adduct_rules | Adduct rule table |
adducts | Adduct table |
buildBaseDB | Build the base database |
build.BLOODEXPOSOME | Build BLOOD EXPOSOME DB |
build.BMDB | Build BMDB |
build.CHEBI | Build CHEBI |
build.DIMEDB | Build DIMEDB |
build.DRUGBANK | Build DRUGBANK |
build.ECMDB | Build ECMDB |
build.EXPOSOMEEXPLORER | Build EXPOSOME EXPLORER |
buildExtDB | Build external database using a given base database |
build.FOODB | Build FOODB |
build.HMDB | Build HMDB |
build.KEGG | Build KEGG |
build.LIPIDMAPS | Build LIPID MAPS |
build.LMDB | Build LMDB |
build.MACONDA | Build MACONDA |
build.MASSBANK | Build MASSBANK DB |
build.MCDB | Build MCDB |
build.METABOLIGHTS | Build METABOLIGHTS DB |
build.METACYC | Build METACYC |
build.mVOC | Build mVOC db |
build.NANPDB | Build ANPDB |
build.PAMDB | Build PAMDB |
build.PHARMGKB | Build PharmGKB |
build.PHENOLEXPLORER | Build PHENOL EXPLORER DB |
build.REACTOME | Build REACTOME db |
build.RESPECT | Build RESPECT |
build.RMDB | Build RMDB (deprecated) |
build.SMPDB | Build SMPDB |
build.STOFF | Build STOFF db |
build.T3DB | Build T3DB |
build.VMH | Build VMH |
build.WIKIDATA | Build Wikidata |
build.WIKIPATHWAYS | Build WikiPathways |
build.YMDB | Build YMDB |
checkAdductRule | Check for combined adduct rules |
chemspiderInfo | Find more info through ChemSpider. |
cleanDB | Uniformize database and remove invalid formulas/SMILES |
countAdductRuleMatches | Check which structures are OK according to given adduct rules |
doAdduct | Generate adduct for given structure |
doBT | Run Biotransformer on SMILES. |
doIsotopes | Generate isotopes for given formula |
downloadBT | Download biotransformer jar file. |
filterFormula | Apply seven golden rules to a vector of formulas |
getFormula | Find possible formulas for a given m/z |
getPredicted | Get predicted formulas and adducts from m/z value |
iatom.to.charge | Get formal charge from iatomcontainer |
iatom.to.formula | Get molecular formula from iatomcontainer |
iatom.to.smiles | Get SMILES from iatom container |
is.empty | Is this item 'empty'? |
isotopes | Weights of all isotopes of all elements used |
lmdb | LMDB |
openBaseDB | Create/open and prepare SQLite database |
pubChemInfo | Find additional info on a PubChem ID. |
removeDB | Remove database |
removeFailedStructures | Remove structures where isotope generation failed. |
revertAdduct | Break formula apart into adduct and main formula |
sdfStream.joanna | Adjusted sdfStream version for databases that store their... |
searchCMMR | Search CMMR |
searchFormula | Find matches based on molecular formula |
searchFormulaWeb | Find web hits for a molecular formula |
searchMZ | Find matches for m/z value in given database |
searchMZonline | Find m/z matches with CMMR, ChemSpider or PubChem |
searchRev | Reverse searching |
showAllBase | Show all compounds in base db |
smiles.to.iatom | Get iatom containers from SMILES |
writeDB | Write table to SQLite database |
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