test bow-vs-matt compares the structural neighbors detected by a search on BOW vectors verus the structural neighbors detected by the Matt structural aligner.
The test only produces the output of the comparison, but does not say how similar they are.
The comparison is that of ordering. Namely, given some protein chain A, find the closest structural neighbors returned by two different methods: structural alignment and BOW searching.
This is done by first creating a BOW database from the given list of PDB files. (This requires that 'create-pdb-db' is in your PATH.) Then, output a file for every protein chain that contains a ordering of all structural neighbors using both search techniques.