Graphical user interface

This tool to provide the possibility to perform the tree search on a single compound using a GUI through a Jupyter notebook. If you are unfamiliar with notebooks, you find some introduction here.

To bring up the notebook, use

jupyter notebook

and browse to an existing notebook or create a new one.

Add these lines to the first cell in the notebook.

from aizynthfinder.interfaces import AiZynthApp
app = AiZynthApp("/path/to/configfile.yaml")

where the AiZynthApp class needs to be instantiated with the path to a configuration file (see here).

To use the interface, follow these steps:

  1. Executed the code in the cell (press Ctrl+Enter) and a simple GUI will appear

  2. Enter the target SMILES and select stocks and policy model.

  3. Press the Run Search button to perform the tree search.

_images/gui_input.png

  1. Press the Show Reactions to see the top-ranked routes

_images/gui_results.png

You can also choose to select and sort the top-ranked routes based on another scoring function.

Creating the notebook

It is possible to create a notebook automatically with the aizynthapp tool

aizynthapp --config config_local.yml

which will also automatically opens up the created notebook.

Analysing the results

When the tree search has been finished. One can continue exploring the tree and extract output. This is done by using the finder property of the app object. The finder holds a reference to an AiZynthFinder object.

finder = app.finder
stats = finder.extract_statistics()

Clustering

There is a GUI extension to perform clustering of the routes. Enter the following a new cell

%matplotlib inline
from aizynthfinder.interfaces.gui import ClusteringGui
ClusteringGui.from_app(app)

A GUI like this will be shown, where you see the hierarchy of the routes and then can select how many clusters you want to create.

_images/gui_clustering.png