Reaction-MQL: line notation for functional transformation.

Representation of chemical reactions is pivotal for different purposes in cheminformatics. We present an extension of the molecular query language (MQL), which combines readable style with meaningful rules for string representation of reactions and unambiguous product formation. The concept of functional groups is used to describe the transformations. Functional groups are defined in terms of substructure queries and are processed by graph transformations. Molecular educt graphs are transformed by application of beginning-, end-, and reaction-matrices to obtain the product graph without consideration of stereochemistry. Both directions of a transformation are possible. We implemented the concept of Reaction-MQL in Java employing the Chemistry Development Kit.