness, so
	that it agrees with numbers generated by 
	MarvinNOEPotential::updateNoeCompleteness.  Also reports 
	specifically on accuracy of explicit exceptions that do not
	correspond to a peakAssignment (ie., were generated by network
	filtering, or diagonal exclusion) 
       -added proc to group shiftAssignments by residue, which is used
        in a few places (eg., netFilter's intraresidue neighborhoods)

  tcl/talos_tools.tcl
       -Added proc to read in a TALOS .tab file and write out an xplor
	cdih table. Previous code reads TALOS and creates dihedral
	restraints directly, with no chance to output an
	xplor-formatted file.  This isn't pretty, but it'll do 
	for now.  Useful when going to python scripts, where TCL
	readTalos isn't convenient.
       -Added ability to skip commented lines

************** Parameter/Topology updates **************

  toppar/nucleic-1.1.par toppar/nucleic-1.1.top
	intended changes somehow got dropped from the previous version
	version string in note updated
	added missing impropers for NH2 base groups and H2'/''
	bumped minor version number
	fixes to stereochem defs to match IUPAC - contributed by J. Doreliejers

  toppar/nucleic-2.0.par toppar/nucleic-2.0.top
	naming corrections
	added missing impropers
	version number bump to 2.0

  toppar/protein-2.0.par toppar/protein-2.0.top
	naming corrections
	added missing impropers
	version number bump to 2.0

************** VMD interface changes **************

  vmd/vmdInter.cc
	remove some ill-advised radius-setting statements


------------------------------------------------------------
		     Changes from 2.15 to 2.16

General 

 now provide native intel/Mac binary package

 documentation:
   XPLOR reference manual has significant updates
   various updates/corrections to Python reference manual

 mailing list now searchable from 
   http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih -- thanks to Gmane.

 pty-xplor:
  added the -xhost command-line option
 
 xplor, pyXplor scripts:
   now protect space, special characters in command-line arguments

XPLOR interface

 added pseudo-CSA (PCSA) potential term, test case from A. Grishaev
  see A. Grishaev, J. Ying, A. Bax (2006) "Pseudo-CSA restraints for
  NMR refinement of nucleic acid structure" J. Am. Chem. Soc. 128,
  10010-10011. 
 
 
 source/ccalls.c
  frename: now remove trailing spaces from old as well as new
    (contributed by J. Howarth)
  frtn_gethostname: workaround for some broken gethostname
  added new FRTN_CLOCK c function
 
 source/cstran.f,v
  changed dihe restrain info message, and now print to DUNIT
 
 source/fantalin.f
 source/fantacross.f
  output fixups, inspired by J. Howarth
 
 source/hbdb.f
  fixed array bounds error noted by J. Howarth
 
 source/orientations.f
  added ugly hack/memory leak to get working on Darwin_x86
 
 source/saxs.f
  saxsinit2:
    initialize glocc array to 0
    rearrange argument decl's, variable definitions to normal conventions
 
 source/linuxtime.f
 source/x86_64time.f
  change VCPU to call new FRTN_CLOCK c function
 
 source/xdipolar_coup.f,v
  fixed rhomicity definition in help text
 
 source/xplor.c
  changed argument treatment: now all options we know about are
  removed from the arg list (except for -tcl)
 
Python Interface

 builtin xplor module
  added helper function xplor.parseArguments() for argument parsing and 
  validation. 
 
 varTensor:
   will now throw exception if Rh (rhombicity) is specified outside the legal 
   range
 
 cdsVector:
   added constructor taking size and fixed value arguments
 
 findPython:
   USE_MACOSX_FRAMEWORKS is now an env var
 
 ivm.py:
  subtle change to breakBond: in 1st arg passed to convertToSelectionIndices
 
 protocol.py:
  matchInexactAtomEntry:
    -added rule matching H to HN
    -added matching rule, examining final character. Came from ILE
     difference in XPLOR, charmm22 ff.
  fixupCovalentGeom:
    -change treatment of sel argument: do not re-evaluate selection
    -save and reset mass values
    -placed default tolerances in argument list
    -split constraints interaction selection line so that longer
     selections are possible before COMAX errors.
    -exit: fixup exit message, and customize the exception thrown
  initCoords: 
    added optional erase argument
 
 psfGen.py:
  dna residueType: added URI residue
  deduceSeqType: 
    differentiate DNA/RNA by presence of URI
  pdbToSeq:
    fixed extraction of the resid field to get all four characters.
  pdbToPSF: 
    changed seqToPSF to not deprotonateHIS- can be done in pdb
 
 pyConvert.hh:
   added toPy(FloatPair)
 
 pyXplor.cc:
  pythonStartup:
    now employ xplorInit.py to do initial argv parsing
  python_interp:
    now executes xplor.scriptName (instead of first item on argv),
    if it's not empty.
  change:
    now run xplorInit.py in the context of the module ``xplor.''
  xplorInit:
    much less is now enclosed in strings
    added parseArguments helper
 
 sansPotTools.py:
  exchangableName: 
    now print warning message if residue is not supported, don't crash
  moved solventVolumeSet definitions to solnScatPotTools
  create_SANSPot:
    added preweighted option
    added radiusScale (now properly treat excluded volume)
    added fractionD2O (now deal with D2O solvent)
    added exchangeFraction (to deal with exchangable protons in D2O)
    added normalizeIndex argument
    now clip negative I values to zero
  added useGlobs function and glob defs.
   -support separate proton globbing
  changed scattering length units by 10
    also fixed units in comments.
  changed used SolnScatPot version from complex to real
  added specialized useGlobs frontend
 
 simulationTools.py:
  genFilename:
    updated to use xplor.scriptName.
  StructureLoop:
    added averageSortPots argument - terms to use to sort structures
    genAveStats: 
      now call averageContext inside stats loop
    added averageTopNum as alternative to averageTopFraction
    added averageAccept function argument to report on only allowed structures.
  StructureLoop.genAveStats:
    deal properly with the case of no acceptable structures
    change location of averageContext call: now done for each structure,
    so that things like globCorrect() get set properly.
  added convertToPotList function
  testGradient: added alwaysPrint option
  documentation update
 
 socketComm.py
  startServer: write message to console on failure
 
 python/solnScatPot.i
  added pairDistribution function
  added import during module initialization
 
