Add transform method to Nucleotide

[debeshmandal]

Nucleotide should be able to accept a 4x4 matrix to translate, transform it. The function should look something like this:

class Nucleotide:
...
def transform(matrix: np.ndarray):
        self.pos_com = np.matmul(matrix, self.pos_com)
        ...
    return

Another thing that can be done is creating an Abstract Class called Transformable that Polygon and Nucleotide classes can subclass, to ensure there is no copy and pasting of transformation methods