Pymultitool is a Python extension that provides a high-level interface to IBM Rational ClearCase MultiSite, suitable for scripting solutions. Pymultitool links directly against ClearCase libraries, saving you from the extra processing usually encountered in scripts that interact with ClearCase MultiSite, where the creation of a multitool subprocess is required to handle a request.
Wat2ions is complementary to DelPhi, the renowned solver of the Poisson-Boltzmann equation. The electrostatic potential map pre-computed by DelPhi is used to replace a certain number of the water molecules of the bath, surrounding a solvated macromolecule, with ions. The potential on the oxygens of the water molecules is estimated using a 3D cubic spline interpolation of the pre-computed potential. The waters with the largest potential are replaced with chlorides, and the waters with the smallest potential, with sodii. No two ions are placed closer than a certain distance to each other. The coordinates of the macromolecule, the water bath (except the replaced waters), and the placed ions are output to a new PDB file.
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.