
BALL Utilities
==============

This directory contains some little utilities which are handy for everyday
use in molecular modeling:

assign_bond_orders:
	Compute bond orders for ligand molecules based on atomic valence
	penalty scores.

add_hydrogens:

	Add missing hydrogens to PDB files and minimizes them while fixing all
	other atoms.

assign_charges_from_rules:

	Assign charges to a PDB file given a charge rule file.

assign_radii_from_rules:

	Assign radii to a PDB file given a radii rule file.

assign_typenames_from_rules:

	Assign typenames from rule files.

atomtyper:

	Create a GAFF typization for a given ligand molecule.

calculate_RMSD:

	Calculate the RMSD between two given PDB files.

compute_connected_components:
	
	Split a given ligand file into its connected components.

dcd2dcd:

	Converts CHARMm "enhanced" DCD trajectory files to simpler X-PLOR type
	DCD files. Use this program if some DCD reader does not know how to
	handle your (AMBER-generated) DCD file. It might help.

export_fragment:

	Reads a HyperChem or PDB file and creates a fragment database skeleton
	file with at least atom entries depending on the content of the input
	files.

fdb_load:

	Parse the content of a FragmentDB-xml file.

file_converter:
	
	Convert ligand file between different file formats.

hin2mol2: (obsolete, deprecated by file_converter)

pdb2amber_naming:

	Converts standard PDB files to PDB files which are conform to the AMBER
	naming scheme, i. e. usable for AMBER calculations. The resulting files
	will not necessarily be correct since there are some ambiguous cases
	which will not be resolved by this program. Instead a standard case will
	be assumed (like CYX for CYS residues which built a sulphur bridge).

pdb2dcd:

	Converts a bunch of PDB files to a dcd file containing the spatial
	information of these PDBs as trajectory information.
	
reconstruct_fragment:

  Reconstruct degraded residues from fragment database information. If you
	happen to have a PDB file which lacks some atoms, use this program to fix
	it.

rigid_docking:

	Run a rigid docking for two systems using the algorithm GeometricFit.
	There are two possible ways to store the docking results.

solvent_accessibility:
	
	Compute for a given PDB file which residues are solvent exposed by 
	summing up atom-based solvent-accessible surface areas. 
	Further print all residues along with their solvent-accessible
	surface area and mark all residues with an area below 10 A^2 as buried.

