Defining a custom measure

The Measure base class

The abstract class Measure defines one abstract method that any derived class must implement:

However, this is not especially helpful as a guide for implementing the method itself. It might be more helpful to look at one of the basic classes provided with Tailor : the DistanceMeasure.

The DistanceMeasure class

This class simply measures the distance between two atoms. This is actually done in the measure method of the class, as seen below.

    public Measurement measure(Structure structure) 
   	                                  throws DescriptionException {
        Vector a = this.descriptionA.findStructureCenter(structure);
        Vector b = this.descriptionB.findStructureCenter(structure);
        
        double distance = Geometry.distance(a, b);
        return new Measurement(this.getName(), new Double(distance));
    }
    

The class holds a pair of Description references - descriptionA and descriptionB - that it uses to find points. These points (actually, Vector objects) are passed to a standard distance method. Finally, the result is wrapped in an instance of a Measurement.

Parameters for the measure method

The structure parameter passed to the measure method is a fragment found by the search for the motif. Any descriptions used by the measure must therefore be able to be found within such a fragment. If there is some problem finding it, the method can throw a DescriptionException.