Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into remote

Conflicts:
	includes/MolecularModeling/assembly.hpp
	src/MolecularModeling/assembly.cc
Merge branch 'refactoring' of /clients1/alireza/Projects/repos/../Gmml/Dev/gmml-refactoring into remote

Conflicts:
	includes/MolecularModeling/assembly.hpp
middle_of_chain attribute has been added to unrecognizedresidue, additional topology file export functions have been implemented, some should be modified
Pdb parser modification for the sake of pdb preprocessing
Merge branch 'remote' of /clients1/delaram/Projects/gems/gmml into refactoring

Conflicts:
	src/MolecularModeling/assembly.cc
Merge branch 'refactoring'