Release Notes 1.4 Series

BALL 1.4.2

Changes since BALL 1.4.1

• Buildsystem:

• Fixed debug builds
• Bundle a python installer for Windows
• Improvements in packaging
• Fixes for recent GCC and Clang versions
• Improved dependency detection
• Compile flags are now correctly exported

• Core:

• Fix Flourine being classified as a metal
• Optimizations in Composite
• Optimizations in SCWRLRotamerFile
• Fixed compiler warnings generated by Clang
• Build with libsvm >= 3.0
• Add a DNAMutator class
• Add an AmiraMesh file parser
• Fixed bugs and crashes in the FPT backend of the AssignBondOrderProcessor
• Use empty() instead of size() == 0 when checking for the emptiness of STL containers
• Fix many memory leaks
• Fix many uninitialized variables
• Prevent loading the same plugin twice
• Made MOLFile Parser compatible to Pipeline Pilot SDFs without fully padded lines.
• Added missing dynamic library exports for various classes
• Much improved PubchemDialog
• Fixed a nasty memory overlay caused by LineBasedFile
• Fixed compilation of the QuEasy utilities

• BALLView:

• Fix crashes related with NULL pointer dereferenciation
• Fix handling of UNC paths
• Fix Povray export
• Update the visuals of the PluginDialog
• Improvements in trajectory file handling. (Mainly .trr files can now be loaded into BALLView)

• Python Bindings:

• Minor fixes
• Python bindings for SDGenerator and SmilesParser
• Fix the interfaces of MOL2File and XYZFile
• Fix SIP warnings about deprecated annotations

BALL 1.4.1

Changes since BALL 1.4.0

• Buildsystem:

• Better detection of installed libsvm and ASIO
• Improved Windows installer generation
• Fix compilation for GCC 4.6
• Install a CMake configuration file for BALL
• Improved Doxygen documentation

• Core:

• Parse and store PDB comments in a PDBInfo object
• Added a peptide cap processor
• Fixed PTE_::getElement(Position), it now returns Elements in order of their atomic number
• Fixes for 64bit systems (mainly Windows related)
• Updated PDB and DCD parser
• Fixed MOL2Files with unknown Sybyl atom-types
• Allow arbitrary whitespace delimiters in option files
• Bugfixes in the QSAR component
• Improvements in the NMR Component
• Further elimination of throw specifiers
• Fixed segmentation fault in HashGrid3
• Bugfix for SecondaryStructureProcessor
• Better handling of UNC paths under Windows
• Probably fixed solvent placement in periodic boundary conditions
• HETATMs read from PDB are now flagged as such
• Fix for SMBM bonds in MMFF94
• Fixed various memory leaks
• Fixed File::createTemporaryFilename(). It now generates different filenames during successive calls.
• Fixed a bug in NumericalSAS.
• Fixed possibly dangerous bugs in String.
• BALL Debug builds work again

• BALLView:

• Editor for PDBInfo objects
• Added a startup dialog to select the BALL_DATA_PATH
• Add a widget for editing named properties
• German translation improvements
• Improved Python interpreter widget
• Improved startup time by factor of about 2
• ColorByGrid finally works again
• Fixes for reading electron densities
• Fixed a crash concerning shortcuts
• Fixed various memory leaks
• Fixed orthographic projection mode not working on application startup
• Updated PubChem downloader (work in progress)

BALL 1.4

Changes since BALL 1.3.2

• Buildsystem:
  • Removed the old autotools based build system
  • Many fixes to the new CMake based build system
  • Visual Studio 2010 support
  • GCC 4.5 support
• Core:
  • Added a linear algebra library (experimental)
  • Added support for reading BMRB files as used for NMR
  • Implemented chemical shift prediction (ShiftX like)
  • Added a NameConverter class to switch between atom naming standards
  • Support for reading Antechamber files
  • Added crystallographic data structures
  • Added NamedPropertyIterator
  • Extended QSAR code
  • Merged support for the MPI interface
  • Removal of the static atom attributes vector (prevents crashes resulting from certain usage patterns)
  • Rewrote the SDGenerator
  • Optimized memory footprint of HashGrid
  • Improved performance and memory footprint of SES generation
  • Introduced various convenience functions in core classes (System::getProtein, Protein::getResidueByID, ...)
  • Support for alternative location markers in PDB files
  • Support for crystallographic information in PDB files
  • Improved MOL2 parser (Correctly output SYBYL types)
  • Improved HBondProcessor
  • Added the SimpleDownloader class for easy file downloads.
  • Some fixes as suggested by Cppcheck
  • Made files non copyable/assignable
  • Deprecation of the BALL::List class
  • Removal of deprecated functions (NumericalSAS/SES and Quaternion)
  • Fixes in MMFF94 atom type assignment
  • Fixed various bugs in the SES surface generation
  • All unit tests pass under Windows and MacOS
  • Removal of dead code
  • Fixed many warnings
• BALLView:
  • New IconLoader class
  • Improved icons in !BALLView
  • Usability improvements in the edit mode
  • Beginning i18n/translation support
    • German
    • Chinese
  • Possibility to switch between orthographic/perspective projection
  • Better full screen code
  • Relayouting of many dialogs
  • Improved color buttons
  • Merging of duplicated widget code
  • Improved !SDWidget
  • Improved PubChem download dialog
  • Improved downloading of e.g. PDB files
  • Support for transparent labels
• Python:
  • Improved Bindings
  • Compatibility with new SIP versions
  • More python example scripts
  • Wrapped HashGrid (as AtomHashGrid)