NP-likeness scorer - Web application

Author: Maria Sorokina, maria.sorokina@uni-jena.de

Last modified: 06.03.2020

NP-likeness scorer is a web application to compute natural-product-likeness for a given set of molecules. The computation of NP-likeness is based on

Sorokina, M., Steinbeck, C. NaPLeS: a natural products likeness scorer—web application and database. J Cheminform 11, 55 (2019). https://doi.org/10.1186/s13321-019-0378-z
Vanii Jayaseelan, K., Moreno, P., Truszkowski, A. et al. Natural product-likeness score revisited: an open-source, open-data implementation. BMC Bioinformatics 13, 106 (2012). https://doi.org/10.1186/1471-2105-13-106

This README describes the steps on how to setup and run a local instance of the NP-likeness scorer web application.

Project tree

NPlsWeb
├── archive
├── docker-compose.yml
├── Dockerfile
├── molimg
├── mvnw
├── mvnw.cmd
├── mysql
├── NPlsWeb.iml
├── pom.xml
├── README
├── src
├── target
├── upload-dir
└── volume

Prior of running

verify that the file NPlikenessDB.sql is in the "mysql" folder (can be downloaded here: https://zenodo.org/record/2652356)
compile the project with Maven by running: "mvnv clean package" from the project root
verify that there are ".ser" files in the "archive" folder
in the docker-compose.yml remplace "VIRTUAL_HOST: nplsscorer.cheminf.uni-jena.de" by "VIRTUAL_HOST: yourwebsite.de" or remove this part to run the web application locally (don't forget to cite us!)
in the docker-compose.yml remove "LETSENCRYPT_HOST" and "LETSENCRYPT_EMAIL" unless you want to have your NPLSweb instance to be certified by Let's Encrypt.
in the docker-compose.yml remplace the MYSQL_ROOT_PASSWORD if necessary

nginx

The project is build to run with nginx as server and reverse-proxy on a Docker "nginx-network". For more details see for example here: https://medium.com/@francoisromain/host-multiple-websites-with-https-inside-docker-containers-on-a-single-server-18467484ab95

Project execution`

sudo docker-compose build
sudo docker-compose up -d
sudo docker exec -it mysql_npls bash
mysql -uroot -proot1234 NPLikenessDB < /mysqldata/NPLikenessDB.sql
exit

After this, the web application will run either on the URL you specified in the docker-compose.yml either on localhost:8090

Source code

The unarchived source code for this project is available at https://github.com/mSorok/NPlsWeb and can be recompiled as a maven project. Here can be

modified the MySQL instance the web application connects on (in the application.properties file)
modified the maximum number of molecules per submitted file via the web interface (currently max 200 molecules - to modify in the SDF and SMILES readers)
if the plots need to be recomputed (due to changes in the database): in the NPlsWebController.java change private boolean newPlot = false to true (when the plots recomputed, don't forgive to change the newPlot back to false!).