2014-11-11 development

config.py:
 -added a further-alignment-style option
connect.py:
 -fixed realignment so will align in correct direction now, i.e. not
creating overlaps
 -refactored to allow for additional further alignment methods
genmethods.py
 -new method to determine connectivity of a given atom in a molecule
molecule.py:
 -new addCharge method to add given amount of charge to an atom, and
keep track of how much has been added.