This software calculates the total normalized energy of a protein
structure based on effective statistical potentials.
For further information see [1].

* Usage:
---------
The software received the following input data:

	./effective <potential> <omega> <file> <chain> 

* Input data:
-------------

<potential>     : file containing a potential energy function.
		  The format is organized in four columns,
	 	  from left to rigth: 
			. atom type 1
			. atom type 2
			. distance class
			. pseudoenergy

		  and it looks like this:	


		   1    5    1     3.6321 
		   1    5    2     3.6321 
		   1    5    3     3.6321 
		...   
		...
		   1    5   15     0.5460 
		   1    5   16    -0.7935 
		   1    5   17    -0.9982 
		   1    5   18    -0.6269 
		   1    5   19    -0.0449 
		...
		...
		   1    5   34     0.7769 
		   1    5   35     0.8159 


		  For further examples, see the directory POTENTIALS/.
 		  The file names are coded as follows:
	
			"pot_<omega>_<distance-range>.de"

		  The distance-rage is set to 7.0 Angstroms.
	

<omega>         : Shielding angle. It specifies the angle at which
  		  effective atomic interactions are defined. In principle
                  it can be any value between 0 and 180 degrees. See [1].

<file>          : Structure file in pdb format.

<chain>         : Chain identifier. If not '_'.

		  

* Output:
--------
  The program prints the following data to the stdout:

  "total-energy"	"total-contacts"	"normalized-energy"


* Examples:
----------

>./effective POTENTIALS/pot_090_07.0.de 90 STRUCTURES/1AKZ.pdb A
>-251.32880000	2706.000000	-0.092878


>./effective POTENTIALS/pot_180_07.0.de 180 STRUCTURES/135l_3.pdb X
>-36.36630000	15818.000000	-0.002299



* Reference:
------------
[1] Ferrada, E. and Melo, F. "Effective knowledge-based potentials" (2009).