Orange3 Chemoinformatics is an add-on for the Orange3 data mining suite. It provides extensions for embedding molecule dataset annotated with SMILES through a pre-trained deep neural networks.

This is fork of the original Chemoinformatics widget with custom embedder. Embedder widget implements four different methods: substructure, circular, topological fingerpritns and and encoder of the autoencoder.

Orange3-Chemoinformatics requires RDKit, that is conda-installable running

conda install -c rdkit rdkit

and NumPy based deep learning package (https://github.com/PrimozGodec/ndf)

To install the add-on from source run

python setup.py install

To register this add-on with Orange but keep the code in the development directory (do not copy it to Python's site-packages directory) run

python setup.py develop

You can also run

pip install -e .

which is sometimes preferable as you can pip uninstall packages later.

After the installation the widgets from this add-on are registered with Orange. To run Orange from the terminal use

orange-canvas

or

python3 -m Orange.canvas

New widgets are in the toolbox bar under the Chemoinformatics section.

Example of an annotated database: https://s3-us-west-1.amazonaws.com/deepchem.io/datasets/molnet_publish/clintox.zip