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.
For most Unix systems, you must download and compile the source code. The same source code archive can also be used to build the Windows and Mac versions, and is the starting point for ports to all other platforms. Download the latest Python 3 and Python 2 source.
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 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: For using visualization under Windows, you need Mark Hammond's Win32 extensions, available at Mac OS X: - The most convenient way to use MMTK with MacOS X is through the MacPorts project, which is located at 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.
Mmtk Python Download For Mac Mac
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 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 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. Copy lines. Copy permalink. Go.
VMD-L Mailing List From: Justin Gullingsrud Date: Sun Apr 16 2006 - 21:32:48 CDT. Next message:.
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Reply:. Messages sorted by: John, I didn't have to do anything unconventional to install Numeric on my (10.4) system. Just unpack the Numeric source package and run 'python setup.py build; sudo python setup.py install' as usual.
This should install Numeric into /System/Library/Frameworks/Python.framework. Cheers, Justin On 4/15/06, John Stone wrote: HiWell, it appears that the problem with loading module.so files on MacOS X with the older revs of Python is not specific to VMD. I've tried a number of things to make the builds work with the older Python library, but they didn't pan out. The recommended solution appears to be to use the framework builds of Python on OSX, as these get around the.so loading problems that can occur with the plain unixy Python builds. I could compile the Mac versions of VMD against the Apple-provided Python frameworks, the main issue with that is that they don't provide the Numeric module in the system Python, even in 10.4.6.
There are various pages that describe how to add Numeric into the system Python, though I'm a bit leery of basing VMD builds off of a hacked version of the Apple frameworks: What I may end up doing is disabling Python in the default MacOS X buildand then do a second build that has it turned on, linked against the same Python framework that MMTK or one of the other popular packages are using. I'd be interested to hear from Mac Python users as to which Python framework you want to see VMD binaries linked against, or if you'd prefer to just build from source for yourselves? John Stone On Wed, Apr 12, 2006 at 09:25:37PM -0500, John Stone wrote: Hi guysThe tar error is innocuous in that it's complaining about restoring some file state on the the python interpreter binary (which isn't used by VMD anyway) and you can run the unpacked binary, so I'm not sure if it's some Apple specific modification to tar, but it doesn't seem to matter.
I also get the same errors you guys are getting with an updated 10.3 machine, but the same Python libs worked fine on this same box previously. (the same machine they were compiled on) I'm wondering if some change that Apple made since 10.3 came out broke these shared libs. Digging deeper, the problem occurs with all of the Python modules which are built with.so files in that library.
'import time', 'import math', 'import dbm'.) I'll have to get back to you on this after I do more testing. John On Wed, Apr 12, 2006 at 05:02:22PM -0700, Justin Gullingsrud wrote: Same thing happens to me - tar errors on unpack, and errors when I try to import the math module. I verified that I'm indeed loading the correct math shared library from the pylibs package. Here is the output: vmd gopython Info) Starting Python. Numeric Python module numpy not found; vmdnumpy module not available.
ImportError: Failure linking new module Info) Text interpreter now Python Traceback (most recent call last): File ', line 1, in? File '/Applications/VMD 1.8.3.app/Contents/vmd/scripts/python/Tkinter.py', line 59, in? import tkinter # If this fails your Python may not be configured for Tk ImportError: No module named tkinter import math Traceback (most recent call last): File 'VMD', line 1, in? File 'VMD', line 1, in? ImportError: Failure linking new module import string string '/Users/justin/Desktop/libMACOSX-numpy/lib/python2.2/string.pyc' The failure to load the numpy module is probably related to the failure to load the math library. Justin On 4/11/06, Grischa Meyer wrote: HiI am using VMD 1.8.3 and 1.8.4b11 on Mac OS X 10.4.6.
I wrote a little python script that needs to do a sqrt, so needs the math library. How can I fix VMD to make it import it? I tried various things, including downloading the pylib package from the vmd site (which, btw, reports errors when untarring), but none was successful. CheersGrischa - Grischa Meyer, BSc (Hons) PhD student, Prof Boris Martinac Group School of Biomedical Sciences University of Queensland Brisbane, Australia phone: +61 7 3346 1224 fax: +61 7 3365 1766 (attn. To me) - Studying texts and stiff meditation can make you lose your Original Mind.
A solitary tune by a fisherman, though, can be an invaluable treasure. Dusk rain on the river, the moon peeking in and out of the clouds; Elegant beyond words, he chants his songs night after night. - Ikkyu, 'The Fisherman' - NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N.
Mathews Ave, Urbana, IL 61801 Email: Phone: 217-244-3349 WWW: Fax: 217-244-6078 - NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: Phone: 217-244-3349 WWW: Fax: 217-244-6078 - Studying texts and stiff meditation can make you lose your Original Mind. A solitary tune by a fisherman, though, can be an invaluable treasure. Dusk rain on the river, the moon peeking in and out of the clouds; Elegant beyond words, he chants his songs night after night. Ikkyu, 'The Fisherman'. Next message:. Previous message:.
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