Atoms                   Operations on Atoms
Molecule                Operations on molecules
bpdata                  Boiling Point Data
cdk.version             Get the current CDK version used in the
                        package.
cdkFormula-class        Class cdkFormula, ac class for handling
                        molecular formula
compare.isotope.pattern
                        Compare isotope patterns.
convert.implicit.to.explicit
                        Convert implicit hydrogens to explicit.
copy.image.to.clipboard
                        copy.image.to.clipboard
do.aromaticity          do.aromaticity
do.isotopes             do.isotopes
eval.atomic.desc        Compute descriptors for each atom in a molecule
eval.desc               Compute descriptor values for a set of
                        molecules
generate.2d.coordinates
                        Generate 2D coordinates for a molecule.
generate.formula        generate.formula
generate.formula.iter   generate.formula.iter
get.adjacency.matrix    Get adjacency matrix for a molecule.
get.alogp               Compute ALogP for a molecule
get.atom.count          Get the number of atoms in the molecule.
get.atom.index          get.atom.index
get.atomic.desc.names   Get class names for atomic descriptors
get.atomic.number       get.atomic.number
get.atoms               Get the atoms from a molecule or bond.
get.bond.order          Get an object representing bond order
get.bonds               Get the bonds in a molecule.
get.charge              get.charge
get.chem.object.builder
                        Get the default chemical object builder.
get.connected.atom      Get the atom connected to an atom in a bond.
get.connected.atoms     get.connected.atoms
get.connection.matrix   Get connection matrix for a molecule.
get.depictor            get.depictor
get.desc.categories     List available descriptor categories
get.desc.names          Get descriptor class names
get.element.types       Obtain the type of stereo element support for
                        atom.
get.exact.mass          get.exact.mass
get.exhaustive.fragments
                        Generate Bemis-Murcko Fragments
get.fingerprint         Generate molecular fingerprints
get.formal.charge       get.formal.charge
get.formula             get.formula
get.hydrogen.count      get.hydrogen.count
get.isotope.pattern.generator
                        Construct an isotope pattern generator.
get.isotope.pattern.similarity
                        Construct an isotope pattern similarity
                        calculator.
get.isotopes.pattern    get.isotopes.pattern
get.largest.component   Gets the largest component in a disconnected
                        molecular graph.
get.mcs                 get.mcs
get.mol2formula         get.mol2formula
get.murcko.fragments    Generate Bemis-Murcko Fragments
get.natural.mass        get.natural.mass
get.point2d             get.point2d
get.point3d             get.point3d
get.properties          Get all properties associated with a molecule.
get.property            Get a property value of the molecule.
get.smiles              Generate a SMILES representation of a molecule.
get.smiles.parser       Get a SMILES parser object.
get.stereo.types        Obtain the stereocenter type for atom.
get.stereocenters       Identify which atoms are stereocenters.
get.symbol              get.symbol
get.title               Get the title of the molecule.
get.total.charge        get.total.charge
get.total.formal.charge
                        get.total.formal.charge
get.total.hydrogen.count
                        Get total number of implicit hydrogens in the
                        molecule.
get.tpsa                Compute TPSA for a molecule
get.volume              Compute volume of a molecule
get.xlogp               Compute XLogP for a molecule
iload.molecules         Load molecules using an iterator.
is.aliphatic            is.aliphatic
is.aromatic             is.aromatic
is.connected            Tests whether the molecule is fully connected.
is.in.ring              is.in.ring
is.neutral              Tests whether the molecule is neutral.
isvalid.formula         isvalid.formula
load.molecules          Load molecular structures from disk or URL
matches                 matches
parse.smiles            Parse SMILES strings into molecule objects.
rcdk-deprecated         Deprecated functions in the rcdk package.
remove.hydrogens        Remove explicit hydrogens.
remove.property         Remove a property associated with a molecule.
set.atom.types          set.atom.types
set.charge.formula      set.charge.formula
set.property            Set a property value of the molecule.
set.title               Set the title of the molecule.
smiles.flavors          Generate flag for customizing SMILES
                        generation.
view.image.2d           view.image.2d
view.molecule.2d        view.molecule.2d
view.table              view.table
write.molecules         Write molecules to disk.
