Small Cleanup

A small comment and code cleanup of mainly rotations.py, but also
genmethods.py
2014-11-10 home cleanup

connect.py:
 -changed rotations to using function call on molecule

molecule.py:
 -new method to rotate (part of) a molecule using a given rotation
matrix

rotations.py:
-renamed functions + arguments to be more general usage
-switched longAxis to return a normalised vector
Merge branch 'develop' into cleanupAndModularisation

Conflicts:
	.gitignore
2014-11-12 cleanup

connect.py:
 -completely broken out the rotations so is a molecule call now
genmethods.py:
 - slight clean up and improved logically of stuff
rotations.py:
 - all cleaned up
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
2014-11-14

Lots of new parameters
201-11-16 new fragments

New unsaturated fatty acid chain fragments
few new parameters
Merge branch 'cleanupAndModularisation' into develop
stuff