Release Notes 1.3 Series

BALL 1.3.2

Changes since BALL 1.3.1

• Buildsystem:
  • Fix some issues with CMake
• Core:
  • Fix a bug in the SES generator
  • Add a safeguard to StructureMapper in order to avoid numeric instabilities
• Python:
  • Fix compilation with Sip 4.10

BALL 1.3.1

Changes since BALL 1.3.0

• Buildsystem:
  • Added a CMake based buildsystem
  • Fixed autoconf to work with newer distros.
• Core:
  • Dramatic speed up of SES triangulation
• Python:
  • Fixed the StringHashMap bindings
  • Added some missing classes
  • Fix compilation with Sip 4.9
• BALLView:
  • Minor fixes all over the place

BALL 1.3.0

Changes since BALL 1.3 RC 1

• Core:
  • Replaced gSoap with an own implementation due to licensing issues
  • Removed MD5Hash in favour of Qt's implementation
• General:
  • Improve the documentation
• Bugfixes:
  • Prevent a crash in ResidueRotamer set
  • Fix POVRay export

BALL 1.3 RC 1

Changes since BALL 1.3 beta 2

• Core:
  • Add a warning to the RNG::setup() routine if invalid seeds were specified
  • Better algorithm for determining fragment names (Now DNA bonds are reconstructed correctly in BALLView)
  • Hopefully fixed all LC_NUMERIC issues
  • Improvements to the AssignBondOrderProcessor
• Buildsystem:
  • Some fixes when building with libtool
• BALLView:
  • Splitted the 3D toolbar
  • Updated the documentation
• Bugfixes:
  • The SecondaryStructure processor could produce too many secondary structure elements
  • Calls to exit() have been removed.
  • The hash function for BALL::String in Python does now work correctly
• General:
  • Cleanup and polishing everywhere
  • Split the Python module into a BALLCore and a VIEW part
  • Small fixes to the Python bindings
  • Make the Python module compatible with SIP 4.8

BALL 1.3 beta 2

Changes since BALL 1.3 beta 1

• Core:

  • Removed calls to exit()
  • Improvements to the plugin system
  • Fixed various parts of the PersistenceManager
  • Fixed bugs in the BondOrderAssigner
  • Add the convenience function: float Atom::getDistance(const Atom&)

• Buildsystem:

  • Various fixes in the Autotools build system

• BALLView:

  • Fixes to the OpenGL visualization in BALLView
  • Fixed the POVRay Exporter
  • Changing the PDB download URL works again
  • Made off screen rendering work better than ever
  • Reworked some icons to play better with dark colorthemes
  • Improved the SpaceNavigatorPlugin (MacOS support)
  • Fixes to the Stereo mode

• General:

  • Fixed various Windows specific bugs
  • Much improved MacOS support
  • Improved the documentation (which is now available under: http://ball-docs.bioinf.uni-sb.de/V1.3-beta2/)

BALL 1.3 beta 1

Changes since BALL 1.2 This is the first public release of BALL 1.3. It offers several significant new features, many bugfixes and optimizations as well as code cleanup. Most notable changes include (not necessarily complete):

• Buildsystem

  • The Python module has been split into a Core and a VIEW part
  • Reduce the size of the computed dependencies
  • Improvements allowing to create binary packages
  • Cleanup of the m4 macros
  • Optionally use libtool for building BALL
  • Add a bootstrap script for regenerating configure and friends
  • Support for DESTDIR when doing a make install

• Core:

  • Improved handling of DNA/RNA (further improvements scheduled for version 1.4)
  • Replaced home brew hash map by the tr1 implementation (either from gcc or boost)
  • Added a dependency on boost:
    • Quaternions replaced by Boost Quaternions
    • Use boost mutexes
    • Optionally use the boost ASIO library (allows to read compressed data)
    • Optionally use the boost hash map
  • Added a hard dependency on GSL
  • A GAFF implementation (experimental)
  • DNAMutator class allowing to exchange bases in DNA strand (experimental)
  • Automated bond order assignment via ILP or A* algorithm (BALL and BALLView)
  • Added plugin-system (experimental)
  • Removal of many throw specifiers that lead to unexpected behaviour (details)
  • HashGrid Iterator improved/replaced
  • HashBox Iterator improved
  • Solved some licensing issues:
    • Code for icosaeder refinement rewritten (used in NumericalSAS)
    • New MMFF94 parametrization files/file format
  • Exposed more data structures to the Python bindings
  • Slightly optimized PDB file loading
  • Atom containers can now delete unselected atoms, as well as remove atoms with certain properties
  • Add a hybridization processor (experimental)
  • Added a deprecation mechanism
  • Bonds have a property isAromatic() now
  • Fix compilation with GCC 4.3
  • Fix compilation with newer Intel compilers
  • Fixes for building against Qt 4.5
  • Made the Windows support a first class citizen
  • Fixed various compiler warnings

• BALLView:

  • Improved stereo capabilities 3D StereoSettings:
    • New stereo mode: "Side-by-side on different displays" (allows the use of an additional operator window for live presentations)
    • Introduced a dialog for fine tuning/computing the stereo settings (adapt screen sizes, user distance, etc.)
  • Separation of renderers from scene data:
    • Multiple render windows are possible
    • Other renderers than OpenGL are possible
  • Input Devices (experimental):
    • Spacenavigator plugin
  • Optionally write binary Project files
  • Introduced thread locking into the gui to prevent race situations
  • Customizable shortcuts
  • Add an option to load all models from a PDB file (e.g. PDB files generated from NMR data can be coped with)
  • Add VRML export for further editing or 3D printing
  • Improved handling of light sources
  • Start to work on more consistency in the GUI
  • Accelerate working with representations
  • Line smoothing can now be disabled. This makes the line representation look less cluttered.
  • Added a nice splashscreen :-)

• Bugfixes:

  • Removal of many valgrind errors
  • Fixed the Amber force field setup dialog. Choosing a parametrization file was not possible.
  • Fixed bugs in the FFT module
  • Fixed crashes when reading and writing mol2 files
  • RMSDMinimizer:
    • Fixed computation of translation matrices (translations were concatenated in the wrong order)
    • Fixed a memory leak (bug #68)
  • Fixed a huge memory leak in Triangulated surface (SES and SAS computation, bug #81)
  • Do not create a BALL and Stick model when entering edit mode (bug #78)
  • Fixed the "moving toolbars"
  • Fixed the usage of strncpy in PDBFile
  • Fixed OutOfGrid Exception in molecularSurfaceGrid (Bug #103); Patch due to H. Zellner.
  • Fixed problems with LC_NUMERIC != "."

• General:

  • New homepage
  • Setup a Trac system for project coordination:
    • New bug tracker
    • Wiki
  • Started a wiki containing tutorials, examples and code snippets
  • Public read-only git repository at http://ball-trac.bioinf.uni-sb.de/browser