The Gnome Chemistry Utils includes the following programs: a 2D chemical editor (GChemPaint), a chemical calculator (computes raw formule, molar weight, mass composition, and isotopic pattern), a 3D molecule viewer using OpenGL to display molecular models, a crystal structure viewer and editor, a spectrum viewer, and a periodic table of the elements.
GAMGI (General Atomistic Modelling Graphic Interface) is a program to build, view, and analyze atomic strucures such as molecules, crystals, glasses, liquids, etc. It aims to be useful for: the scientific community working in Atomistic Modelling that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; the scientific community at large studying chemistry, physics, materials science, geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; teaching chemistry and physics in secondary schools and universities; science promotion in schools, exhibitions and science museums.
uLan Driver provides 9-bit character message- oriented communication protocol that is transferred over an RS-485 link. The physical layer consists of one twisted pair of leads, and RS-485 transceivers. Supported hardware includes OX16C954 PCI based add-on cards, USB-to-uLan converters, the i82510 RS-485 card, or simple active converter dongle for standard PC RS-232 ports. The whole set of libraries and support tools is available for building embedded devices. They range from low level firmware boot-loaders and debugging tools up to object oriented properties browsing and manipulation and process data communication channels mapping.
Freesteam is a library that allows you to calculate water and steam properties using the industry-standard IAPWS-IF97 steam tables. It is a library of C++ classes which can be integrated into your code. Plug-ins to allow freesteam to be integrated with spreadsheets and other applications are under development. The included unit tests assure compliance with published property values. IAPWS-95 (scientific use) correlations are also included and used as part of this validation.
xylib is a portable C++ library for reading files that contain x-y data from powder diffraction, spectroscopy, or other experimental methods. Supported formats include plain text (CSV or TSV), Crystallographic Information File for Powder Diffraction (pdCIF), Siemens/Bruker UXD, Siemens/Bruker RAW v1/2/3, Philips UDF, Philips RD (raw scan) V3, Rigaku DAT, Sietronics Sieray CPI, DBWS/DMPLOT data file, Canberra MCA, XFIT/Koalariet XDD, RIET7/LHPM/CSRIET/ILL_D1A5/PSI_DMC DAT, Vamas ISO14976, and Princeton Instruments WinSpec SPE.
iNA is a computational tool for quantitative analysis of fluctuations in biochemical reaction networks. Such fluctuations, also known as intrinsic noise, arise due to the stochastic nature of chemical reactions and cannot be ignored for when some molecules are present only in very low copy numbers as is the case in living cells. The SBML-based software computes statistical measures such as means and standard deviations of concentrations within a given accuracy using the analytical system size expansion. The result of iNA’s analysis can be tested against the computationally much more expensive stochastic simulation algorithm.
The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.
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.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.