Adun Documentation

This is version 0.83 of the Adun Documentation.

Adun is a platform for developing tools related to molecular simulation and also a molecular simulation program. See our home-page at http://adun.imim.es.

Note: This documentation is an eternal "work-in-progress". Although the code coverage is high i.e. most classes/functions etc. are documented in some way, the documentation may be sparse/out-of-date/difficult to understand in places. If you encounter any of these situations please contact us at adun-.nosp@m.dev@.nosp@m.gna.o.nosp@m.rg or file a support request at https://gna.org/support/?group=adun

This documentation describes the main frameworks and libraries available. These are:

• AdunBase Library
  • Pure C library
  • Includes functions for evaluating standard molecular mechanics potential energy terms and their derivatives
• AdunKernel Framework
  • Contains classes and functions for creating molecular simulation applications
  • NB: A number of important additional classes are described in the AdunCore Program section
• FFML Library
  • Contains classes for parsing, modifying and quering FFML (force-field) files.
• ULFramework
  • Contains classes that provide non-graphical functionality for Adun's GUI.
  • Includes database, process management and system creation.

Adun also supplies the third-party MolTalk framework for parsing, querying and creating PDB files, which is not described here.

All the classes and functions provided these frameworks/libraries can be used by Adun plugins and controllers. In addition, Adun scripts can utilize all the frameworks (AdunKernel, FFML, MolTalk, ULFramework) but not AdunBase.

Note:

The classes that compose Adun's GUI are described in Interface.