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First Polymer class implementation

Changing particularities of Polymer class vs Molecule class

Method Align first implementation
Cleared problems with references

Test now works but align fnuction was not tested yet.
Fixing updates functions and making tests
There was a typo mistake of _old_orientation and old_orientation that was causing not holding new orientations.
Start to put everything in Unit Tests and Asserts
Implemented a test for the method Rotate
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