Natural Products Online is an open source project for Natural Products (NPs) storage, search and analysis. This repository contains code for LOTUS, the naturaL prOducTs occUrrence databaSe, one of the biggest and best annotated resources for NPs occurrences available free of charge and without any restriction. LOTUS is a living database which is hosted in parallel at Wikidata and here. The Wikidata version allows for community curation and addition of novel data. The current version allows a more user friendly experience (such as structural search, taxonomy oriented query, flat table and structures exports).
docker exec -it npoc-mongo-db bash
mongo --port 27019
use NPOC2021
db.dropDatabase()
exit
cd mongodata/NPOC2021/NPOC2021/
mongorestore --port 27019 --db=NPOC2021 --noIndexRestore .
mongo --port 27019
use NPOC2021
db.lotusUniqueNaturalProduct.createIndex( {lotus_id:1})
db.lotusUniqueNaturalProduct.createIndex( {inchi:"hashed"})
db.lotusUniqueNaturalProduct.createIndex( {inchikey:1})
db.lotusUniqueNaturalProduct.createIndex( {smiles: "hashed"})
db.lotusUniqueNaturalProduct.createIndex( {inchi2D:"hashed"})
db.lotusUniqueNaturalProduct.createIndex( {inchikey2D:1})
db.lotusUniqueNaturalProduct.createIndex( {smiles2D: "hashed"})
db.lotusUniqueNaturalProduct.createIndex( {molecular_formula:1})
db.lotusUniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"})
db.lotusUniqueNaturalProduct.createIndex( {fragments:"hashed"})
db.lotusUniqueNaturalProduct.createIndex( {molecular_weight:1})
db.lotusUniqueNaturalProduct.createIndex( {fsp3:1})
db.lotusUniqueNaturalProduct.createIndex( {lipinskiRuleOf5Failures:1})
db.lotusUniqueNaturalProduct.createIndex( {heavy_atom_number:1})
db.runCommand(
{
createIndexes: 'lotusUniqueNaturalProduct',
indexes: [
{
key: {
iupac_name:"text", traditional_name:"text", allTaxa:"text", allChemClassifications:"text", allWikidataIds:"text"
},
name: "superTextIndex",
weights: { traditional_name:10, allTaxa:5 }
}
]
}
)
db.lotusUniqueNaturalProduct.createIndex( {npl_score:1})
db.lotusUniqueNaturalProduct.createIndex( { pubchemBits : "hashed" } )
db.lotusUniqueNaturalProduct.createIndex( {deep_smiles: "hashed"})
db.lotusUniqueNaturalProduct.createIndex( { "pfCounts.bits" :1} )
db.lotusUniqueNaturalProduct.createIndex( { "pfCounts.count" : 1 })
docker-compose up -d --no-deps --build lotus-online