msorok / lotusfiller

LOTUS filler for MongoDB

To fill all from scratch:

java -Xmx16288m -jar lotusfiller-0.0.1-SNAPSHOT.jar ~/Projects/NP/LOTUSonline/LOTUSfiller/data/platinum.part.tsv ~/Projects/NP/LOTUSonline/LOTUSfiller/fragments/fragment_without_sugar.txt ~/Projects/NP/LOTUSonline/LOTUSfiller/fragments/fragment_with_sugar.txt > latest.logs.feb9.txt &

on Ponder:

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( {lotus_id:1}) db.lotusUniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"}) db.lotusUniqueNaturalProduct.createIndex( {fragments:"hashed"})

db.runCommand( { createIndexes: 'lotusUniqueNaturalProduct', indexes: [ { key: { iupac_name:"text", traditional_name:"text", allTaxa:"text" }, name: "superTextIndex", weights: { name:10, synonyms: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 })

java -Xmx16288m -jar lotusfiller-0.0.1-SNAPSHOT.jar /media/data_drive_big/maria/Projects/NP/LOTUSonline/LOTUSfiller/data/platinum.tsv /media/data_drive_big/maria/Projects/NP/LOTUSonline/LOTUSfiller/fragments/fragment_without_sugar.txt /media/data_drive_big/maria/Projects/NP/LOTUSonline/LOTUSfiller/fragments/fragment_with_sugar.txt > latest.logs.feb19.txt &

java -Xmx16288m -jar lotusfiller-0.0.1-SNAPSHOT.jar cleanRecomputeMissing /media/data_drive_big/maria/Projects/NP/LOTUSonline/LOTUSfiller/fragments/fragment_without_sugar.txt /media/data_drive_big/maria/Projects/NP/LOTUSonline/LOTUSfiller/fragments/fragment_with_sugar.txt

indexes:

db.lOTUSSourceNaturalProduct.createIndex( {inchi3D:"hashed"}) db.lOTUSSourceNaturalProduct.createIndex( {inchikey3D: "hashed"}) db.lOTUSSourceNaturalProduct.createIndex( {inchikey2D:1}) db.lOTUSSourceNaturalProduct.createIndex( {smiles3D:"hashed"}) db.lOTUSSourceNaturalProduct.createIndex( {smiles2D:"hashed"})

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( {lotus_id:1}) db.lotusUniqueNaturalProduct.createIndex( {fragmentsWithSugar:"hashed"}) db.lotusUniqueNaturalProduct.createIndex( {fragments:"hashed"})

db.lotusUniqueNaturalProduct.createIndex( {traditional_name:"hashed"})

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 })

db.fragment.createIndex({signature:1})

db.fragment.aggregate([ { "$group": { "_id": { "signature": "$signature", "withsugar":"$withsugar" }, "dups": { "$push": "$_id" }, "count": { "$sum": 1 } }}, { "$match": { "count": { "$gt": 1 } }} ]).forEach(function(doc) { doc.dups.shift(); db.fragment.remove({ "_id": {"$in": doc.dups }}); }); db.fragment.createIndex({signature:1, withsugar:-1}, {unique:true, dropDups : true})

lotusfiller's Issues

[PMID]

Hi Maria,

On this page, we can see the DOI and PMID links. As far as I remember (I can be wrong...it is old now) we did not provide you any PubMed ID (now we have some). Are you generating them?
Sadly it seems that it leads to an incorrect article... might be out of nowhere but since I felt on it randomly I report it! :)

Best