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 the index of an atom in a molecule. Acces
                        the index of an atom in the context of an
                        IAtomContainer. Indexing starts from 0. If the
                        index is not known, -1 is returned.
get.atomic.desc.names   Get class names for atomic descriptors
get.atomic.number       Get the atomic number of the atom.
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 the charge on the atom. This method returns
                        the partial charge on the atom. If charges have
                        not been set the return value is 'NULL',
                        otherwise the appropriate 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 atoms connected to the specified atom
                        Returns a 'list" of atoms that are connected to
                        the specified atom.
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 the formal charge on the atom. By default
                        the formal charge will be 0 (i.e., 'NULL' is
                        never returned).
get.formula             get.formula
get.hydrogen.count      Get the implicit hydrogen count for the atom.
                        This method returns the number of implicit H's
                        on the atom.  Depending on where the molecule
                        was read from this may be 'NULL' or an integer
                        greater than or equal to 0
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 the 2D coordinates of the atom. In case,
                        coordinates are unavailable (e.g., molecule was
                        read in from a SMILES file) or have not been
                        generated yet, 'NA''s are returned for the X &
                        Y coordinates.
get.point3d             Get the 3D coordinates of the atom. In case,
                        coordinates are unavailable (e.g., molecule was
                        read in from a SMILES file) or have not been
                        generated yet, 'NA''s are returned for the X, Y
                        and Z coordinates.
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 the atomic symbol of the atom. Get the
                        atomic symbol of the atom.
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            Tests whether an atom is aliphatic. This
                        assumes that the molecule containing the atom
                        has been appropriately configured.
is.aromatic             Tests whether an atom is aromatic. This assumes
                        that the molecule containing the atom has been
                        appropriately configured.
is.connected            Tests whether the molecule is fully connected.
is.in.ring              Tests whether an atom is in a ring. This
                        assumes that the molecule containing the atom
                        has been appropriately configured.
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 the CDK atom types for all atoms in the
                        molecule Calling this method will overwrite any
                        pre-existing type information. Currently there
                        is no way to choose other atom typing schemes
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.
