CML allows you to mark a bond as single (S), double (D), triple (T), but also as aromatic (A). The latter has the downside that one looses the localization of the double bonds, often used in 2D diagrams, e.g. in JChemPaint.
The CDK addresses this by storing the aromaticity as additional property on the bond:
Assistant professor at the Dept of Bioinformatics - BiGCaT at NUTRIM, Maastricht University, studying biology at an unsupervised but atomic level. Open science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and Wikipathways. ORCID:0000-0001-7542-0286. Posts on G+ are personal.