Getting started

Right now the only things that are needed to run the pipeline are the script parse_and_run.py and the DNAProDB database as downloaded from http://dnaprodb.usc.edu. You can download the latest database with the following command:

wget http://dnaprodb.usc.edu/data/dnaprodb_1.0.7z

then unzip the database using whatever tools you prefer for doing so. It's easiest to just extract the file that DNAProDB recommends on their website:

7z e dnaprodb_1.0.7z Assuming that the downloaded file is in the current directory.

Dependencies

parse_and_run.py currently relies upon keras and tensorflow to work correctly, and has only been tested with Python version 3.6.5.

Run the model

After downloading the DNAProDB database and unzipping it, running the script is as simple as:

python /path/to/parse_and_run.py /path/to/collection.txt

Where collection.txt is the locally downloaded DNAProDB database. This script reshapes the input data and filters DNAProDB for cocrystal structures involving multiple chains and structures with no interacting chains with the DNA. While running, the script will periodically pipe progress messages to sys.stderr .