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| adducts | Adduct table |
| adduct_rules | Adduct rule table |
| build.ANPDB | Build ANPDB |
| 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 |
| 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.METABOLOMICSWORKBENCH | Build REACTOME db |
| build.METACYC | Build METACYC |
| build.mVOC | Build mVOC db |
| 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 |
| buildBaseDB | Build the base database |
| buildExtDB | Build external database using a given base database |
| 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 compounds in SDF format |
| 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 |