The Molecular Modelling Toolkit (MMTK)

The Molecular Modelling Toolkit (from now on referred to as MMTK) presents a new approach to molecular modelling. It is not a "modelling program" with a certain set of functions that can be used by writing more or less flexible "input files", but a collection of library modules written in an easy-to-learn high-level programming language, Python.

• Why MMTK? A few words of motivation.

MMTK is still in an early stage of development, and therefore some common functions in molecular modelling are not yet implemented. However, the existing functions are very well usable and include features that in the classical modelling packages are nonexisting or difficult to use. This manual describes version 1.1b1 of MMTK, where "b1" stands for "beta 1" and indicates the first public test release of version 1.1.

Using MMTK requires a basic knowledge of object-oriented programming and Python. Newcomers to this subject should have a look at the introductory material in this manual and at the Python tutorial (which also comes with the Python interpreter). There are also books on Python that are useful in getting started. Even without MMTK, Python is a very useful programming language for scientific use, allowing rapid development and testing and easy interfacing to code written in low-level languages such as Fortran or C.

• Introduction to object-oriented programming and Python

MMTK User's Guide

The user's guide explains how to perform standard tasks that do not require a knowledge of MMTK interna.

• MMTK Overview
• Defining molecules in the database
• Constructing a molecular system
• Minimization, molecular dynamics, and normal modes
• Analysis and manipulation
• Miscellaneous operations
• Examples

MMTK Developer's Guide

The developer's guide deals with topics that require a good knowledge of Python and perhaps some study of the MMTK source code. It is not yet complete - please be patient.

• Introduction and module overview
• Module descriptions
  • Chemical objects and the database
  • Collections and universes
• Recipes for common extensions
  • ...
• Glossary

Useful information

Pointers to information around the Web that could be of interest to MMTK users.

• The MMTK homepage (check from time to time for new versions etc.)
• The Python homepage
• The Python numerics extension that is used everywhere in MMTK
• The graphical user interface PTUI
• The netCDF format and library used by MMTK for trajectory files
• The AMBER force field used by MMTK
• The visualization programs VMD and XMol, for which MMTK contains special support
• The NSC routines that MMTK uses for the calculation of molecular surfaces and volumes.
• The DPMTA library used in MMTK for fast-multipole electrostatics.

The following books have been published on Python:

• Mark Lutz: Programming Python, O'Reilly 1996, ISBN: 1-56592-197-6
• Aaron Watters, Guido van Rossum, James Ahlstrom: Internet Programming with Python, MIS Press 1996, ISBN: 1-55851-484-8
• Martin von Löwis, Nils Fischbeck: Das Python-Buch, Addison-Wesley-Longman 1997, ISBN: 3-8273-1110-1 (in German)