Primary paper figures

Code to produce the main figures of the paper.

• Figures in .AI, .PDF and .PNG format are accessible at results.
• Executable IPython Notebooks to produce most panels related to this figures can be found in notebooks.
• Panels are stored in the assets folder.

Installation

All dependencies related to these notebooks are pip-installable and you should be able to install them on-the-go as you encounter them. Some modules you may want to install are fragmentembedding, mini-automl, mini-xai and stylia:

git clone https://github.com/ligand-discovery/fragment-embedding
cd fragment-embedding
python -m pip install -e .

git clone https://github.com/ligand-discovery/mini-automl
cd mini-xai
python -m pip install -e .

git clone https://github.com/ligand-discovery/mini-xai
cd mini-xai
python -m pip install -e .

python -m pip install git+https://github.com/ersilia-os/stylia.git

Disclaimer

• This repository is likely to evolve as figures are revised over manuscript iterations. Therefore, it is possible that, before publication, panel names in assets do not correspond to panels in the final figures.
• Likewise, some panels produced in the executable notebooks may not be part of any final figure.
• Also, please note that some figure panels were not produced with executable notebooks (e.g. in-fluorescence gels, or networks laid out with Gephi).
• There are some custom paths associated to Supplemental Figures, since the data related to them is large and computations were conducted elsewhere.
• Similarly, for Figure 6 data is read from the results of the interactome-signatures repository.