Quick start guide

Once you have succesfully installed the package, you can start using it.

Downloading the dataset

For this tutorial we will work with the GLASS dataset

To download it, we will use the following code:

python workflow/scripts/get_datasets.py glass --min_num_aa 250

Since this is a dataset of GPCRs, we do not accept protein structures with less than 250 aminoacids.

This will create a new folder in datasets/glass/resources, which will contain all the necessary information.

Running the Snakemake pipeline

Once our dataset is downloaded, we can run the snakemake pipline with the following command:

snakemake -j 10 --use-conda --configfile config/snakemake/glass.yaml

This will create the final pickle file for the GLASS dataset, which will be located in datasets/glass/resources/prepare_all folder.

Note

Some parts of the config rely on more than just the base file downloaded in the previous step.

Running the training

We can run the training script with the following code:

python train.py config/dti/glass.yaml

This will start the training process, which will take a while.

You can monitor the progress of the training by running the following command:

tensorboard --logdir=tb_logs