kavrakilab/dinc-bin
Docker for Mac or Windows: https://www.docker.com/products/docker-desktop
Docker for Linux: https://docs.docker.com/install
$ docker pull kavrakilab/dinc-bin
Before running this command, you might want to create a folder in which you want all the results to be saved. And you can share that (host) folder with the container.
$ mkdir ~/test-dinc
$ cd ~/test-dinc
$ docker run --rm -v $(pwd):/home/data -it kavrakilab/dinc-bin
This step will share the content of your current folder (host machine), with the folder /home/data inside the container. Your terminal will change to indicate you are now inside the running container. Your terminal should look something like this:
(dinc) root@49c85e870b36:/home#
The dinc binary is located at /dinc. In /dinc/example you will also find the defaults.yml file with the standard dinc parameters. You must have a copy of this file inside the folder you are running DINC (do not rename this file). You also need the ligand (mol2 or pdb) and receptor files (pdb or pdbqt). You can change the parameters to better suit your needs, and your system. For instance, you should increase num_threads to match the number of threads in your system. Or select the best distribution of threads for num_threads and num_cpu. For instance, if you have 32 threads, you could use num_threads: 16 and num_cpu: 2.
There are also example files in the /dinc/example folder. Since the folder we shared with the host machine is /home/data/, lets copy some demo files there.
# cd data/
# cp /dinc/example/1ohr_* .
# cp /dinc/example/defaults.yml .
# dinc -l 1ohr_ligand.mol2 -r 1ohr_receptor.pdb -p defaults.yml
Alternatively, the dinc_job.py script runs DINC on every sub-directory containing a ligand (in mol2 format) and a receptor (in pdb format), according to the default.yml parameter file. A summary of jobs executed will be written to job-out.log at the end of the job. Example files to run a test virtual screening are also provided.
# cd data/
# unzip /dinc/example/screening-data.zip
# nohup /dinc/dinc_job.py -o job-out.log > nohup.out &
docker pull kavrakilab/dinc-bin