Moved the Graph class to graphs.py file.
Moved implementation of DomainGraph class to graphs.py file.
Moved implementation of PeptideGraph class into graphs.py file.
Moved implementation of Vertex class into vertices.py file.
Moved implementation of DomainVertex class into vertices.py file.
Moved implementation of PeptideVertex class into vertices.py file.
Briefly renamed the Examples folder Examples2 to fix a case sensitivity issue.
Changed the name of Examples2 to examples.