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BKchem BKchem is a chemical drawing program written in Python. It is platform independent.

Biskit Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.

Chemtool Chemtool is a GTK+-based 2D chemical structure editor for X11. It draws organic molecules easily and store them as a X bitmap file. You can export drawings in XFig format for further annotation, or as Postscript files (using xfig's companion program transfig). The distribution includes a set of sample molecular structure drawings. The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file.

E-CELL Simulation Environment E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

EMAN EMAN is a scientific image processing suite designed mainly to perform single-particle reconstructions of individual molecules. In this method, a transmission electron microscope is used to collect images of thousands of individual molecules. A complex series of algorithms then turns the individual 2D images into a high-resolution 3D structure of the molecule. The core of EMAN is a C++ based scientific image processing library.

Fityk Fityk is nonlinear curve-fitting and data analysis software. It supports 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 common bell-shaped functions (Gaussian, Lorentzian, Pearson 7, Voigt, Pseudo-Voigt) and polynomials, but more sophisticated formulae can be added if needed. It also enables background substracting, data calibration and task automation with a simple script language. It is being developed to analyze powder diffraction patterns, but can be used to fit analytical functions to any kind of data.

GAMGI 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.

GDIS "GDIS' is a GTK/OpenGL based program for displaying isolated molecules, periodic systems, and crystalline habits. It also acts as a GUI to packages such as GAMESS, GULP, and POVRay to provide energy minimizations and publication quality rendering.

GElemental gElemental is a periodic table viewer that provides detailed information on the chemical elements. It is a port of GPeriodic to C++ and gtkmm, and it offers an improved UI, an updated and corrected data set, a better data format, a list view, and easier coloration.

GPeriodic GPeriodic is a periodic table application for GNU/Linux. It allows you to browse through a periodic table of the elements, and view detailed information on each of the elements. 118 elements are currently listed.

GROMACS GROMACS simulates molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids that have many complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) it is also used for research on non-biological systems, e.g. polymers. GROMACS is user-friendly, with topologies, parameter files, and error messages written in clear text format. There is a lot of consistency checking, but no scripting language: all programs use a simple interface with command line options for input and output files.

Gabedit 'Gabedit' is a graphical interface to the Molpro and Gaussian computational chemistry packages, running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported, and graphics can be exported in many formats.

Gdpc 'gdpc' is a tool for visualising the output files of a molecular dynamic simulation. It can be customized to read almost any input file format, animate it, and output images of each frame.

GenChemLab 'GenChemLab' is an OpenGL-based application intended to simulate several common general chemistry laboratory exercises. It is meant to be used to help students prepare for actual lab experience. Supported experiments include titration, calorimetry, freezing point depression, vapor pressure, electrochemistry, and spectrophotometry.

Ghemical Ghemical is a molecular modelling software package with a GUI (one for the GLUT library, and another for GNOME), and some nice 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included.

Jmol Jmol is a molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. It can read a variety of file types and print and export images. It can animate the results of simulations.

Kci The kc program is a "kinetic compiler". This means it is able to transform chemical equations into simulation programs.

Lamprop 'lamprop' calculates some properties of fiber-reinforced composite laminates. It calculates engineering properties like Ex, Ey, Gxy, thermal properties CTE_x and CTE_y, physical properties like density and laminate thickness, and stiffness and compliance matrices.

MayaChemTools MayaChemTools is a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs. The current release of MayaChemtools provides command line scripts for the following tasks:

• Manipulation of SD, CSV/TSV, Sequence/Alignments, and PDB files
• Analysis of data in SD, CSV/TSV, and Sequence/Alignments files
• Information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
• Exporting data from Oracle and MySQL tables into text files
• Properties of periodic table elements, amino acids, and nucleic acids
• Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
• Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
• Calculation of similarity matrices using a variety of similarity and distance coefficients
• Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors and acceptors, logP (SLogP), molar refractivity (SMR), topological polar surface area (TPSA), and so on

Melting Melting computes, for a nucleic acid duplex, the enthalpy and entropy of the helix-coil transition, and then its melting temperatures. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program uses the method of nearest-neighbors. The set of thermodymanic parameters can easily be changed, for instance following an experimental breakthrough. The program is coded in ISO C and can be compiled on any operating system. Some Perl scripts are provided to show how melting can be used as a block to construct more ambitious programs.