This is some work we are doing with colleagues at the University of Portsmouth to investigate adding nominal, ordinal and continuous data into fingerprints. This allows similarity measures not only based on structure but also on other properties or attributes. E.g. what reactions are there similar to my target but also occur about room temperature. You may be willing to have a weaker substructure match if you going to boost similarity on occuring at room temperature. Hopefully we will be able to present preliminary results.
Link to Presentation