BALL examples


This directory contains some short examples illustrating some of BALL's
capabilities.
Just type "make" to build the examples. When called without arguments,
each example prints out the required syntax. Please have a look at the
source code of each example.

Further examples can be found in the folder "BALL/source/APPLICATIONS/UTILITIES/". 

addHydrogens:
=============
	This example reads a PDB-file, normalizes the atoms names, builds bonds, 
	adds missing hydrogens and minimizes the all hydrogens employing a 
	conjugate gradient minimizer.

amberEnergy:
============
	This example reads a PDB-file and optionally an AMBER-option-file, normalizes
	the atoms names, builds bonds, computes and prints nicely all AMBER energy 
	contributions.

BALLVIEWClient:
==============

  This example illustrates the simple visualization using the BALLView 
  stand-alone viewer. It reads a PDB file and sends its contents to the
  BALLView-application running somewhere on the network. On this viewer,
  the molecule is then inserted and drawn in the current representation
  (please make sure, the VIEW server is activated - check the settings in
  Display/Preferences/Network).

bindingEnergy:
==============
	This example reads two PDB-files, normalizes the atoms names, adds missing
	bonds, and computes the binding energy according to the following equation:
			(ACE_AB - ACE_A - ACE_B) + (ES_AB - ES_A - ES_B)
	where ACE denotes the _A_tom _C_ontact _E_nergy of the molecules and 
	the complex (Zhang et al. "Determination of atomic desolvation energies from 
	the structures of crystallized proteins". J. Mol. Biol., 267:707-726, 1997) 
	as well as the electrostatic energy analogs.


energy:
=======
  This example shows an examplary energy function as used in Althaus 
  et al. "A branch and cut algorithm for the optimal solution of the 
  side-chain placement problem", 2000.
  
  It reads a PDB-file and calculates "the" bonded energy using a force
  field and "the" non-bonded energy (electrostatics only) by solving 
	the Poisson-Boltzmann equation.


PDB2Discover:
=============
	This example reads a PDB-file, adds hydrogen atoms where needed and
	converts the atom names to the Discover naming scheme, and finally 
	writes everything to the given outfile.


PDBChecker:
===========
	This example reads a PDB-file, converts the atom names from several naming
	conventions to the standard PDB names, reconstructs the bonds from templates 
	in the fragment database (since PDB files normally do not contain bond 
	information) and checks all residues for valid bond distances, charges and 
	missing or superfluous atoms in a residue.



proteinMapper:
==============
	This example reads two PDB-files and maps the backbone of the two proteins 
	(Calpha atoms) onto each other. The Calpha atoms are recognized by their 
	name (CA).

	Optional parameters are:
  	<upper> (double):
    	 upper bound for triangle side length use by the mapper
  	<lower> (double):
     	lower bound for triangle side length use by the mapper
  	<tolerance> (double):
     	maximum distance between two (mapped) Calpha atoms in Angstrom

	Defaults for the optional parameters are:
    upper     = 8
    lower     = 4
    tolerance = 0.6

ramachandran:
=============
 
  This example reads a PDB-file and calculates all backbone torsion angles.
  From the output of the program, a Ramachandran plot can be created that
  shows the torsion angle distribution.


