functions to process pdb files with multiple models and output pdb files with one model have been added in pdbfile and pdbpreprocessor classes. Initial implementation (still has issues) of topology file export from central data structure.
Amino acid chain extraction has been changed
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into refactoring

Conflicts:
	includes/Resolver/PdbPreprocessor/pdbpreprocessor.hpp
	src/Resolver/PdbPreprocessor/pdbpreprocessor.cc
Charge calculation of each residue in a model and the whole model
Gap extraction in pdb preprocessor has been changed and additional functions have been added to PdbFile to handle gap and amino acid chain extraction
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into refactoring

Conflicts:
	includes/Resolver/PdbPreprocessor/pdbpreprocessor.hpp