File	Date	Author	Commit
README.txt	2013-05-07	Gerald Lushington	[b0ab2c] Initial commit
allih.log-results.mol2	2013-05-07	Gerald Lushington	[b0ab2c] Initial commit
allih.log-results_tab.log	2013-05-07	Gerald Lushington	[b0ab2c] Initial commit
arange.py	2013-05-07	Gerald Lushington	[b0ab2c] Initial commit
cfile.pm	2013-05-07	Gerald Lushington	[b0ab2c] Initial commit

Read Me

Git contents:

README.txt
		This file.

arange.py
		This is the python code.  It takes as input the output of
		Surflex docking simulations (see allih* files below),
		analyzes the location of ligand atoms across all poses and
		assigns favorability weights for the different chemical
		elements as a function of docking score.  It outputs 
		element-specific PyMol scripts (see c.pm for example) that
		can be visualized in PyMol.

allih.log-results.mol2
		Surflex docked conformer molecular structure file (can be
		directly loaded into PyMol).

allih.log-results_tab.log
		Surflex docking log, reporting the binding scores which are
		analogous to predicted binding free energies.

c.pm		PyMol graphical objects script that translates the spatial
		and scoring information from Surflex into a visual
		representation that can be interpreted and depicted by PyMol.
		One *.pm script is generated for each of the following atoms:
		Carbon (c.pm), Nitrogen (n.pm), Oxygen (o.pm), Fluorine
		(f.pm), Phosphorus (p.pm), Sulpher (s.pm), Chlorine (l.pm)
		and Bromine (b.pm).  In each, the favorable positions (on a
		1 Angstrom grid) in the vicinity of which to find a given atom
		type are colored green, while those grid points near 
		unfavorable areas are colored red.  The size of the sphere
		reflect the magnitude of the favorability or unfavorability
		(large is very favorable or unfavorable).