Download Marvin JS from ChemAxon site https://chemaxon.com/products/marvin-js/download
Click Download Packaged Archive
extract it as mjs and put into project directory
tested with marvinjs-22.1.0-all
docker build -f Dockerfile_with_jupyter . -t repathdb:jupyter
docker run -d -p 5432:5432 -p 5000:5000 -p 7474:7474 -p 7687:7687 -p 9999:9999 repathdb:jupyter
port 5432 for postgres connections
port 5000 for RePathDB visualisation
port 7474 for web interface of neo4j
port 7687 for bolt connection of neo4j
port 9999 for jupyter connection
Install last version of neo4j 3 and postgres 10
Create virtual environment, activate it and install dash_network and mol3d_dash wheels
Then run pip install -e . in the folder of the project
python -m RePathDB cmd
#initialization of CGRDB
cgrdb init -c '{"user":"your postgres user name","password":"your password","host":"host ip"}'
#creation of table in the CGRDB cgrdb create -n "reactions" -f config.json -c '{"user":"your postgres user name","password":"your password","host":"host ip"}'
neomodel_install_labels RePathDB RePathDB.graph --db bolt://login:pass@host:port
#populate DB from log files (please be sure that you added your own parser to process your files)
python -m RePathDB -f "your folder" -s "files extension" -pg POSTGRES_CONNECTION_INFO ("//user:port@host:port/table") \
-nj BOLT_CONNECTION_INFO"(bolt://login:pass@host:port") populate
#start WEB User Interface (wui) python -m RePathDB -pg POSTGRES_CONNECTION_INFO("//user:pass@host:port/table") -nj BOLT_CONNECTION_INFO("bolt://login:pass@host:port") wui -ls WEB_HOST
