The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, and conversion of different chemical file formats. It is written in 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
Fityk is nonlinear curve-fitting and data analysis software. It allows data visualization, separation of overlapping peaks, and least squares fitting using standard Levenberg-Marquardt algorithm, a genetic algorithm, or Nelder-Mead simplex method. It knows about many functions (mostly bell-shaped, like Gaussian, Loretzian, Pearson 7, Voigt, Pseudo-Voigt, and Doniach-Sunjic) and user-defined functions can be easily added. It also enables background subtracting, data calibration, and task automation with a simple script language. It is mainly used to analyze powder diffraction patterns, chromatography, photoluminescence, infrared, and Raman spectroscopy, but it can be used to fit analytical functions to any kind of data.
GKrellF@H is a GKrellM 1.2.x plugin to monitor the Folding@Home client. It can be configured to display the name of the molecule being folded, the download time of the work unit, and the progress through the work unit. It supports starting and stopping the Folding@Home client and will optionally run a command when a work unit completes.