Overview

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The Molecular Modelling Toolkit

This is release 2.7 of MMTK, the Molecular Modelling Toolkit. For more information about MMTK, look at the manual (in the directories Doc/HTML and Doc/PDF) and at the examples in the directory Examples.

Please remember that MMTK, like Python, comes with neither a price tag nor any warranty (see the file LICENSE for details). I use it for my own work, and I consider it reasonably stable, but your mileage may vary. If you find any problems with MMTK, please let me know, but understand that I cannot promise extensive support (I am a scientist, not a programmer, and much less a software distributor!). I also gratefully accept additional example applications and other code donations.

Installation

Prerequisites: Python 2.5 or higher, ScientificPython 2.6 or higher,
NumPy between 1.6 and 1.8.

MMTK is NOT compatible with NumPy 1.9 or later, because it relies on a submodule of NumPy that was removed in version 1.9.

Note: MMTK is developed and tested using Python 2.7 and NumPy 1.8. However, it should work with Python 2.6 as well.

On most Unix systems, installation requires two commands:

python setup.py build python setup.py install

The second command often requires root priviledges, as MMTK will be installed in the Python library tree. There are many options for building and installing, type

python setup.py build --help

or

python setup.py install --help

for details.

If you want MMTK's MPI support enabled, you must first install ScientificPython with MPI support and then use mpipython instead of python for running the compilation/installation procedure via setup.py. Note that a version of MMTK compiled with MPI support works only with the mpipython executable, not with an ordinary python interpreter. However, there is no overhead for using mpipython on a single processor.

Numeric vs NumPy

There are three nearly compatible implementations of numeric arrays for Python: the original one, Numerical Python (module name "Numeric"), a later rewrite called numarray, and an evolution of Numeric that integrates features from numarray, called NumPy. In the long run, only NumPy will be maintained and further developed.

MMTK was originally written for Numeric, but has supported NumPy as well for quite a while. When MMTK is installed, it checks whether ScientificPython was compiled for Numeric or for NumPy, and uses the same package. MMTK development is done with NumPy, and Numeric support will be removed in a future version. Unless you have a good reason to use Numeric, please use NumPy!

MMTK does not support numarray at all. Since numarray development has stopped, this is not likely to change in the future.

Platform-specific notes

This section is based on information I got from MMTK users in the past. There is a risk that it is not up to date. Any platform-specific information is welcome!

Windows:

MMTK can be compiled under Windows using the free MinGW compiler (available from www.mingw.org). You will need to have MinGW setup properly to compile python extensions, see http://www.python.org/doc/2.2.1/inst/non-ms-compilers.html for details. The option "--compiler=mingw32" must be added when running setup.py.

MMTK can be compiled using Microsoft Visual Studio 6.0 as well. For more information, check the Wiki pages at:

http://dirac.cnrs-orleans.fr/mmtk_wiki

For using visualization under Windows, you need Mark Hammond's Win32 extensions, available at http://starship.python.net/crew/mhammond/win32/Downloads.html

Mac OS X:

The most convenient way to use MMTK with MacOS X is through the MacPorts project, which is located at

http://www.macports.org/

MacPorts provides an install-and-build system for Unix software on the Mac. You will find many other goodies there, including Python and many Python packages.

Of course, MacOS X being a variant of Unix, it is also possible and quite straightforward to install MMTK and all the prerequisites from source code. Just make sure to have Xcode (Apple's developer kit) installed.

Using VMD for visualization under MacOS X

The VMD release for MacOS presents itself as a standard Mac application. Internally, it has the standard Unix command line interface that MMTK expects, but using the two together requires some particular steps:

  1. Create a script called "vmd" in a directory on your shell's search path (e.g. /usr/bin) containing the following two lines:

#!/bin/bash xterm -e '/Applications/VMD 1.8.2.app/Contents/Resources/VMD.app/Contents/MacOS/VMD' $*

Don't forget to make this file executable (chmod 755 vmd).
  1. Set the environment variable PDBVIEWER to "vmd". The most general method to do this is by editing the file ~/.MacOS/environment.plist. The most convenient tool to edit (or create) this file is the Property List Editor (in Applications/Utilities), but if you feel comfortable editing XML files, any text editor will do. Note that changes to this file become active only after the next login.
  2. When using VMD from MMTK, make sure to have X11 running (because the script uses xterm). One way not to forget this is to put X11 (in /Applications/Utilities) into your startup item list with the "hide" option selected.

External programs

MMTK uses external programs for visualization and animation. The names of these programs must be supplied via environment variables. If no names are provided, the visualization functions will do nothing. The environment variables are

  • PDBVIEWER to specify a program that can show the contents of a file in the PDB format. The program will be called with the name of a PDB file as a command line argument.
  • VRMLVIEWER to specify a program that can show a file in the VRML format. The program will be called with the name of a PDB file as a command line argument.

Animation is implemented only for the programs VMD and XMol. It is sufficient to specify one of these programs as PDBVIEWER in order to have access to animation functions.

Documentation

The MMTK manual is included in HTML (Doc/HTML) format. The source code for the Spinx documentation tool is also included. A list of changes along MMTK development versions can be found in Doc/CHANGELOG.

Useful tools

The directory Tools/TrajectoryViewer contains a small program for viewing trajectories. It allows that quick inspection of energies, thermodynamic quantities, etc., as well as animation via an external viewer.

Web site

The MMTK home page can be found at

http://dirac.cnrs-orleans.fr/MMTK/

Mailing list

To be informed about updates to MMTK, and to communicate with other MMTK users, you should subscribe to the MMTK mailing list via the Web page

http://starship.python.net/mailman/listinfo/mmtk

This is a low-traffic list; there is little reason not to subscribe.

License

MMTK is licensed under the CeCILL-C license. See the file LICENSE for the text of this license.

Acknowledgements

The DCD reader was contributed by Lutz Ehrlich, and uses a C library for reading DCD files (files Src/ReadDCD.c and Src/ReadDCD.h) which was written by Mark Nelson at the University of Illinois.

The MolecularSurface module was contributed by Peter McCluskey.

Patches to make MMTK work under Windows were provided by Jon Michelsen.

Peter Cook contributed Windows code, examples, code improvements, and good suggestions.

Chris Ing translated the documentation to Sphinx, wrote test cases, and made lots of good suggestions.

Routines for matrix diagonalization were taken from LAPACK, and for the erfc function from the CEPHES library.

Konrad Hinsen Centre de Biophysique Moleculaire (CNRS) Rue Charles Sadron 45071 Orleans Cedex 2 France

E-Mail: hinsen@cnrs-orleans.fr