 python/solnScatPotTools.py
  add Pr function:
    weighted pairwise distance distribution function.
    supports EnsembleSimulations with proper averaging.
  useGlobs:
    added verbose entry which turns on single-glob atom listing
 
 python/solnXRayPotTools.py
  useGlobs: support for verbose argument
  moved solventVolumeSet definitions to solnScatPotTools
  moved useGlobs from solnXRayPotTools.py to solnScatPotTools.py and
    generalized, then placed wrapper back in solnXRayPotTools.py
 
 python/varTensorTools.py
  calcTensor:
    now able to calculate the tensor from an ensemble of structures (not
    necessarily an EnsembleSimulation)
 
 python/xplorInit.py
  fixed up to deal with command-line options, arguments
  added xplor.parseArguments:
    uses writeConsole to print command-line error message
  change:
    now run xplorInit.py in the context of the module ``xplor.''
    much less is now enclosed in strings
 
 eginput/gb1_rdc:
   .py files updated
   StructureLoop in .py files now implements averageSortPots argument
 
 eginput/protG:
   added calcTensor.py to calculate alignment tensor from expt rdcs + structure
   grid_search.inp - add comments on use
   tang.py - updated to deal with segids, unknown resid types
 

TCL interface

 tcl/Makefile
  deal with empty TK_INIT_DIR def
 
 tcl/findTCL
  handle case of missing tk_library
  USE_MACOSX_FRAMEWORKS is now an env var
 
C++ Layer Changes

 rdcWavePot:
   updated
 
 atomSel.cc:
   reimplemented intersects() method for speed.
 
 noePot.cc:
   updated defaults to be consistent with those in noePotTools
   change: now default to HARD potType
   NOE tables
     increased maximum distance to 10^6 (in ASSIgn statement)
     added a check that atom selections don't intersect.
     allow zero distances
 
  


		     Changes from 2.14 to 2.15

General

 * Parallel job synchronization now uses tcp communication
     - allows some nodes to be down at startup (will ignore those
       hosts). Also allows for xplor-nih or whole machines to crash
       and not hang the parallel calculation- structures scheduled on
       those nodes will be ignored. 
     - requires communication over port 9021 (or that specified by the
       -pport option)


 *Changes to the command-line xplor script:

  -fixed -smp so that -parallel need not be specified.

  -support for new socket communication facility:

     added support for socketComm functionality with -pport, -phost options
     and XPLOR_PPORT, XPLOR_PHOST env vars.

     added -crash_on_startup flag to cause crash if a process doesn't
     report in at startup

     (for parallel jobs) now redirect file descriptor 9 to stdout
     before redirecting to the log file so that we're able to send
     messages to the user: parallel calcs now print cpu info summary 
     to stdout at exit


  -remove LD_ASSUME_KERNEL hack - this caused problems on newer
   distributions. This change may break things on FC2.


 *startup message: now include the hostname

 *Parameter changes:

   -protein-1.0.par:
     added missing angle parameter for SP patch
   
   -protein-1.0.top:
     fixed the YP patch 1cz 1oh 2p angle definition
  

Python Interface

  Binaries now built with Python version 2.4. Source also builds with
    version 2.3

 ./configure: now always performs Python precompilation to avoid race
   condition on parallel startup. Also precompile files in bin.$ARCH
   Fix XPLOR scripts so that sure we're always using optimization.

  atomSelAction: Fit: 
    fixed ugly bug which could cause the rotation matrix to become an
    inversion matrix.
  
  most C++ potential terms with restraints:
    added numRestraints() method
    added showAllRestraints boolean - if set all restraints are output
    in the showViolations() method (but violated terms are flagged).
  
  PDBTool: added support for PDB MODEL records
    read() now returns list of unmatched PDB ATOM entries
  
  PotList: 
    change to rms(): now use individual terms' scale() to weight
                     the rmsd calc, if the terms are all of the same PotType.
                     also weight by # restraints.
    Also made a fix to violations().
  
  Simulation::atomString:
    output has been rationalized.
  
  SimulationWorld:
    added cpuTime method
  
  XplorPot:
    added delegate so that rms(), violations() methods return useful values
  
  XplorWrap:
    select() will now raise an exception if there is an error.
    added fastCommand() method
  
  
  PREPot:
    update adding SUM restraints - PRE contributions from
    distinguishable groups which contribute to the same relaxation process
  
  SolnXRayPot: renamed to SolnScatPot. 
    Now supports complex scattering amplitudes
    added glob defs for DNA.
  
  cdsMatrix:
    fixes to *, - operators
  
  cdsVector:
    fixes to - operator
  
  ensembleSimulation:
    added helpers: singleThread, multiThread, commBarrier
    better EnsembleSimulation cleanup at exit
    Modified behavior with EnsembleSimulation fixed
    
  protocol.py:
    initCoords: 
      added support for optional model parameter
      added support for unmatched pdb ATOM entries. guessing logic-
        togther with the with matchInexactCoords helper.
    initDihedrals: fixed default chi2 restraint definitions.
    initTopology: fix to allow pathnames relative to pwd and TOPPAR (and absolute
                  names too).
    added initRandomSeed, initialRandomSeed helpers
       Distribute seed value to other parallel processes if the seed if
       not explicitly specified. 
  
    torsion/cartesianTopology:
      added oTensors argument which takes a list of VarTensors to set up
      according to the setFreedom() method.
  
  psfGen:
    cisPeptide: fixed so that it actually works for the non-proline case.
    seq2PSF: fix in several patchings to deal properly w/ multiple segids.
  
  pyInterp:
   allow triple-single quotes in scripts redirected from stdin.
   Python shell: better handling of error conditions- exceptions are now 
   thrown back to C++, proper exit status is returned
  
  python startup:
    errors in startup will now throw exception. Previously only a
    warning message was printed.
  
  rdcPotTools:
    fixes to dipolar coupling scaling.
    Allow using correct gyromagnetic ratio signs.
    added DaScale helper function
  
  restraintStats:
    fixes for violation amounts
    now accumulate and print crossTerms separately from main potList
  
  simulationTools:
    StructureLoop: 
      added averageCrossTerms argument to constructor - so that
        non-refined-against terms are listed in statistics, average
        printouts
  
      allow averagePotList, crossTerms to be plain python sequences
  
      added new optional paramter: structureNums. Can use
        this instead of numStructures, startStructure
  
      calcAverageStructure:
       now treat ensembles correctly: calculate the average of the
         ensemble-averaged structure.
  
