The GRASP Project has created an algorithmic-level graphical representation for software called the Control Structure Diagram (CSD). The CSD was created to improve the comprehension efficiency of Ada source code and, as a result, improve software reliability and reduce software costs. Since its creation, the CSD has been expanded and adapted to include other languages. GRASP provides the capability to generate CSD's from Ada 95, C, C++, Java, and VHDL source code in both a reverse and forward engineering mode with a level of flexibility suitable for professional application. GRASP has been integrated with the GNU family of compilers for Ada (GNAT) and C (gcc), and Sun's javac compiler for Java. Use of GRASP is not restricted to these compilers, however. This has resulted in a comprehensive graphically-based development environment for these languages. The user may view, edit, print, and compile source code as CSDs with no discernible addition to storage or computational overhead.
Dynamic Probe Class Library (DPCL) is an object-based C++ class library that provides the necessary infrastructure to allow tool developers and sophisticated tool users to build parallel and serial tools through technology called dynamic instrumentation. DPCL takes the basic components needed by tool developers and encapsulates them into C++ classes. Each of these classes provide the member functions necessary to interact and dynamically instrument a running application with software patches called probes. Dynamic instrumentation provides the flexibility for tools to insert probes into applications as the application is running and only where it is needed.
The GotoBLAS codes are a fast implementation of the Basic Linear Algebra Subroutines. The advantage is fast calculation. Note that the actual performance depends in part on the code from which you call the GotoBLAS subroutine(s), and on the combination of architecture and operating system under which you are running. Your own tuning can make a big difference.
Open Watcom consists of the famous Watcom C++ and WATFOR compilers -- now open source. Open Watcom is mainly used for developing embedded, DOS, and ncurses software. Open Watcom includes the C/C++/Fortran IDE from Watcom for DOS and a full set of command-line tools for compilation, including the superb Watcom debugger. Open Watcom emits easy-to-understand errors and warnings when things go wrong. Open Watcom generates small statically linked binaries for Linux, Win32, Win16, OS/2, QNX, NetWare, and MS-DOS real and protected mode, among other targets. However, Open Watcom is still only beta-quality on Linux and BSD. The two most serious issues are imperfect C++ template support and an inability to dynamically link with shared libraries built by GCC. Also, Open Watcom is released under the Sybase Open Watcom Public License, which is considered non-free by most Debian Linux developers. NOTE: Open Watcom binaries for Linux are not available anywhere. You must build it yourself. 1.5 has known build issues on Linux; use version 1.4 or the current daily build instead.
APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.