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https://github.com/khinsen/mmtk

The Molecular Modelling Toolkit
https://github.com/khinsen/mmtk

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The Molecular Modelling Toolkit

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README 

        
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

============



Note: the following are step-by-step instructions for installing

from source code. The only package manager that offers an

up-to-date version of MMTK is [Guix](https://guix.gnu.org/)

for Gnu/Linux. With Guix, installing MMTK is a matter of typing

```

guix install python2-mmtk

```

Otherwise, for Unix-like systems you may prefer to use the

[mmtk_install](https://github.com/roygroup/mmtk_install)

script for some automation, but be aware that it installs the

[path_integral branch](https://github.com/khinsen/MMTK/tree/path_integrals)

rather than the [master branch](https://github.com/khinsen/MMTK/tree/master),

which may not be what you want/need. You can change this in line 111

of the script.



Manual installation from source code

-------------------------------------



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).



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.



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: [email protected]