BALL

• Interactive molecular drawing and conformational editing (+)
• Reading and writing of molecular file formats (PDB, MOL2, MOL, HIN, XYZ, KCF, SD, AC)
• 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, WII-based head tracking*, OpenSim*)
• Molecular graphics (3D, stereoscopic viewing, ray tracing*)(+)
• comprehensive documentation (Wiki, code snippets, online class documentation, bug tracker)
• comprehensive regression tests
• BALL project format for presentations and collaborative data exchange (+)
• QSAR*
• NMR
• editable shortcuts (+)

(*) Experimental function of the next version (+) Function of BALLView

The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It has been carefully designed to meet the needs of programming experts and novices. Users can exploit BALL's rich functions, while being offered an extensive framework of C++ data structures and algorithms, and a variety of standard structural bioinformatics algorithms. New algorithms can be added easily.

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 well-tested by many developers.

File import-export

BALL supports a rich variety of molecular file formats like 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

Fast and stable 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).

A variety of standard structural bioinformatics algorithms are offered and new algorithms can be easily added.

The following program reads a PDB file, adds missing information like bonds and hydrogens, optimizes the hydrogen positions using the AMBER force field, and writes the resulting molecule into a second pdb file.

 using namespace std;
 using namespace BALL;
 
 int main() 
 {
   // read a PDB file
   PDBFile file("test.pdb");
   System S;
   file >> S;
   file.close();
 
   // add missing information
   // e.g. hydrogens and bonds
   FragmentDB fragment_db("");
   S.apply(fragment_db.normalize_names);
   S.apply(fragment_db.add_hydrogens);
   S.apply(fragment_db.build_bonds);
 
   // check for charges, bond lengths,
   // and missing atoms
   ResidueChecker checker(fragment_db);
   S.apply(checker);
 
   // create an AMBER force field
   AmberFF FF;
   S.deselect();
   FF.setup(S);
   Selector selector("element(H)");
   S.apply(selector);
 
   // optimize the hydrogen's positions
   ConjugateGradientMinimizer minimizer;
   minimizer.setup(FF);
   minimizer.setEnergyOutputFrequency(1);
   minimizer.minimize(50);
 
   // write a PDB File
   file.open("test_out.pdb", ios::out);
   file << S;
   file.close();
 }

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, so porting code that uses BALL from C++ to Python, and vice versa, is usually a trivial task.

For instance, the above C++ code translates to:

# Example
file = PDBFile("test.pdb")
system = System()
file.read(system)
file.close()
 
# Add missing information
# e.g. hydrogens and bonds.
fragment_db = FragmentDB("")
system.apply(fragment_db.normalize_names)
system.apply(fragment_db.add_hydrogens)
system.apply(fragment_db.build_bonds)
 
# Check for charges, bond lengths,
# and missing atoms.
checker = ResidueChecker(fragment_db)
system.apply(checker)
 
# Create an AMBER force field.
FF = AmberFF()
system.deselect()
FF.setup(system)
selector = Selector("element(H)")
system.apply(selector)
 
# Optimize the hydrogen's positions.
minimizer = ConjugateGradientMinimizer()
minimizer.setup(FF)
minimizer.setEnergyOutputFrequency(1)
minimizer.minimize(50)
 
# Write a PDB file.
outfile = PDBFile("test_out.pdb", File.MODE_OUT)
outfile.write(system)
outfile.close()

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 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. BALLView allows loading several molecules at the same time and all representations can be hidden or shown at will. A large part of the functionality of the library BALL can be applied directly to the loaded molecule in BALLView.

BALLView supports several modern visualization and input methods like, for example, 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]

• List of molecular graphics systems
• List of free and open-source software packages
• Comparison of software for molecular mechanics modeling
• Molecular design software
• Molecular graphics
• Molecule editor

• Hildebrandt, Andreas; Dehof, Anna Katharina; Rurainski, Alexander; Bertsch, Andreas; Schumann, Marcel; Toussaint, Nora C; Moll, Andreas; Stockel, Daniel; Nickels, Stefan; Mueller, Sabine C; Lenhof, Hans-Peter; Kohlbacher, Oliver (2010). "BALL - Biochemical Algorithms Library 1.3". BMC Bioinformatics. 11: 531ff. doi:10.1186/1471-2105-11-531. PMC 2984589. PMID 20973958.
• Kohlbacher, Oliver; Lenhof, Hans-Peter (2000). "BALL—rapid software prototyping in computational molecular biology". Bioinformatics. 16 (9): 815–24. doi:10.1093/bioinformatics/16.9.815. PMID 11108704.
• Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver (2005). "BALLView: a tool for research and education in molecular modeling". Bioinformatics. 22 (3): 365–6. doi:10.1093/bioinformatics/bti818. PMID 16332707.
• Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver (2006). "BALLView: an object-oriented molecular visualization and modeling framework". Journal of Computer-Aided Molecular Design. 19 (11): 791–800. doi:10.1007/s10822-005-9027-x. PMID 16470421.

• Official website
• BALLView web page
• Code Library
• Gallery
• Tutorials