Molmodel™ API Reference Documentation

What is this page?

You are looking at the main page for the reference documentation of the Molmodel API. This documentation was generated by Doxygen directly from the Molmodel source code as annotated by the original programmers so it is both accurate and comprehensive. As you will quickly realize if you look around, this is a large system providing a great deal of functionality. It is, however, very easy to use if you know where to begin -- and this reference documentation is most definitely not the place to start if you want to learn how to use Molmodel. Instead, start with the tutorials that are available at the Molmodel project site https://simtk.org/home/molmodel, "Documents" tab. If you have specific questions, use the Molmodel help forum under the "Advanced" tab. You can also file bug reports and make feature requests using the tools provided there.

What is Molmodel?

Molmodel is a high-performance, industrial-grade open source C++ library providing sophisticated modeling of biomolecular systems as a set of articulated rigid bodies with motion modeled in internal coordinates. It makes use of the Simbody internal-coordinate multibody dynamics package (https://simtk.org/home/simbody) to produce coarse-grained mechanical models of molecules, and the OpenMM GPU-accelerated force field package (https://simtk.org/home/openmm) to efficiently calculate the forces that act on the bodies. Molmodel also contains its own very-flexible molecular force field framework, and provides access to Simbody's arbitrary force and constraint capabilities, resulting in an extremely broad set of capabilities for application developers.

Molmodel has a powerful but easy-to-learn API that is intended to be used in building special purpose biomolecular applications. It is used in the RNABuilder application (https://simtk.org/home/rnatoolbox) to enable combined knowledge- and physics-based structural modeling of RNA molecules.

Molmodel's use of Simbody allows it to employ a minimal coordinate recursive formulation of the equations of motion, providing computation of system dynamics with O(N) computational complexity for N interconnected bodies (not N atoms).

Molmodel is part of the SimTK biosimulation toolkit originating from Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. Molmodel is hosted on the simtk.org biosimulation community site, at https://simtk.org/home/molmodel and is a community resource available for unrestricted academic, commercial, government, and personal use.

Molmodel was conceived by Christopher Bruns and Michael Sherman (Sherm). It was implemented primarily by Christopher, with substantial contributions from Sherm and Peter Eastman, all of the Simbios Center at Stanford. Many others have contributed to the software, support, training, and documentation and we invite well-engineered community contributions.

How to use this documentation

If you know the name of the class, method, or other symbol for which you want information, you can enter it into the search box above and click directly to the documentation for that symbol. You can also enter words or partial symbols and get a list of names that include your search key. Unfortunately Doxygen does not currently provide a full-text search capability. Another approach is to select the Classes tab to get an alphabetical listing of all the class names, and there is a tab below that providing a class hierarchy view.

If you would like to see some more logical groupings of Molmodel classes with some limited overview material, select the Modules tab to see groupings that made sense to the authors. You can also look at the Related Pages to see other general topics.

Molmodel's API documentation also contains references to Simbody's and the lower-level SimTK classes. These will not be listed in the main class list but you can find them in the class hierarchy and can click on them when they appear in the Molmodel API. Generally Molmodel classes, modules, and pages will be shown with bold links while the lower-level ones are quieter.

License

We encourage the broadest possible use of Molmodel for any purpose by using the extremely permissive MIT License. We would appreciate some acknowledgement if our work has been helpful in yours, but our license does not require that. For more information see our license page.