      averageCompSel changed from "not hydro" to "not name H*"
      genAveStats: now print out the rmsd values for fitted selection in
                  addition to the comparison selection. Also write out
                  these two strings.
      writeStructure: 
        added extraRemarks argument
        now writes out seed from protocol.initialRandomSeed
   
     now report pos. rmsd to ave. of calcd struts

  analyze():
    can now give a single Pot as an argument (doesn't have to be a sequence)

 varTensorTools:
   calcTensor:
     no longer reset oAtom to origin- rather, keep it at its current
     position.
     fixed handling of non-NH normalized restraints
     fixed handling of restraints w/ more than one bond vector
   analyze:
     fixed calculation of Euler angles
   added xyzFromEuler helper
   configIVM_fixAxis/RhToOther:
     fixes for ensemble simulations.

 vmdInter.py:
    VMDObject.labels: now allow sel arg to be string
    change to object naming so that using file in subdir works

 xplorPotTools: now supports COLL term

 added minimize.py - optimization algorithms


 various small updates to the examples
   gb3_ensemble: added order.py example script - refine against order
   parameters 


Platform Specific

 *Darwin: 
   -threads now supported in VMD interface
   -updated to be compilable by gfortran
   -rationalized Python libraries linking- they no longer need to be
    linked to the xplor binary 

 *better support for running on Scyld clusters:
    -can now specify SCYLD_PROCESSES env var and command-line -parallel
    -now eval $cmd so that redirection works on scyld clusters

XPLOR Interface

  *enbond: moved NCSOP to heap, removed MNCSYM parameter
  
  *hbdb: removed naamax parameter, and now allow it to grow dynamically.
         fixed an array range underflow in hbdbpatt
    
  *plane: PLNINR: reinitialize PLN_NUM to 0 so that the init statement works.
  
  *xplor.f: change behavior for case in which a filename is specified:
    now redirect it into stdin, so that the PYTHon and TCL XPLOR
    commands work in this mode. 

  *new variables are defined: START_TIME, START_DATE variables
  
  *tutorial/nmr_ensemble:
    filled in missing contents

  *multiple modifications to modernize the code - thanks to J. Howarth.



		     Changes from 2.13 to 2.14


XPLOR interface changes

  new XPLOR SAXS module from Alex Grishaev
     A. Grishaev, J. Wu, J. Trewhella, and A. Bax, JACS 127, 16621 (2005)

  ncs.fcm:
    removed MAXNGR static arrays - now dynamically allocated
  
  hbdb.f:
    removal of pause statements, prompted by J. Howarth
  
  XPLOR tests:
    added new sani and saxs tests
  

Python Interface changes

  new solnXRayPot module for refinement of SAXS and large-angle xray scattering
  data.
  
  improved support for Potential terms derived from C++ terms. Eliminates 
  the step of reconstituting a Python wrapped object by deducing its type.
  
  XplorPot:
    threshold, rms(), and violations() methods now work for supported terms.
    simulationTools.xplorThreshold has been removed.
  
  XplorWrap:
    added new methods: disableOutput, enableOutput to manipulate
      XPLOR's echo and wrnlev variables
    for convenience, xplorInit places references to these in the global xplor
    module.
  
  IVM:
    fix for error condition in buildNode:
      better identify bend atoms in bad hinge specification
      null out IVM's tree_ member when throwing an exception -
         so that it doesn't get destructed in this state (causes crash)
    
  python cdsMatrix module:
    added CDSMatrix_complex
  
  cdsVector: 
    added dot(), __mul__(float), __pow__(), sum()
  
  analyze functions: now work better with AvePot terms
  
  noePotTools:
    create_NOEPot: now initialize aveType to "sum"
  
  nonBondTools.py:
    made messages from XPLOR interface a bit less verbose
  
  rdcPotTools:
    specified different nucleic acid NH distance to use in calcing 
    Da_prefactor.
  
  protocol module:
    initNBond:
      added selStr argument. onlyCA is now deprecated.
      omit ANI residues in constraints interaction statements
    initDynamics: 
      added parameters eTol_minimum, etol_factor
    added addDisulfideBond helper function
    torsionTopology: modified to call selectTools.breakDisulfides()
  
  structureLoop module:
    StructureLoop:
      updated so that calcing ave. struct. works for EnsembleSimulations
      when generating violation statistics, now only use averageTopFraction
        structures (not all structures)
      disable creating backups for fit structures if averaging or taking stats
    StructureLoop.pdbFile():
      now use old object if the name has not changed. This necessary to
      retain remarks info.
    better per-restraint statistics over all calculated structures.
  
  varTensorTools:
    fixes for fixAxisToOther function
    added orthogonalize() helper function
  
  Python Swig change for C++ ACCESSOR and MODACCESSOR modules resulting
   in large size decreases, simplification in coding.

  added posSymmPot: position symmetry- a more powerful version of the NCS term.

  Python tests:
    added rdcPotTest3, mat3Test, solnXRayTest

  Python docs: 
    csaPot: fixed def. of csa tensor atom s in assignment table.
    mat3: updated SymMat3 constructor, element access member docs
  
  
TCL Interface changes

  PASD/Marvin:
    renamed class Restraint to Peak.
  
  tclPosnSymmPot:
    Support for Atom and AtomSel based accessors

Changes to the eginput example scripts:

    PSF generation: added complex circular peptide example

    dna_ref: added refine_full.py script

    gb1_rdc: added standalone analyze.py script
             anneal.py: changed noe setup so extra terms can be added easily 
                        updated for XplorPot threshold change
    protG: anneal.py: updated to produce .viols, stats files
           anneal.inp: removed spurious NOE parameter clause 
                       (thanks to Francesca Marassi)
  


Parameter/Topology changes
  
  nucleic-1.0.par
  changed the 5-terminus H'-H'' improper angle values to match it's
  minimized value
  
  protein-1.0.top
  phosphorylating patches: fixed patch SP, added patch YP
  
  
low-level changes:

  CDSlib/complex.hh:
    added operator-=
    added operator*(Complex,T)
    added function IEXP(floatType)
  
  CDSlib/mnbrak.cc:
    small fix
  
  vec3.hh:
    added explicit constructor from integer, so the literal ``0'' can be used.

  modified.cc:
    registerTo: don't register sim if it's already been registered.
  
  avePot.cc/hh:
    fixed calcEnergy/Derivs s.t. the scale factor is not applied twice.
  
    overide scale, threshold accessor methods to use values from the
    subpot. Note that the wrong value will be obtained  if the object is
    accessed as a Pot (the base class). Virtual methods might be a better idea.
  
