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