From a7c52aa530b61aa64c40ebc98c3744bb7faa97a5 Mon Sep 17 00:00:00 2001 From: "Genheden, Samuel" Date: Tue, 13 Apr 2021 14:17:04 +0200 Subject: [PATCH] Update doc of clustering tool. --- README.md | 4 ++-- docs/index.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index be8e173..8c9150d 100644 --- 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 index 41d2277..e34dcff 100644 --- 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