searching for substructure + electron-flow arrows

We want to write an algorithm that will determine whether a particular MDocument contains a reference substructure with particular electron-flow arrows. The reference substructure could include "ANY" atoms as well as the usual elements.





One way we could do it is to find all cases of the substructure in the MDocument, then examine each one for the presence of the electron-flow arrows.





We are worried that this method would be computationally time-consuming and expensive if there are a lot of substructure matches.





We thought about replacing the source and sink atoms of the substructure with particular pseudoatoms, but that would preclude the using "ANY" atoms in bond-making or -breaking.





Searching is your bread and butter. Do you have any insights?

My two pence:

• ANY atoms will match pseudo atoms also, so this probably will not be a problem.
  
  
  
• In the future, we will introduce a custom MolComparator interface which will allow you to add your own comparisons of atoms, bonds and hits into the search process. This way you will be able to handle electron-flow objects more efficiently.