  Fortran code:
    removal of arithmetic if statements, (courtesy of J. Howarth)
  
  prePot:
    optimization in inner loop

  build change:
    now should better handle transitive linked shared libraries
  
  now include required lapack, blas source- but it's use is optional.

  mac build now on Darwin_8, (OS X 10.4.4) no longer tested on Darwin_7

  added gamma and rjbesel functions from the specfun netlib library.



		     Changes from 2.12 to 2.13


PASD/Marvin:
  - fixed so that the eginput scripts now work.
  - changed linear pot to have continuous derivatives
  - improved error checking.

eginput scripts:
  added gb1_rdc/violStats.py - script to gather violation statistics
      over multiple structures.
  updated gb1_rdc/anneal.py to collect violation statistics

  updated runAll script so can now specify multiple target directories.

XplorPot:
  a single instance can now specify multiple XPLOR terms. This to work
  around errors when VDW and PVDW are called separately.

noePot:
  added Average PotType

updated Python interface tutorial

Source/lowlevel changes

  created fortlib directory and moved libfft there
  added pppack to fortlib
  template library: added Spline class 

  C++ cleanups. Contribution from Jack Howarth.

  EnsemblePot now derives from ModifiedBase
  
  Pot:
    now derives from ModifiedBase
    added threshold MODACCESSOR.
  
  EnsembleSimulation:
    fixed up addDependent, removeDependent, markAsModified methods
  
  Pair class is now a template in CDSlib.

  XPLOR interface:
    updated sbound.f to remove NMCTAB parameter
    nbonds.f: don't print close atom warning messages if messages=off.
  
  bin/makedepend:
    now omit entries which end with a slash (/) so it doesn't create
    dependencies on directories.
  
  testDist:
    now remove WORKDIR before running tests
  
  noePot, rdcPot, csaPot, jCoupPot:
    now have direct access to list of Restraint objects 
    added violation value to printViolations() header
  
  
  Python interface:
    added spline module
  
  Python Interface:
    fixed violation reporting in *Tools.py:
     threshold values are no longer reset to 0 before analysis.
  
  monteCarlo.py:
    bug fix for randomizeTorsions (affected Marvin/PASD)
  
  split off nonBondTools.py from simulationTools.py
  
  protocol.py:
    contributed by Greg Zornetzer:
    fix for fixupCovalentGeom():
      specifying a selection with bonds to a non-selected region would
      mess up the interface region.
    addUnknownAtoms():
      added arguments: dyn_stepsize, dyn_numStepMull, verbose
      reduced default stepsize to 0.02ps
  
  simulationTools.py:
    StructureLoop: 
    added genViolationStats flag to constructor, for printing out
    violation statistics.
    if averaging structures, overwrite the calculated structures with
    versions fit to the first structure.


		     Changes from 2.11.2 to 2.12

Frontend Scripts

 - seq2psf: 
    added -amidate_cterm option
    multiple chains are now supported
  
 - xplor script:
    more relaiable treatment of the PYTHONHOME env variable


Parameters

 -  added fixed nucleic.top/par topology/parameter files.


IVM

 - fixed bug for torsion angle dynamics with a bond which is initially 
   *exactly* parallel to the xz plane.


Python Interface

  - new functionality in protocol.py:
    addUnknownAtoms() see example in eginput/PSF_generation/addAtoms.py 
  
  - simulationTools.py:
    StructureLoop:
      added writeStructure() method which creates a .viols file for each structure

  - testGradient:
    fixed so that it works with an non-ensemble Simulation
    
  - changed PotName for some terms to be more consistent
  
  - atomAction.py:
    SetProperty: fix so that properties with Capitalized letters (such as
      residueName) are handled properly.
  
  - cdsVector.py:
    norm: now always reduces to a float_type scalar return value
    added vec_norm(): performs a norm on each element of a vector
    added log()
  
  - simulationTools.py:
    analyze(): terms now register themselves for reporting using 
               registerTerm(), and simulationTools doesn't need to know 
               about them.
    fixes for nonbonded analysis for repel=off
  
    added fileSuffix global variable
    used when creating temporary files to avoid races in EnsembleSimulation
    calculations
  
  - simulationWorld.py:
    added pure-python world() function to access the simulationWorld()
    static function.
  
  - trace.py:
    added function addModuleName() to make tracing arbitrary modules easier.
 
  
  - protocol.py:
    fixupCovalentGeom: allow sel argument to be a plain string
  
    initDynamics(), initMinimize(): 
       no longer set ivm's constrainLengths. This is part of the topology setup.
  
    added cartesianTopology() helper for ivm setup.
  
    added initTopology()
    initParams/initTopology(): will now take sequence type specifiers which
      use the new parameters, topology files configured in module local 
      dictionaries.
  
  - psfGen.py:
    now add remark to autogenerated PSFs - to denote their origin 
    * seqToPSF:
      now use protocol.initParams/Topology for initialization.
      added the amidate_cterm option
      changed default seqType to 'auto'
      added disulfide_bonds/bridges arguments.
      added support for seqType 'rna'
    * pdbToPSF:
      now use seqType 'auto' in call to seqToPSF
  
  - pyPot:
    rewrote the PyPot constructor to remove need to supply the
    second self argument.

  - added tests: tkInterTest, ivm3, bigPatch
    note that tkInterTest will fail if DISPLAY is not set (or X11 access is 
    otherwise not available)  .


XPLOR interface

  - optional output reduction improvements
  
  - updates to allow extra-large residues in patching (removed SEGDIM 
      parameter from segmnt.f) 
  
  - fixes to problems in Fortran code discovered by Darwin's GuardMalloc
  
  - fixes to some paraRestraints code
  
  - fixes to machine dependent code found by gfortran developers
  
  - fixes to deal correctly with case (>8 bonds)
  
  - torsion angle database term: fixed bugs caught by Guillermo Bermejo

VMD-XPLOR interface

  - fixed race condition which caused errors when trying to follow the 
    dynamics of an ensemble.

