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The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.
GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.
QuantimSim is a physics simulation engine. Some aspects of astrophysics, electromagnetism, relativity, thermodynamics, statistical mechanics and quantum mechanics will be included in the simulation library.
...Analysis tools involve 1D, 2D and 3D data binning (histograms), volumetric data handling, etc. A small library, libmd, is an abstraction layer that serves data exchange among different tools.