route-distances documentation

route-distances contains routines and tools to compute distances between synthesis routes and to cluster them.

This is a project mostly targeting developers and researchers, not so much end-users.

There is one command line tool to process AiZynthFinder output:

cluster_aizynth_output --files finder_output1.hdf5 finder_output2.hdf5 --output finder_distances.hdf5

This will add a column to table in the merged hdf5 file called distance_matrix with the tree edit distances, and another column called distances_time with the timings of the calculations.

To cluster the routes as well add the --ncluster flag

cluster_aizynth_output --files finder_output1.hdf5 finder_output2.hdf5 --output finder_distances.hdf5 --nclusters 0

Giving 0 as the number of clusters will trigger automatic optimization of the number of clusters. Two columns will be added to the table: cluster_labels and cluster_time holding the cluster labels for each route and the timings of the calculation, respectively.