  - pty-xplor: set pager to cat- real pagers cause pty-xplor to hang in 
    python mode

  - added findXcookie to bin files distributed - for more reliable remote 
    Xplor-NIH/ VMD-XPLOR execution.

Low-Level Changes

 - atomSel:
   added intersects() operator==() methods,

 - template libraries:
   cdsIterator.hh: mods so that can be re-assigned.
   cdsString.cc: added copy() method which returns a non-reference counted copy.
   cdsVector.hh: added scale() method for symmetry with CDSMatrix class

 - compilation/development
   added support for intel Fortran/C++ compilers, version 9

   added version 1.3.25 to list supported swig versions

   findPython: now also defines PYTHON_VERSION

PASD/Marvin:

  - Significant changes to the Marvin/PASD code -
     *** old scripts will need to be modified ***

  - note carefully the following change to the initial matching script:
       now, the spectral range must be specified by giving the actual
       beginning and end of the spectrum (in ppm) along each dimension.

  - introduce new datatype, ShiftAssignment 
    * represents a single entry (or pair of covalently bonded entries)   
      in a chemical shift table.  
    * facilitates analysis of the likelihood of a particular spin's
      location in the structure and/or the likelihood of its chemical
      shifts being correct.  
    * note difference from the previous version, which only kept track
      of the likelihood of a particular assignment of a particular NOE
      peak being correct. 

  - full discussion of these changes will be available in an upcoming
    paper.




		     Changes from 2.11.0 to 2.11.2

PASD/Marvin fixes to correctly handle symmetry peak filter.

Platform specific updates:
  - Darwin version 8 (Tiger) is now supported
  - amd64: added some support for use of Pathscale fortran

frontend xplor script
  - consistent use of TMPDIR env variable, if it is set. 
  - semaphore cleanup:
    grep for current user- to avoid permission violation messages.

Python Interface:

  protocol.initNBond():
    added onlyCA flag to enable only CA-CA repulsion.
  
  gb1_rdc/refine.py example script:
    - further improvements s.t. no explicit parameter configuration is
      performed in the structure loop.
    - now will compute average structure.
    - increased the rdc force constant
  
  simulationTools.analyze():
    - now report the number of vdw violations
    - now print violation info in a .viols file.
  
  simulationTools:
    - added waitForProcess() barrier function.
    - StructreLoop:
      * added capability to compute average of all structures
      * added analyze method which prints violation info to a
        file with the structure filename + a '.viols' suffix.
      * added StaticRamp class
      * added InitialParams, FinalParams class, which initialize or
        finalize ramped parameters.
  
  fix to CDSMatrix::resize to copy old contents
  
  added CDSVector_int to cdsVector.py

  CDSString: optimization of operator+=(CHAR)
  
  PotList:
    added a copy() method

  EnsembleSimulation input multiplexer (using stdin) - now only use if
  *both* stdin and stdout are ttys.


XPLOR source:
  - removed/converted blanket SAVE statements in darwintime.f and dynio.f
  - ccalls.c: frtnchdir:
    reworked to use Fortran's string length argument.
  - update from A. Grishaev - updates the segm statement.
  - nbonds.f:
    * added DECLAR statements for REPEL nbond parameters
    * removed limit on iatmx (max num of bonded atoms) by overloading the
      CMPLTD return code of MAKINB.
  - combined xlftime.f and darwintime.f --> darwintime.f
  - noe.f:
    reduced the severity of error of calling PRINT for classes in which 
    POTEntial is set to SYMM, HIGH, or 3DPO.

parameters:
  added patches, parameters for phosphoserine, phosphocysteine to the
  standard protein.top/par files.

  

		     Changes from 2.10 to 2.11

- xplor run script: 
  added the -scyld cmd-line argument for running on scyld clusters.
  added the PROTSHIFTS env var for access to proton chemical shift database.
  under Linux, now cleanup unused Semaphores at startup.

low-level:
  - fixed error in reference-counted classes which rendered them
  non-thread safe.  
  - fixed Solaris-specific ensemble bugs.
  - fix for strange Solaris /bin/sh behavior

 - pty-xplor (used by Xplor-NIH) fixups under Solaris

Python interface
 
 - now correctly build and test Tkinter package.

 - pyXplor script: now properly protect spaces in command-line arguments.

 - psfGen module:
   added the dAmino() function to convert a residue to a D-amino acid.

 - simulationTools:
   now perform NOE analysis.

 - added NOEPotTools- helper functions including create_NOEPot()

 - protocol.py: 
   initMinimizie: added added dEPred to argument list.
   added initCoords() helper function.

 - varTensorTools:
   added calcTensorOrientation function

 - xplor (toplevel) module:
   added the requireVersion() function

 - added posRMSDPot potRMSDPotTools
   for both RAP and bfactor refinement.


XPLOR interface:

 - hbdb: fixes for problems with long filenames.

 - more robust determination of username.

 - Darwin:
   fix so that file versioning works properly.


Examples in the eginput subdirectory:

 - added gb1_rdc simple examples using NOEs and multiple
   RDCs. Included are both XPLOR and Python scripts.

 - protG/anneal.inp: fixed bug in vdw loop.

 - PASD/Marvin: fixups in eginput/marvin/il4 example data.

 - improvements to runAll script.

Low-level changes:

 - RandomNum: added integerInRange() member.
 
 - jCoupPot:
   fixed variance calculation.
 
 - AtomSel: added reevaluate, constainsAtom and isMonomericallyEqualTo
   members.
 
 - Pot: added resetPotName() method.
 
 - IVM:
   small changes to Powell minimizer.
   added vel/setVel accessors.
 
 - cdsVector module:
   added sqrt function.
 
 - VMD:
   better cleanup of vmd atom selections.
 
 - EnsembleSimulation:
     added input multiplexer for the case in which stdin is a tty. This
     allows proper interactive behavior for numthreads>1, and should help
     with debugging.



