The Molecular Modelling Toolkit
This is release 2.4 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 COPYRIGHT 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.
NOTE: This is likely to be the last MMTK release compatible with Python 1.5. I don't use Python 1.5 any more on any machine, which means that I am no longer able to verify compatibility. Moreover, I do use Python 2.x features in new code I write.
Installation
Prerequisites: Python 1.5 or higher, ScientificPython 2.2 or higher. With Python 1.5.x, the Distutils package must be installed (starting from Python 1.6, it is part of the Python distribution).
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.
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.
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 fink project, which is located at
Fink 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.
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:
- 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).
2) 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.
3) 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.
Mac OS X compilation hint:
(You can disregard this if you use the fink version.)
Under at least some releases, the file /usr/include/pthread.h must be modified to make MMTK compile (probably this affects all Python extension modules that use threads). Search for the following two lines (around 239)
int pthread_key_create __P((pthread_key_t key,
void (destructor)(void *)));
and modify the second one to read
void (*)(void *)));
(i.e. remove the word "destructor"). This should have no adverse effects on anything.
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) and PDF (Doc/PDF) formats. 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/
or at
http://starship.python.net/crew/hinsen/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 GNU Lesser Public License. See the file LICENSE for the text of this license. The DPMTA library (everything in the directory Src/dpmta-2.7) is not part of MMTK and therefore not subject to 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.
The DPMTA library used for electrostatic multipole calculations (everything in the directory Src/dpmta-2.7) was written by William T. Rankin at Duke University. Check the file dpmta-2.7/README and the Web page http://www.ee.duke.edu/Research/SciComp/Docs/Dpmta/dpmta.html for more information about this library. Note that MMTK does not contain the whole DPMTA distribution; the documentation, Fortran interface, and test code were left out to reduce the size of the MMTK distribution. You can obtain the full DPMTA distribution at the Web address given above.
Patches to make MMTK work under Windows were provided by Jon Michelsen.
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