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BALL (Biochemical Algorithms Library) is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
BALL has evolved from a commercial product into free-of-charge open-source software licensed under the GNU Lesser General Public License (LGPL). BALLView is licensed under the GNU General Public License (GPL) license.
BALL and BALLView have been ported to the operating systems Linux, macOS, Solaris, and Windows.
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.
The BALL project is developed and maintained by groups at Saarland University, Mainz University, and University of Tübingen. Both the library and the viewer are used for education and research. BALL packages have been made available in the Debian project.[1]
Key features
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)
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]
See also
Free and open-source software portal
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
References
"Debian -- Details of source package ball in sid". Retrieved 9 August 2021.
"BALLView with real-time raytracing capabilities demonstrated at official Intel press conference," BALL website, 3 March 2009. Archived 25 July 2011 at the Wayback Machine Accessed 12/13/10.
Further reading
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. S2CID 22875661.
External links
Official website
BALLView web page
Code Library
Gallery
Tutorials
vte
Computational chemistry software
Cheminformatics
Free software
Avalon Cheminformatics Toolkit Bioclipse Blue Obelisk Chemistry Development Kit ECCE JOELib OELib Open Babel RDKit
Proprietary
Canvas Chemicalize Discovery Studio
Chemical kinetics
Free software
APBS Cantera KPP
Proprietary
Autochem Chemical WorkBench CHEMKIN COSILAB DelPhi Khimera
Molecular modelling
and
visualization
List of molecular graphics systems
Free software
Ascalaph Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol
Proprietary
Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow EzMol Gaussian Maestro MarvinSketch MarvinView MODELLER Molecular Operating Environment SAMSON Spartan UCSF Chimera VMD
Molecular docking
List of protein-ligand docking software
Free software
AutoDock AutoDock Vina FlexAID rDock
Proprietary
Glide LeDock Molecular Operating Environment
Molecular dynamics
Free software
CP2K GROMACS LAMMPS OpenMM PLUMED
Proprietary
Abalone AMBER CHARMM CPMD Desmond GROMOS NAMD
Quantum chemistry
List of quantum chemistry and solid-state physics software
Free software
ABINIT ACES (CFOUR) AIMAll BigDFT COLUMBUS CONQUEST CP2K Dalton DIRAC DP code FLEUR FreeON MADNESS MPQC NWChem Octopus OpenMolcas PARSEC PSI PyQuante PySCF Quantum ESPRESSO (PWscf) RMG SIESTA VB2000 YAMBO code
Proprietary
ADF AMPAC DMol3 CADPAC CASINO CASTEP CPMD CRUNCH CRYSTAL Firefly GAMESS (UK) GAMESS (US) Gaussian Jaguar MOLCAS MOLPRO MOPAC ONETEP OpenAtom ORCA PLATO PQS Q-Chem Quantemol Scigress Spartan TeraChem TURBOMOLE VASP WIEN2k XMVB
Skeletal structure drawing
Free software
JChemPaint Molsketch XDrawChem
Proprietary
ACD/ChemSketch BIOVIA Draw ChemDoodle ChemDraw ChemWindow JME Molecule Editor MarvinSketch
Others
Aqion Eulim EXC code GenX GSim Mercury CrystalExplorer ICM (ICM-Browser) Materials Studio Molden OpenChrom SASHIMI
Hellenica World - Scientific Library
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