----------------------------------------------------------------------
		     Changes from 2.9.9 to 2.10

general:

  new parameter/topology file naming convention:
    NMR protein refinement should now use protein.top / protein.par
  new command: tclXplor
    calls xplor -tcl. Can be used as command interpreter
  Darwin/ MacOSX change: version number now only includes the first digit. 
    This so the arch/equivList doesn't need to be updated so often.
  Darwin: 
    fixed Xplor-NIH-as-tcl-extension functionality
  xplor master script: 
    - now can specify parallel machines using the MACHINES env variable
      instead of the -machines option on the command line.
    - updated Linux ARCH def to deal with minor dot release numbers.
    - IRIX: properly treat LD_LIBRARYN32_PATH if it is set.
  eginputs:
   - added runAll script to run (most) scripts in eginputs.
   - fixed up scripts to use protein.top/par files.
   - minor updates to protG/anneal.inp

  
  
Python Interface:

  EnsembleSimulation:
    - can now specify nonuniform weighting.
    - fixed issue in which coordinate changes made in XPLOR shell were
      not propagated back to EnsembleSimulation.
  
  PotList:
    - change in behavior when an attempt is made to add a term with an
      instanceName already contained in the list: now the code throws an
      exception (previously, the second term was silently ignored).

  OrderPot:
   - new potential term to enable refinement again order parameters.
  
  CSAPot:
   - atomOrder accessor changed to support 15N CSAs.
   - fixed variance calc.
  
  AtomProb:
   - now normalize output map so that the largest map value is 1.
  
  PrePot:
   - update from Junji Iwahara
  
  ShapePot:
   - fixes- deal better with apparent singularities in angle diff. calc.
   - new degenerateTol member- determination of eigenvector/value
     pairing is now modified close to degeneracy- chose such that
     eigenvectors are those which align most closely with those in
     ensemble member 0.
   - added Pairwise target type- minimize pairwise differences.
  
  Python CDSVector:
    added fromList accessor.
  
  ivm:
    - added stepsizeThreshold member. If set, will try to avoid small
      timesteps by performing minimization when the stepsize falls below
      this value.
  
  mat3:
   - added trace function.
   - added rows()/cols() accessors.
  
  protocol: 
    initParams(): 
      - added optional weak_omega argument to allow
        small deformations of the peptide bond.
      - added optional reset parameter to clear any previous parameters
    fixupCovalentGeom():
      - made a bit more robust.
    genExtendedStructure():
      - added pdbFilename argument
      - fixed up the use of the optional sel argument.
    added covalentMinimize(), initHBDA() helpers.

  psfGen:
    pdbToPSF(): the pdbRecord argument may now be a filename instead of
                a string
    seqToPSF(): added optional deprotonateHIS argument.
    added cisPeptide() function to make cis-peptide bonds.
  
  ShapePot:
    added analyze tools.
  
  SimulationTools:
    better handling of analysis of existing files. No need to specify 
       numStructs. 
    added testGradient() helper.
  
  JCoupPot:
    added jCoupPotTools including create_JCoupPot() and analyze() helpers.
  
  PotList:
    analyze summary now prints sum of violations, not average.
  
  varTensorTools:
    added massSetup() helper.
    analyze(): print out more Da/Rh info, if using an ensemble.

XPLOR interface:

  hbdb update from Alex Grishaev:  
   adds ability use multiple segments
   other fixes to prevent crashes
  
  fixup time reporting under AMD64, Solaris

  SET MESSages statement: 
    now allow NONE to be a valid keyword (same as OFF).
 
  xplor command: allow XPLOR script to be specified as an argument. It
                 no longer needs to be redirected through stdin.

----------------------------------------------------------------------
		     Changes from 2.9.8 to 2.9.9

XPLOR interface:

  fixed problem in which Xplor-NIH would clobber /dev/null if the program was 
     run as root.
  plane.fcm: removed static arrays from planarity restraints.

general:
  configure script: added -symlinks option
  pdf2psf: fixup in reading arguments.
  seq2psf: added disulfide bond support with 
           -disulfide_bond and -disulfide_bridge options

PASD/Marvin fixup for problems at startup.

Python Interface

  updated eginputs/protG/anneal.py
  cdsVector, mat3, vec3 updates. Need documentation.
  python interpreter speedups (large) when tracing is off.
  python: added version, version_info to xplor module.
  XplorPot term now supports the scale() accessor.

----------------------------------------------------------------------
		     Changes from 2.9.7 to 2.9.8


XPLOR interface

  added support for set PRINT=off end statement, to suppress (most) output.
  related- now reroute much output through PUNIT instead of unit 6 (stdout).


Python interface

  protocol.py:
    added 
     genExtendedStructure() - generates a random initial structure.
     fixupCovalentGeom()    - corrects bonds, angle, dihe, atom overlap.
    modified
     initNBond()       - added optional nbxmod, tolerance parameters.
     torsionTopology() - added optional parameter to fix omega angle.

  psfGen.py:
    re-enabled and fixed the terminal atom chain break code
    seqToPSF(): now takes sequence as list or string
  
  rdcPotTools:
    added support for CAHN expts. provided by Alex Maltsev
  
  ringGeom, structureTools: structure analysis tools.
  
  selectTools:
    IVM_groupRigidSidechain(), convertToSelectionIndices():
      optimizations
    updated the following to correctly deal with multiple segments:
      IVM_breakProlines, IVM_breakRiboses, IVM_breakDisulfides, 
      IVM_groupRigidBackbone, groupRigidSel
    rigidProteinSelections: 
      ARG entry:   removed CE atom from rigid group list
  
  simulationTools:
    StructureLoop constructor: added the startStructure argument, fixes
  
  trace:
    fixes to work better with non-XplorNIH python interpreter
  
  varTensorTools:
    calcTensor(): fixes, now works with CSA expts too.

  replaced readline with editline (license issues).

  pyXplor script now treats cmd line arguments correctly.

  PDBTool: fixed a memory leak, added addRemarks() method to Python interface.


PASD/Marvin auto-assignment

  added AENEAS (Automated Experimental NoE Assignments based on Shifts):
    -accepts chemical shift, NOE peak position tables, matches them up, 
    filters them in reasonable ways, to produce an initial NOE restraint table.
    -now the primary input mechanism for Marvin.  
    -examples of use in the interleukin-4 and cyanovirin example cases.

