Initial test of changing to numpy
Fix test job template
Add to multi_job test to check the job files
Remove duplicate tests
Add test for writing single job
Add actual comparison of job text for multi_job
Change triple bond spacer to use single bonds instead of Ar
Fix 3D rotations

The 3D rotations are mostly done in 4 steps

1. Calculate the "bond" vectors
2. Calculate the difference in their azimuth and altitude
3. Generate a rotation matrix based on those values
	(do an xy axis rotation to remove the Z then a Z rotation)
4. Apply rotation matrix to all atoms in the fragment

Before, steps 2 and 3 were mixed together and the wrong base rotation
matrix was used (assumed all rotations were on the x,y,z axes). This
is fixed by instead having an xy rotation and a z rotation.
Remove timers from tests
Merge branch 'rotationfix'

Conflicts:
	chemtools/molecule.py