The molecule viewer BALLView, also developed by the BALL project team, is a C++ application of BALL using Qt, and OpenGL with the real-time ray tracer RTFact as render back-ends. For both, BALLView offers three-dimensional and stereoscopic visualizing in several different modes, and applying directly the algorithms of the BALL library via its graphical user interface.
Reading secondary data sources e.g. (DCD, DSN6, GAMESS, JCAMP, SCWRL, TRR)
Generating molecules from and matching of SMILES- and SMARTS expressions to molecules
Geometry optimization
Minimizer and molecular dynamics classes
Support for force fields (MMFF94, AMBER, CHARMM) for scoring and energy minimization
Python interface and scripting functionality
Plugin infrastructure (3D Space-Navigator)
Molecular graphics (3D, stereoscopic viewing)
comprehensive documentation (Wiki, code snippets, online class documentation, bug tracker)
comprehensive regression tests
BALL project format for presentations and collaborative data exchange
NMR
editable shortcuts
BALL library
BALL is a development framework for structural bioinformatics. Using BALL as a programming toolbox allows greatly reducing application development times and helps ensure stability and correctness by avoiding often error-prone reimplementation of complex algorithms and replacing them with calls into a library that has been tested by many developers.
File import-export
BALL supports molecular file formats including PDB, MOL2, MOL, HIN, XYZ, KCF, SD, AC, and secondary data sources like DCD, DSN6, GAMESS, JCAMP, SCWRL, and TRR. Molecules can also be created using BALL's peptide builder, or based on SMILES expressions.
General structure analysis
Further preparation and structure validation is enabled by, e.g., Kekuliser-, Aromaticity-, Bondorder-, HBond-, and Secondary Structure processors. A Fragment Library automatically infers missing information, e.g., a protein's hydrogens or bonds. A Rotamer Library allows determining, assigning, and switching between a protein's most likely side chain conformations. BALL's Transformation processors guide generation of valid 3D structures. Its selection mechanism enables to specify parts of a molecule by simple expressions (SMILES, SMARTS, element types). This selection can be used by all modeling classes like the processors or force fields.
Molecular mechanics
Implementations of the popular force fields CHARMM, Amber, and MMFF94 can be combined with BALL's minimizer and simulation classes (steepest descent, conjugate gradient, L-BFGS, and shifted L-VMM).
Python interface
SIP is used to automatically create Python classes for all relevant C++ classes in the BALL library to allow for the same class interfaces. The Python classes have the same name as the C++ classes, to aid in porting code that uses BALL from C++ to Python, and vice versa.
The Python interface is fully integrated into the viewer application BALLView and thus allows for direct visualization of results computed by python scripts. Also, BALLView can be operated from the scripting interface and recurring tasks can be automated.
BALLView
BALLView is BALL's standalone molecule modeling and visualization application. It is also a framework to develop molecular visualization functions.
BALLView offers standard visualization models for atoms, bonds, surfaces, and grid based visualization of e.g., electrostatic potentials. A large part of the functionality of the library BALL can be applied directly to the loaded molecule in BALLView. BALLView supports several visualization and input methods such as different stereo modes, space navigator, and VRPN-supported Input devices.
At CeBIT 2009, BALLView was prominently presented as the first complete integration of real-time ray tracing technology into a molecular viewer and modeling tool.[2]