  Support for 3dC, 3dN, 4dCC and 4dCN NOESY data

  Automatic detection of solvent lines

  Terminology change:  Rather than refer to, for example, Hi, Ci, 
    and Hj in a 3dC experiment, they're now referred to as fromProton, 
    fromCarbon, and toProton.  

  Reduced output during covalent geometry cleanup.

  Improved energy minimization.


Other various potential terms:

  Ensemble calculations:
    children now ignore the terminal suspend signal.
    performance, robustness improvements.
  
  CSAPot:
    fixups, cleanups
    restraint: corrected the tensor() method
  
  NOEPot:
    fixed segfault when reading a bad restraint (in code compiled with
    Intel compilers).
  
  RDCWavePot: 
    bugfixes
  
  ShapePot: 
    performance improvements.

  paraRestraints code fixes


Examples/Documentation

  documentation additions, fixups
  protein G example:
    update anneal.py: cleanup, modernization. Now psf and initial coords are
    generated on the fly from sequence info.
    added tang.py script for pretty printing of torsion angles from an
    ensemble of structures.

Architecture specific notes:

  combined Darwin+other os distribution should now work.
  Darwin build: 
    python libs now linked against xplor executable, rather than shared
    libs so that extension module has a better chance of working.

  Linux builds:
    workaround for segfaults in recent Redhat 2.4 kernels which incorporate 
    the back-ported thread library.

    The 2.2 kernel binary package has been discontinued. Please
    contact us if you are affected by this decision.

Parameters

  parnah1er1_mod_new.inp:  contribution from Zeena Johar:
    new impropers added to define chirality of ribose carbons


Running Xplor-NIH

  added xplor_mpi - helper script for running Xplor-NIH under MPI.
  testDist: now doesn't clean up if a failure occurs.

Low-level code

  CDSMap- added iterator over key/value pairs

  CDSStringStream, fdstream- 
    fix for memory leak (beyond my control) under Intel compilers

  FixedMatrix- added setDiag(vector)

  added EnsemblePot base class for ensemble potentials
    allows for code reuse and simplifies the use of synchronization
    barriers, with better performance characteristics.

  Modified update: support for telling which aspect is modified
  (simulation or potential variable)

  XplorWrap: add pid to temp filenames (used to communicate with XPLOR),
    to avoid resource contention. (e.g. MPI jobs on local host).

  support for SWIG version 1.3.22


     ------------------------------------------------------------
		     Changes from 2.9.6 to 2.9.7

General changes

  new documentation page at http://nmr.cit.nih.gov/xplor-nih/doc/current/

  documentation page with update Python documentation

  also available at the command-line via xplor -pydoc

  XPLOR manual updates
	
  added two scripts: 
    -bin/pdf2psf to generate a structure file from a pdb file.
    -bin/pyXplor to facilitate using Xplor-NIH as a Python interpreter.

  new architecture supported: AMD64/X86_64 (Opteron/Athlon64).


Python interface changes:

  protocol.py: updated, added torsionTopology()

  selectTools.py: added getResids()

  surfaceTools.py: added calcSA()

  rdc/csa orientational tensor setup for IVM simplified with freedom()
          accessor, and varTensorTools.topologySetup()


XPLOR interface changes

  define four variables: $echo $prev_echo, $messages $prev_messages
    to better control echoing, messaging.
  
  suppress many messages when messages==off

  csa.f: fixed rmsd calculation

  segmnt.f: added NUMBer statement to the SEGMent statement - to allow
            starting resid to be specified - without renumbering.


Marvin/PASD changes: 
  
  allow import from nmrDraw, NMRSTAR, XEASY, and PIPP data formats.

  initial matchup of NOE peak locations and chemical shift tables is 
    now handled by Marvin:
    - STAPP no longer needed.
    - symmetry-related peaks are detected.
    - restraints/assignments fully annotated with NOE peak, chemical shift
      source info.

  eginputs/marvin/cvn and eginputs/marvin/il4 were re-worked
    to illustrate the new data import facility.


Parameter changes

  topallhdg.dna: swapped ADE H61|H62 positions and CYT H41|H42 positions


Other changes

  ensemble calculations: -improved performance by not blocking instead of
                          spin for num_threads>1
                         -added singleThread(), multiThread() methods
                         -better treatment of irregular shutdowns
                         -subtle IVM bug: different ensemble members could
                          have different temperatures.
                         -fixup for JCoupPot for Ne>1
                         -new ability to share python objects across an
			  ensemble.

  surfaceArea: many fixes and improvements including approximations and 
               data-caching to improve performance.

  pdbTool: xplorAtomName now better translates * characters.
           will now read/write to a string buffer.

  added rms() and violations() as required entries in the Pot interface




     ------------------------------------------------------------
		     Changes from 2.9.5 to 2.9.6

General changes

 removed limits on all PSF parameters- the arrays have been moved from
 Fortran common blocks to the heap. Xplor-NIH startup size is now about
 25MB smaller, and it will handle systems as large as your computer's
 memory will allow. 

 Removed the CSTACK- and the associated summary line at exit.

PASD/Marvin
  - improved memory cleanup
  - improvements to peak picking code.
  - general fixups.

Developer changes

  added source/i1mach.c for machine constants

  XplorVars changed to a singleton class

  removal of SWIG type registration code- replaced by calls to TypeQuery.

     ------------------------------------------------------------
		     Changes from 2.9.4 to 2.9.5

General changes

 merged isac code for floating RDC alignment tensor.
   [from H.J. Sass, G. Musco, S.J. Stahl, P.T. Wingfield and S.Grzesiek,
     J. Biomol. NMR 21: 275-280 (2001). ]

 merged hbdb code from A. Grishaev. 
   ``An empirical pseudo-potential that encodes for the relative
     arrangement of two protein peptidyl units linked by a
     backbone-backbone hydrogen bond.''

  faster program startup by lazy initialization - only start
  python/tcl when they're needed.

  bin/testDist now prints and tallies CPU times of the tests

  Linux_2.4_i686 build verified working on 2.6 kernels, and on AMD64 (opteron) 
  processors.

