AP-class                Class "AP"
APset-class             Class "APset"
DUD                     Database Connections
ExtSDF-class            Class "ExtSDF"
FP-class                Class '"FP"'
FPset-class             Class '"FPset"'
SDF-class               Class "SDF"
SDF2apcmp               'SDF' to 'list' for AP generation
SDFDataTable            SDF Data Table
SDFset-class            Class "SDFset"
SDFset2SDF              'SDFset' to list with many 'SDF'
SDFset2list             'SDFset' to 'list'
SDFstr-class            Class "SDFstr"
SMI-class               Class '"SMI"'
SMIset-class            Class '"SMIset"'
addDescriptorType       Add Descriptor Type
addNewFeatures          Add New Features
ap                      Return atom pair component of 'AP/APset'
apfp                    Frequent Atom Pairs
apset                   Atom pairs stored in 'APset' object
apset2descdb            'APset' to list-style AP database
atomblock               Return atom block
atomcount               Molecular property functions
atomprop                Standard atomic weights
atomsubset              Subset SDF/SDFset Objects by Atom Index to
                        Obtain Substructure
batchByIndex            Batch by Index
bondblock               Return bond block
bonds                   Bonds, charges and missing hydrogens
browseJob               Open ChemMine Tools Job in Web Browser
bufferLines             Buffer File Input
bufferResultSet         Buffer Query Results
byCluster               By Cluster
canonicalNumbering      Canonical Numbering
canonicalize            Canonicalize
cid                     Return compound IDs
cluster.sizestat        generate statistics on sizes of clusters
cluster.visualize       visualize clustering result using
                        multi-dimensional scaling
cmp.cluster             cluster compounds using a descriptor database
cmp.duplicated          quickly detect compound duplication in a
                        descriptor database
cmp.parse               Parse an SDF file and compute descriptors for
                        all compounds
cmp.parse1              Parsing an SDF file and calculate the
                        descriptor for one compound
cmp.search              Search a descriptor database for compounds
                        similar to query compound
cmp.similarity          Compute similarity between two compounds using
                        their descriptors
conMA                   Bond Matrices
datablock               Return data block
datablock2ma            SDF data blocks to matrix
db.explain              Explain an atom-pair descriptor or an array of
                        atom-pair descriptors
db.subset               Subset a descriptor database and return a
                        sub-database for the selected compounds
dbTransaction           DB Transaction
desc2fp                 Fingerprints from descriptor vectors
draw_sdf                draw_sdf
exactMassOB             Exact Mass (Monoisotopic Mass)
findCompounds           Find Compounds in Database
findCompoundsByName     Find compound by name
fingerprintOB           Fingerprints from OpenBabel
fold                    Fold
foldCount               foldCount
fp2bit                  Convert base 64 fingerprints to binary
fpSim                   Fingerprint Search
fptype                  fptype
fromNNMatrix            From Nearest Neighbor Matrix
genAPDescriptors        Generate AP Descriptors
genParameters           Generate Parameters
generate3DCoords        Generate 3D Coords
getAllCompoundIds       Get ALl Compound Ids
getAtomAttr             getAtomAttr
getBondAttr             getBondAttr
getCompoundFeatures     Get Compound Features
getCompoundNames        Get Compound Names
getCompounds            Get Compounds From Database
getIds                  Import Compounds from PubChem
grepSDFset              String search in 'SDFset'
groups                  Enumeration of Functional Groups and Atom
                        Neighbors
header                  Return header block
initDb                  Iinitialize SQL Database
jarvisPatrick           Jarvis-Patrick Clustering
jarvisPatrick_c         Jarvis Patrick Clustering in C code
jobToken-class          Class '"jobToken"'
largestComponent        Largest Component
launchCMTool            Launch a Tool on ChemMine Tools
listCMTools             List all available ChemMine Tools
listFeatures            List Features
loadSdf                 Load SDF and SMILES Data
makeUnique              Uniquify CMP names
maximallyDissimilar     Maximally Dissimilar
nearestNeighbors        Nearest Neighbors
numBits                 numBits
obmol                   obmol
openBabelPlot           Plot compound structures
parBatchByIndex         Parallel Batch By Index
plotStruc               Plot compound structures
propOB                  Properties from OpenBabel
pubchemCidToSDF         Import Compounds from PubChem
pubchemFPencoding       Enncoding of PubChem Fingerprints
pubchemInchi2cid        Query pubchem by InChI sttrings and return CIDs
pubchemInchikey2sdf     Query pubchem by InChIKeys sttrings and get SDF
                        back
pubchemName2CID         Translate compound name to pubchem compound id
pubchemSDFSearch        PubChem Similarity (Fingerprint) Search
pubchemSmilesSearch     PubChem Similarity (Fingerprint) SMILES Search
read.AP                 Read Atom Pair/Fingerprint Strings
read.SDFindex           Extract Molecules from SD File by Line Index
read.SDFset             SD file to 'SDFset'
read.SDFstr             SD file to 'SDFstr'
read.SMIset             SMILES file to 'SMIset'
regenerateCoords        Re-generate 2D Coordinates
result                  Obtain the resulting output data from a
                        ChemMine Tools Job
rings                   Ring and Aromaticity Perception
sdf.subset              Subset a SDF and return SDF segements for
                        selected compounds
sdf.visualize           Visualize an SDFset online using ChemMine Tools
sdf2ap                  Atom pair library
sdf2list                'SDF' to 'list'
sdf2smiles              'SDFset' to 'character' Convert 'SDFset' to
                        SMILES ('character')
sdf2str                 'SDF' to 'SDFstr'
sdfStream               Streaming through large SD files
sdfid                   Return SDF compound IDs
sdfsample               SD file in 'SDFset' object
sdfstr2list             'SDFstr' to 'list'
searchSim               PubChem Similarity (Fingerprint) Search
searchString            PubChem Similarity (Fingerprint) SMILES Search
selectInBatches         Select in Batches
setPriorities           Set Priorities
smartsSearchOB          SMARTS Search OB
smiles2sdf              Convert SMILES ('character') to 'SDFset'
smisample               SMILES file in 'SMIset' object
status                  Get Status of a ChemMine Tools Job
toolDetails             Detailed instructions for each ChemMine Tools
                        web tool
trimNeighbors           Trim Neighbors
validSDF                Validity check of SDFset
view                    Viewing of complex objects
write.SDF               SDF export function
write.SDFsplit          SDF split function
write.SMI               SMI export function
