Free chemistry software

Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from [[Java (programming language)|[J]ava]] (the programming language) + [mol]ecules, and also the mol file format.

Molecular builder/editor for Windows, Linux, and Mac OS X

program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry

JChemPaint is computer software, a molecule editor and file viewer for chemical structures using 2D computer graphics. It is free and open-source software, released under a GNU Lesser General Public License (LGPL). It is written in Java and so can run on the operating systems Windows, macOS, Linux, and Unix. There is a standalone application (editor), and two varieties of applet (editor and viewer) that can be integrated into web pages.

The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).

Ghemical is a computational chemistry software package written in C++ and released under the GNU General Public License. The program has graphical user interface based on GTK+2 and supports quantum mechanical and molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools. Ghemical relies on external code to provide the quantum-mechanical calculations — MOPAC provides the semi-empirical MNDO, MINDO, AM1, and PM3 methods, and MPQC methods based on Hartree–Fock calculations.

CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical (AM1, PM3, MNDO, MNDOd, PM6) and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hyb

Java library for chem- and bioinformatics

Chemfig is a LaTeX package used for creating graphical representations of chemical structures, molecules, reaction schemes, and structural formulas. It provides a simple and flexible syntax to define atoms, bonds, angles, rings. It allows for the construction of both organic and inorganic molecules using LaTeX markup.