I have found that certain MDL query features (link nodes in this case) are lost when converting to RDKit or Indigo molecules. I have attached a screenshot showing the SDF string output for (1) the MOL output from the sketched (Marvin Sketch) query; (2) the RDKit version; and (3) the Indigo version (had to add an Indigo->Query Mol node in this case to get the SDF String rendering).
As you can see, in the RDKit and Indigo molecules, the M LIN line is missing (but the atom list query feature - M ALS - is retained). Would it be possible to add support for the link node query feature, and also any other MDL query features that are missing - as I think these are what most chemists are familiar with when sketching query molecules?
(cross-posted on RDKit forum - http://tech.knime.org/forum/rdkit/handling-of-mdl-query-features-link-nodes)