2014-11-13 cleanup

config.py:
 - new MAX_ALIGNMENT_COUNT config option so don’t get into infinite
rotation loops

connect.py:
 - added sanity checking for further rotations so don’t get too many
happening
 - added sanity checking for charge redistribution so only runs if
there is charge to redistribute

genmethods.py:
 - added ability for MTB parsing to create new bonds in the molecule.
No longer relies solely on the PDB file for CONECT records

molecule.py:
 - improved getNumX functions so that they only return counts of X with
all positive integers
 - improved PDB and MTB printing to only print atoms, bonds etc with
positive integers

rotations.py:
 - fixed normCrossProduct to not divide by 0