# Interface to the 'CDK' Libraries

## Documentation for package ‘rcdk’ version 3.6.0

- 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 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
hydrogen | 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
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
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 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.
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.