## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install('biodbChebi') ## ---- results='hide'---------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- chebi <- mybiodb$getFactory()$createConn('chebi') ## ----------------------------------------------------------------------------- entries <- chebi$getEntry(c('2528', '17053', '15440')) ## ----------------------------------------------------------------------------- entries[[1]]$getFieldValue('smiles') ## ----------------------------------------------------------------------------- entries[[1]]$getFieldsAsDataframe() ## ----------------------------------------------------------------------------- mybiodb$entriesToDataframe(entries, fields=c('accession', 'formula', 'molecular.mass', 'inchikey', 'kegg.compound.id')) ## ----------------------------------------------------------------------------- chebi$searchCompound(name='aspartic', max.results=3) ## ----------------------------------------------------------------------------- chebi$searchCompound(mass=133, mass.field='molecular.mass', mass.tol=0.3, max.results=3) ## ----------------------------------------------------------------------------- ids <- chebi$searchCompound(name='aspartic', mass=133, mass.field='molecular.mass', mass.tol=0.3, max.results=3) ## ----------------------------------------------------------------------------- mybiodb$entriesToDataframe(chebi$getEntry(ids), fields=c('accession', 'molecular.mass', 'name')) ## ----------------------------------------------------------------------------- chebi$convCasToChebi(c('87605-72-9', '51-41-2')) ## ----------------------------------------------------------------------------- chebi$convCasToChebi('14215-68-0') ## ----------------------------------------------------------------------------- chebi$convInchiToChebi('InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/t8-/m0/s1') ## ----------------------------------------------------------------------------- chebi$convInchiToChebi('MBDOYVRWFFCFHM-SNAWJCMRSA-N') ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- sessionInfo()