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.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d37b6813f3721c52ccd0afc8e5b91eea
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/index.rst.txt

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+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:
+
+.. code-block:: bash
+
+    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
+
+.. code-block:: bash
+
+    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.
+
+
+
+
+.. toctree::
+    :hidden:
+
+    python
+    route_distances

_sources/modules.rst.txt

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+route_distances
+===============
+
+.. toctree::
+   :maxdepth: 4
+
+   route_distances

_sources/python.rst.txt

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+Python interface
+================
+
+This page gives a quick overview of how to use the Python classes and methods to compute
+distances between routes.
+
+Input format
+------------
+
+The routes or reaction tree are input as dictionaries that can be loaded from e.g. a JSON file.
+The structure of the dictionary follows the output format used by AiZynthFinder, but only a small
+number of fields are necessary. The structure is checked by the code, and if the validation fails,
+an exception will be raised.
+
+The structure definition and validation code can be found in the `route_distance.validation` module.
+
+The input structure should be a the type `MoleculeNode` which is a dictionary with the following
+fields
+
+    * smiles - the SMILES string of the molecule represented by the node
+    * type - should be the string "mol"
+    * children - an *optional* list, containing at most one dictionary of type `ReactionNode`
+
+The `ReactionNode` type is a dictionary with the following fields
+
+    * type - should be the string "reaction"
+    * children - a list of dictionaries of type `MoleculeNode`
+
+It is easy to realize that this is a recursive definition. All extra fields in the dictionaries are ignored.
+And example dictionary is shown below
+
+.. code-block:: python
+
+    {
+        "smiles": "CCCCOc1ccc(CC(=O)N(C)O)cc1",
+        "type": "mol",
+        "children": [
+            {
+                "type": "reaction",
+                "children": [
+                    {
+                        "smiles": "CCCCOc1ccc(CC(=O)Cl)cc1",
+                        "type": "mol"
+                    },
+                    {
+                        "smiles": "CNO",
+                        "type": "mol"
+                    }
+                ]
+            }
+        ]
+    }
+
+
+Calculating TED
+---------------
+
+To compute the distance between two routes, we will first load them from a JSON file
+
+.. code-block:: python
+
+    import json
+    with open("my_routes.json", "r") as fileobj:
+        routes = json.load(fileobj)
+
+Then we will create two wrapper objects that will take care of the calculations
+
+.. code-block:: python
+
+    from route_distances.ted.reactiontree import ReactionTreeWrapper
+    wrapper1 = ReactionTreeWrapper(routes[0], content="both")
+    wrapper2 = ReactionTreeWrapper(routes[1], content="both")
+
+The argument `content` can be `molecules`, `reactions` or `both` and specify what nodes are included
+in the calculation.
+
+To calculate the distance between these two routes, we simple do
+
+.. code-block:: python
+
+    wrapper1.distance_to(wrapper2)
+
+If we have many routes, a distance matrix can be calculate using
+
+.. code-block:: python
+
+    from route_distances.ted.distances import distance_matrix
+    distance_matrix(routes, content="both")
+
+
+The docstrings of all modules, classes and methods can be consulted :doc:`here <route_distances>`

_sources/route_distances.lstm.rst.txt

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+route\_distances.lstm package
+=============================
+
+Submodules
+----------
+
+route\_distances.lstm.data module
+---------------------------------
+
+.. automodule:: route_distances.lstm.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.lstm.defaults module
+-------------------------------------
+
+.. automodule:: route_distances.lstm.defaults
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.lstm.features module
+-------------------------------------
+
+.. automodule:: route_distances.lstm.features
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.lstm.inference module
+--------------------------------------
+
+.. automodule:: route_distances.lstm.inference
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.lstm.models module
+-----------------------------------
+
+.. automodule:: route_distances.lstm.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.lstm.optim module
+----------------------------------
+
+.. automodule:: route_distances.lstm.optim
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.lstm.utils module
+----------------------------------
+
+.. automodule:: route_distances.lstm.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: route_distances.lstm
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/route_distances.rst.txt

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+route\_distances package
+========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   route_distances.lstm
+   route_distances.ted
+   route_distances.tools
+
+Submodules
+----------
+
+route\_distances.clustering module
+----------------------------------
+
+.. automodule:: route_distances.clustering
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.route\_distances module
+----------------------------------------
+
+.. automodule:: route_distances.route_distances
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.validation module
+----------------------------------
+
+.. automodule:: route_distances.validation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: route_distances
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/route_distances.ted.rst.txt

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+route\_distances.ted package
+============================
+
+Submodules
+----------
+
+route\_distances.ted.distances module
+-------------------------------------
+
+.. automodule:: route_distances.ted.distances
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.ted.reactiontree module
+----------------------------------------
+
+.. automodule:: route_distances.ted.reactiontree
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.ted.utils module
+---------------------------------
+
+.. automodule:: route_distances.ted.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: route_distances.ted
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/route_distances.tools.rst.txt

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+route\_distances.tools package
+==============================
+
+Submodules
+----------
+
+route\_distances.tools.cluster\_aizynth\_output module
+------------------------------------------------------
+
+.. automodule:: route_distances.tools.cluster_aizynth_output
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.tools.prepare\_aizynthfinder\_output module
+------------------------------------------------------------
+
+.. automodule:: route_distances.tools.prepare_aizynthfinder_output
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+route\_distances.tools.train\_lstm\_model module
+------------------------------------------------
+
+.. automodule:: route_distances.tools.train_lstm_model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: route_distances.tools
+   :members:
+   :undoc-members:
+   :show-inheritance: