Base methods size penalty calculation

Created base methods and test class. Implemented size penalty
calculation.
Added macrocycle calculation

Using the number of rings with atom count greater than 9 as number of
macrocycles in a molecule
Added sterocomplexity logic

We need a newer version of the library to be able to use it
Migrated from cdk 1.4.19 to cdk 1.5.4

fucking nightmare
RingComplexity score

RingNumber and number of spiro atoms calculated for the score
Merge branch 'ComplexityScore' of https://github.com/garcianavalon/cheminformaticstermproject into ComplexityScore
Added weighted method for complexity score
Merge branch 'ComplexityScore'

Conflicts:
	src/code/InputHandler.java