CTS.externalIdSubset    Select a subset of external IDs from a CTS
                        record.
CTS.externalIdTypes     Find all available databases for a CTS record
RmbDefaultSettings      RMassBank settings
RmbSettings             RMassBank settings
add.formula             Calculations on molecular formulas
addMB                   MassBank-record Addition
addPeaks                Add additional peaks to spectra
addPeaksManually        Addition of manual peaklists
addProperty             Add and initialize dataframe column
aggregateSpectra        Aggregate analyzed spectra
analyzeMsMs             Analyze MSMS spectra
annotator.default       Generate peak annotation from peaklist
archiveResults          Backup 'msmsWorkflow' results
checkIsotopes           Checks for isotopes in a 'msmsWorkspace'
checkSpectra            Check if a spectra set is found, complete,
                        empty
cleanElnoise            Remove electronic noise
combineMultiplicities   Combine workspaces for multiplicity filtering
compileRecord           Compile MassBank records
createMolfile           Create MOL file for a chemical structure
dbe                     Calculate Double Bond Equivalents
deprofile               De-profile a high-resolution MS scan in profile
                        mode.
exportMassbank          Export internally stored MassBank data to files
filterLowaccResults     Filter peaks with low accuracy
filterMultiplicity      filterMultiplicity
filterPeakSatellites    Filter satellite peaks
filterPeaksMultiplicity
                        Multiplicity filtering: Removes peaks which
                        occur only once in a n-spectra set.
findEIC                 Extract EICs
findMass                Calculate exact mass
findMsMsHR              Extract MS/MS spectra for specified precursor
findMsMsHR.direct       Discontinued: find MS/MS spectrum from open raw
                        file
findMsMsHR.ticms2       Extract an MS/MS spectrum from MS2 TIC
findMsMsHRperxcms       Read in mz-files using XCMS
findMz                  Find compound information
findMz.formula          Find the exact mass +/- a given margin for a
                        given formula or its ions and adducts.
findProgress            Determine processed steps
flatten                 Flatten, or re-read, MassBank header blocks
formulastring.to.list   Interconvert molecular formula representations
gatherCompound          Compose data block of MassBank record
gatherData              Retrieve annotation data
gatherDataBabel         Retrieve annotation data
gatherDataUnknown       Retrieve annotation data
gatherPubChem           Retrieve supplemental annotation data from
                        Pubchem
getCSID                 Retrieve the Chemspider ID for a given compound
getCactus               Retrieve information from Cactus
getCtsKey               Convert a single ID to another using CTS.
getCtsRecord            Retrieve information from CTS
getData                 Get data frame with all present peak data
getMolecule             Create Rcdk molecule from SMILES
getPcId                 Search Pubchem CID
is.valid.formula        Check validity of formula
loadInfolists           Load MassBank compound information lists
loadList                Load compound list for RMassBank
makeMollist             Write list.tsv file
makePeaksCache          Generate peaks cache
makeRecalibration       Recalibrate MS/MS spectra
mbWorkflow              MassBank record creation workflow
mbWorkspace-class       Workspace for 'mbWorkflow' data
msmsRead                Extracts and processes spectra from a specified
                        file list, according to loaded options and
                        given parameters.
msmsRead.RAW            Extracts and processes spectra from a list of
                        xcms-Objects
msmsWorkflow            RMassBank mass spectrometry pipeline
msmsWorkspace-class     Workspace for 'msmsWorkflow' data
newMbWorkspace          Create new workspace for 'mbWorkflow'
newMsmsWorkspace        Create new empty workspace or load saved data
                        for 'msmsWorkflow'
order.formula           Order a chemical formula correctly
parseMassBank           MassBank-record Parser
peaksMatched            Select matching/unmatching peaks from aggregate
                        table
peaksUnmatched          Select matching/unmatching peaks from aggregate
                        table
plotMbWorkspaces        Plots mbWorkspaces
plotRecalibration       Plot the recalibration graph.
ppm                     Calculate ppm values
problematicPeaks        Identify intense peaks (in a list of unmatched
                        peaks)
processProblematicPeaks
                        Generate list of problematic peaks
progressBarHook         Standard progress bar hook.
reanalyzeFailpeaks      Reanalyze unmatched peaks
recalibrate             Predefined recalibration functions.
recalibrate.addMS1data
                        Return MS1 peaks to be used for recalibration
selectPeaks             Select peaks from aggregate table
selectSpectra           Select a subset of spectra matching properties
setData                 Set 'RmbSpectrum2' data from data.frame
smiles2mass             Calculate the mass from a SMILES-String
spectraCount            Count MS2 spectra per compound
to.limits.rcdk          Convert formula to Rcdk limits
toMassbank              Write MassBank record into character array
toRMB                   Conversion of XCMS-pseudospectra into
                        RMassBank-spectra
updateSettings          Update settings to current version
validate                Validate MassBank records with a set of Unit
                        tests
