NPMINE

NPMINE package performs semi-automated retrieval of chemical and phylogenetic information from natural products literature.

Installation

Install conda

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh

Create a dedicated conda environment and activate

conda env create -f environment.yml
conda activate nplibrary
pip install git+https://github.com/computational-chemical-biology/npmine.git

Installation with docker

 docker pull ridasilva/npmine:latest

Alternatively one can buil the docker image

docker build . -t npmine 

If a new library needs to be installed, don't forget to update the environment.yml file

conda env export | grep -v "^prefix: " > environment.yml 

Using npmine docker

Go to your npmine/notebooks directory, and execute the commands

docker run -it -p 8888:8888 -v "$PWD":/home/npmine ridasilva/npmine:latest
jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root

Installing packages individually

• Install docker and pull OSRA
• Install gnfinder
• Install oscarpdf2json command line tool

API usage

from npmine.retrieve_chemical_entities import retrieve_chemical_entities
help(retrieve_chemical_entities) 

Contributing

To contribute, fork the repository and make a "Pull Request" with your edits. For major changes, please open an issue first to discuss what you would like to change

License

This project is licensed under the BSD 3-Clause License - see the LICENSE file for details

Datasets

Access Zenodo to download the compounds and nomenclature extracted by NPMINE and the bioactivity data.

Acknowledgements

• OSRA (Optical Structure Recognition Application) - Igor Filippov - 2007, SAIC-Frederick, Frederick National Laboratory for Cancer Research, NIH, DHHS, Frederick, MD

• Image file of the latest OSRA build, based on open-babel and osra - Leonard Morayniss

• gnfinder (Global Names Finder) - gnames

• OSCAR4 (Open-Source Chemistry Analysis Routines) - David M. Jessop, Sam E. Adams, Egon L. Willighagen, Lezan Hawizy, Peter Murray-Rust

• oscarpdf2json - Mark Williamson