Viewmol is a program for building and editing molecules as well as for the visualization of outputs from quantum chemical and molecular mechanics programs. Currently supported are Gaussian 9x, Gamess, Discover, DMol/DSolid/DMol3, Gulp, Mopac, Turbomole, and PDB files. Properties visualized include geometry (with various drawing modes), vibration (animated or with arrows), optimization history/MD trajectories, MO energy level diagram, MOs, basis functions, and electron density. Drawings can be saved as TIFF, HPGL, Postscript, and input files for Rayshade. Viewmol has an embedded Python interpreter for automation. The program is language independent and currently "speaks" English, French, German, Russian, or Spanish.
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.
Esra is a scriptable, scalable, and highly hackable molecular mechanics library for Java. Its primary purpose is the statistical analysis of trajectory data generated with packages such as GROMOS, GROMACS, or AMBER, but it can also be used as a standalone package for performing simple molecular dynamics and Monte-Carlo simulations. It can be scripted with Jython, Mathematica, or Matlab.
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.