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