docker_tutorial.md

Docker tutorial for MaSIF.

Installation

docker pull pablogainza/masif:latest
docker run -it pablogainza/masif

You now start a local container with MaSIF. The first step is to clone the masif_molecule repository:

root@b30c52bcb86f:/masif# git clone https://github.com/jomimc/masif_molecule.git

MaSIF pipeline

Running the pipeline on a protein from a PDB file

Go into the MaSIF-molecule source directory.

cd masif_molecule/source

Running the pipeline on the test data provided "data/2sic.pdb". To extract a single protein (chain) use the "-c" option. Specify output folder with "-o". Run "python main.py --help" to see all options. In this example we compute all possible features and patches with default parameters.

python main.py ../data/2sic.pdb -c E -o test_data --hphob --hbond --patches

If you want to run a prediction on multiple chains you can run without the "-c" option:

python main.py ../data/2sic.pdb -o test_data --hphob --hbond --patches

Running the pipeline on a nanoparticle from a PQR file

Go into the MaSIF-molecule source directory.

cd masif_molecule/source

Running the pipeline on the test data provided "data/np.pqr". To extract a single protein (chain) use the "-c" option. Specify output folder with "-o". Run "python main.py --help" to see all options. In this example we compute all possible features and patches with default parameters.

python main.py ../data/Np.pdb -o test_data --patches