# Interface to the 'CDK' Libraries

## Documentation for package ‘rcdk’ version 3.8.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Atoms | Operations on Atoms
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
charge | Tests whether the molecule is neutral.
compare.isotope.pattern | Compare isotope patterns.
convert.implicit.to.explicit | Convert implicit hydrogens to explicit.
copy.image.to.clipboard | copy.image.to.clipboard
deprecated_rcdk_function | Deprecated functions in the rcdk package.
do.aromaticity | do.aromaticity
do.isotopes | do.isotopes
do.typing | Deprecated functions in the rcdk package.
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
hydrogen | get.hydrogen.count
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
match-SMARTS | matches
matches | matches
Molecule | Operations on molecules
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.
show-method | Class cdkFormula, ac class for handling molecular formula
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.