pyMLP: Molecular Lipophilicity Potential evaluator

pyMLP is a program computing the molecular lipophilicity
potential map of proteins.

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Please include this reference in published work using pyMLP:

Broto P., Moreau G., Vandycke C. - 
`Molecular structures: Perception, autocorrelation descriptor and sar studies.
 System of atomic contributions for the calculation of the n-octanol/water 
 partition coefficients', Eu. J. Med. Chem. 1984, 19.1, 71-78

Laguerre M., Saux M., Dubost J.P., Carpy A. -
`MLPP: A program for the calculation of molecular lipophilicity potential in
 proteins', Pharm. Sci. 1997, 3.5-6, 217-222
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This program was developed in python as a platform independent equivalent of 
MLPP (see references). As a result pyMLP may run on any platform supported by
Python and Numpy.


INSTALLATION

In order to launch pyMLP you will need:
* a working python installation (http://www.python.org) (tested with version
  2.4, 2.5, 2.6 and 2.7)
  (any desktop oriented Linux distribution should have already one installed)
* a working numpy installation (http://numpy.scipy.org/)
  (any scientific friendly Linux distribution should have it in its repository)

(pyMLP was reported to work on win32 with Enthought's Python Sumo-Distribution
for Windows (http://www.enthought.com/))

With a properly configured python + numpy install, you just have to input this
command to the CLI (command line interface):
python pyMLP.py

----------Optional----------
In order to have pyMLP.py available from any directory you can copy it in your
PATH (after enabling direct execution):
chmod +x pyMLP.py
cp pyMLP.py /usr/local/bin/

Then you can directly launch pyMLP that way:
pyMLP.py
----------------------------


USAGE

pyMLP takes a .pdb file as input and output a .dx map file easily visualized in
many molecular visualization packages such as VMD, Pymol, Chimera, ...

Please run "pyMLP.py --help" for detailed instructions.

Simple examples:

* Command to calculate foo.dx the lipophilicity potential map of foo.pdb:
  (assuming pyMLP.py is in your PATH and foo.pdb in the current directory)
pyMLP.py -i foo.pdb
  this command will create foo.dx in the current directory

* Command that will achieve exactly the same thing as the one above but be
  more verbose about what is being done:
pyMLP.py -v -i foo.pdb


FOOTNOTE

Feel free to criticize pyMLP code: it needs some serious refactoring and way
more comments ... alas it works for me ... sorry
(from the quick-n-dirty-dev-dpt)

last modified March 28, 2007 by Julien Lefeuvre

