Some function declarations for export file data structure from central data structure
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into refactoring
Topology structure builder has been modified to build a correct structure
Library file structure extraction from central data structure has been implemented
Coordinate file structure extraction from central data structure has been implemented
Some additional modification to other files in order for maintaining consistency
PDB file mutator, functions for exporting topology file structure
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into refactoring

Conflicts:
	includes/MolecularModeling/assembly.hpp
	src/MolecularModeling/assembly.cc
Error fix
Modification on assembly exporting functions
Pdbpreprocessor bug fix in extraction of library and prep file atom list of a residue