DeepDDIΒΆ

DeepDDI running procedure This project is to develop a framework that systematically predicts drug-drug interactions (DDIs) and drug-food interactions (DFIs).

Features - DeepDDI predicts DDIs and DFIs using names of drug-drug or drug-food constituent pairs and their structural information as inputs - DeepDDI predicts 86 DDI types as outputs of human-readable sentences

Note: This source code was developed in Linux, and has been tested in Ubuntu 14.04

  1. Create and activate virtual environment

$ virtualenv venv
$ source venv/bin/activate

  1. Install packages at the root of the repository

$ pip install pip --upgrade
$ pip install -r requirements.txt

  1. Install [rdkit](http://www.rdkit.org/)

In our case, we installed rdkit in the root of a server using apt-get (i.e., apt-get install rdkit), and created its symbolic link in venv:

$ ln -s /usr/lib/python2.7/dist-packages/rdkit/ ./venv/lib/python2.7/site-packages/

Input files for the DeepDDI

Following working input files can be found in: ./data/. These files were used for the data presented in the manuscript.

Example

$ python run_DeepDDI.py -i ./examples/input_structures.txt -o ./output_dir/