NaturalProductsOnline is the web application for the COCONUT database of openly available natural products structures.
Prior to any further action, a target folder needs to be generated, with the following command:
mvn package
To fire up a local version of it, you need to have Docker installed.
In the directory containing the 'docker-compose.yml' file run the following commands:
docker-compose build
docker-compose up -d
docker exec -it coconut-mongo-db bash
mongo --port 27018
use COCONUT2020-07
db.dropDatabase()
exit
cd mongodata/COCONUT2020-07/COCONUT2020-07/
mongorestore --port 27018 --db=COCONUT2020-07 --noIndexRestore .
mongo --port 27018
use COCONUT2020-07
db.sourceNaturalProduct.createIndex( {source:1})
db.sourceNaturalProduct.createIndex( {simpleInchi:"hashed"})
db.sourceNaturalProduct.createIndex( {simpleInchiKey:1})
db.sourceNaturalProduct.createIndex( {originalInchiKey:1})
db.sourceNaturalProduct.createIndex( {originalSmiles:"hashed"})
db.sourceNaturalProduct.createIndex( {absoluteSmiles:"hashed"})
db.sourceNaturalProduct.createIndex( {idInSource:1})
db.uniqueNaturalProduct.createIndex( {inchi:"hashed"})
db.uniqueNaturalProduct.createIndex( {inchikey:1})
db.uniqueNaturalProduct.createIndex( {clean_smiles: "hashed"})
db.uniqueNaturalProduct.createIndex( {molecular_formula:1})
db.runCommand(
{
createIndexes: 'uniqueNaturalProduct',
indexes: [
{
key: {
synonyms:"text", name:"text", chemicalClass:"text", chemicalSubClass:"text", chemicalSuperClass:"text", directParentClassification:"text"
},
name: "superTextIndex",
weights: { name:10, synonyms:5 }
}
]
}
)
db.uniqueNaturalProduct.createIndex( {annotationLevel:1})
db.uniqueNaturalProduct.createIndex( {npl_score:1})
db.uniqueNaturalProduct.createIndex( {coconut_id:1})
db.uniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"})
db.uniqueNaturalProduct.createIndex( {fragments:"hashed"})
db.uniqueNaturalProduct.createIndex( { pubchemBits : "hashed" } )
db.uniqueNaturalProduct.createIndex( {unique_smiles: "hashed"})
db.uniqueNaturalProduct.createIndex( {deep_smiles: "hashed"})
db.uniqueNaturalProduct.createIndex( { "pfCounts.bits" :1} )
db.uniqueNaturalProduct.createIndex( { "pfCounts.count" : 1 })
db.uniqueNaturalProduct.createIndex( {chemicalSuperClass: "hashed"})
db.uniqueNaturalProduct.createIndex( {chemicalClass: "hashed"})
db.uniqueNaturalProduct.createIndex( {chemicalSubClass: "hashed"})
db.uniqueNaturalProduct.createIndex( {directParentClassification: "hashed"})
db.fragment.createIndex({signature:1})
db.fragment.createIndex({signature:1, withsugar:-1})
exit
exit
In case you want to rebuild the "natural-products-online" container only (because changes have been made to the front- or back-end) run the following:
docker-compose up -d --no-deps --build natural-products-online