Update doc of clustering tool.

MolecularAI · Apr 13, 2021 · a7c52aa · a7c52aa
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diff --git a/README.md b/README.md
@@ -34,10 +34,10 @@ the `route_distances` package is now installed in editable mode.
 
 ## Usage
 
-The tool will install the `calc_aizynthfinder_distances` that is used
+The tool will install the `cluster_aizynth_output` that is used
 to calculate distances and clusters for AiZynthFinder output
 
-    calc_aizynthfinder_distances --files finder_output1.hdf5 finder_output2.hdf5 --output finder_distances.hdf5 --nclusters 0
+    cluster_aizynth_output --files finder_output1.hdf5 finder_output2.hdf5 --output finder_distances.hdf5 --nclusters 0
 
 This will perform TED calculations and add a column `distance_matrix` with the distances and column `cluster_labels` with the cluster labels for each route to the output file.
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -9,7 +9,7 @@ There is one command line tool to process AiZynthFinder output:
 
 .. code-block:: bash
 
-    calc_aizynthfinder_distances.py --files finder_output1.hdf5 finder_output2.hdf5 --output finder_distances.hdf5
+    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
@@ -19,7 +19,7 @@ To cluster the routes as well add the ``--ncluster`` flag
 
 .. code-block:: bash
 
-    calc_aizynthfinder_distances.py --files finder_output1.hdf5 finder_output2.hdf5 --output finder_distances.hdf5 --nclusters 0
+    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