Python interface:

  added CSA potential.

  reworked RDC potential (old scripts will not work - please see
                          eginput/protG/anneal.py for examples of how to
                          fix)
    [tensor moved to a separate VarTensor class ]

  added Gauss-Bonet surface area (with gradient) calculator. See 
  python/tests/saTest.py

  protocol.py:
    added initParams(), initStruct().
    updated initMinimize, initDynamics to be more complete.

  selectTools: 
    added minResid()

  simulationTools:
    added pdbFile() method which generates a pdb file name from a template.

  pdbTool:
    updated so that the filename() accessor actually works.

  XplorPot() - can now specify argument as lower case.

  general:
     atom selection arguments can now be specified as a python string

TCL interface:

  PASD/marvin automatic NOE assignment package updates.

  added DerivList wrapper

Parameters:

  updated dna/rna parameters.

Developer Changes:

 CDSlib update:
  Complex type updates
  cdsList: added pop() method, can now interact with generic vector
  cdsVector: can now interact with generic vector
  cdsSStream: added str_volatile() (old behavior), changed str() to return
              a copy of the streambuf
  chull: convex hull calculator class
  matrixTools: added setRow/Column manipulators

 source ( Fortran source ) updates:
  README: includes style rules for XPLOR Fortran submissions.
  freehp: now clear the heap index (set it to zero).
  added ability to turn off vdw energy

     ------------------------------------------------------------
		     Changes from 2.9.3 to 2.9.4

General changes

  merged the PARArestraints module from  
    http://www.postgenomicnmr.net/SW/PARArestraints.html

  new script: bin/seq2psf to generate psf file from sequence
              do seq2psf --help for info.

  Fixup so compilation with NOTCL=1 actually works

  proton chemical shifts: added setup file to databases/protshifts,
     example in test/protoncshift2.inp

Examples and Tests

  eginput: 
     updated: mef_dna, analysis_SRY, dock_dipolar_chemshift, sry,
	    marvin, DNA-SRY, PSF_generation, SRY_data_preprocessing

     marvin: added cvn example, other script fixups

     protG: important fixes to anneal.inp, anneal.py
  
  Unit tests:
    test: updated carboncshift.inp,
          added    protonchift2.inp, paraRestr.inp, pyCmd.inp, tclCmd.inp
    python: added matTest.py, protocolTest.py
            updated rdcPotTest.py

Python Interface changes:

  important bug fix for IVM

  improved analysis capabilities. See e.g. eginput/protG/anneal.py

  update to RDC potential. Added calcTensor, makeTable helpers

  added additional linear algebra capability

  cleanup of distributed python directory

  now built with Python-2.3.3

  new Dihedral class for measuring dihedral angles

  updated help entries


TCL Interface changes:

  marvin: updates, fixes

  interface fixups

Platform specific:

  Darwin port: support for newer OS versions
               better support for IBM xlf

  ia64 port: support for version 8 of Intel compilers
             fix \0 characters in username

  x86 port: fixups for compilation with pgf77 and g77

Developer changes:

  improved distclean rule

  update to classes: CDSMatrix, auto_ptr, 

  new datastructures, algorithms:
    circular doubly-linked list, convex hull template algorithm
    symmetric heap matrices+support

  support added for swig-1.3.21, but it seems to have problems.

     ------------------------------------------------------------
		     Changes from 2.9.2 to 2.9.3

Core XPLOR code

  Darwin port: now compiled with the ibm xlf compiler- with a big
               speed improvement. Many improvements to build more
               easily with and without fink. A big thanks goes to 
               Jack Howarth (howarth -at- bromo.med.uc.edu) for doing
               most of this work. 

General changes

  eginput: updates, and addition of new example scripts.
  
  ia64 port is improved: full regression tests now report a single
                         error (in the XPLOR interface).


Python Interface changes

 - includes paramagnetic relaxation enhancement module based on the
   modified Solomon-Bloembergen equation and 
   multiple structure representation for paramagnetic groups. This module
   contributed by Junji Iwahara. Please contact him at 
   iwahara-at-helix.nih.gov(replace -at- with a @) for further information.  

 - RDCPotTools:
    -- added the following methods: saupeMatrix, normalizedScalarProduct

 - PotList interface improved to allow use of a simple Python sequence
   in most instances. Also, the potentials returned by indexing a
   PotList object are now cast back to their original type (instead of
   being generic Pots).

 - SimulationTools:
     added analyze() function to analyze terms of a potList and return
     a concise summary appropriate for the remarks section of a PDB file.

 - can now access argv.

 - help files updated.

TCL Interface changes

 - update to interactive interface.

 - can now access argv.

Developer changes

  initial entry point changed from Fortran to C (xplor.c)- so that
  argv is more easily used.

  upgraded to pcre-4.4

  added symlink support for Darwin-7.0, Darwin-7.2

  added XPLOR tests for the TCL and Python interfaces.

  improved Fortran rtl initialization, when needed.



     ------------------------------------------------------------
		     Changes from 2.9.1 to 2.9.2


Core XPLOR code

  constraint inter code: fixed bug encountered when a double selection contains 
                         more than 9999 atoms
  
  ia32/linux port: fixed bug in which \000 would sometimes be written in
                   the username output
  
  sani potential: fixed bug encountered when using the ``square well'' potential
                type

General changes

  a FAQ is included in helplib/faq
  
  eginput: updated protG .inp, .py scripts
           many changes and additions for other examples.
  
  ia64 port is better, but full regression tests still report two errors.


Python Interface changes

  rdcPot: now supports averaging of dipolar couplings
          rdcPotTools.py updated
  
  selectTools.py updated
  
  simulationTools.py: StructureLoop now will deal appropriately if the number
                      of structures is smaller than the number of processes
  
  vmdInter.py: added loadFiles() helper for loading ensemble of structures


Developer changes

  added new install rule. Define INSTALL_DIR in Makefile.loc and make install
    creates an installation of Xplor-NIH separate from that in the source
    directory.
  
  iostream .h headers are now wrapped by .hh versions in CDSlib
  
  symbols in cdsMath.hh changed namespace from CDS to CDSMath
  
  matrixTools: svd matrix size fixed in python interface
  
  moved tcl/python test scripts to tests subdirectories
  
  enumNameMap.hh: added functions to help with conversions
  
  reworked Simulation id code


VMD-XPLOR interface

  py-xplor: now explicitly set intr char to ^C. This had caused problems
            with vmd-xplor on SGIs

  vmdInter code: made color setting more robust.