AP-class                Class "AP"
APset-class             Class "APset"
FP-class                Class '"FP"'
FPset-class             Class '"FPset"'
SDF-class               Class "SDF"
SDF2apcmp               'SDF' to 'list' for AP generation
SDFset-class            Class "SDFset"
SDFset2SDF              'SDFset' to list with many 'SDF'
SDFset2list             'SDFset' to 'list'
SDFstr-class            Class "SDFstr"
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
bondblock               Return bond block
bonds                   Bonds, charges and missing hydrogens
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
desc2fp                 Fingerprints from descriptor vectors
fp2bit                  Convert base 64 fingerprints to binary
fpSim                   Fingerprint Search
getIds                  Import Compounds from PubChem
grepSDFset              String search in 'SDFset'
groups                  Enumeration of Functional Groups and Atom
                        Neighbors
header                  Return header block
jarvisPatrick           Jarvis-Patrick Clustering
makeUnique              Uniquify CMP names
plotStruc               Plot compound structures
pubchemFPencoding       Enncoding of PubChem Fingerprints
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'
rings                   Ring and Aromaticity Perception
sdf.subset              Subset a SDF and return SDF segements for
                        selected compounds
sdf.visualize           Subset a SDFset and visualize selected
                        compounds in a webpage
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
smiles2sdf              Convert SMILES ('character') to 'SDFset'
validSDF                Validity check of SDFset
view                    Viewing of complex objects
write.SDF               SDF export function
write.SDFsplit          SDF split function
