Molecule rigid translate added
Ligand translation and rotation is now working

Code might need further efficiency optimization before apply
The original coordinates are isolated

So that actions on the molecule will not carry onto next transform
This is a unfinished commit

Todo: consider how to store the coordisnates, make it stay alive when
doing twist and transform, but get refresh when next result comes in
Add the test cases for structure manipulation
Single torsion works, but seems multiple torsion fails
The torsions are now in work

The problem comes from shadow copying, fix by deepcopy
Add a simple testing script for coordinates calc
Merge branch 'mol'