Friday, September 18, 2009

Bond order information and aromaticity

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:
<bond atomRefs='a1 a2' order='D'>
  <bondType dictRef="cdk:aromaticBond"/>