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rcdk (version 3.8.2)

Interface to the 'CDK' Libraries

Description

Allows the user to access functionality in the 'CDK', a Java framework for cheminformatics. 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.

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Version

Install

install.packages('rcdk')

Monthly Downloads

3,824

Version

3.8.2

License

LGPL

Issues

Pull Requests

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Repository

https://github.com/CDK-R/cdkr

Maintainer

Zachary CharlopPowers

Last Published

November 30th, 2025

Functions in rcdk (3.8.2)

get.chem.object.builder

Get the default chemical object builder.

Get the atoms from a molecule or bond.

get.atomic.number

get.atomic.number

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.element.types

Obtain the type of stereo element support for atom.

Get descriptor class names

get.desc.categories

List available descriptor categories

get.mol2formula

get.mol2formula

get.isotope.pattern.generator

Construct an isotope pattern generator.

get.murcko.fragments

Generate Bemis-Murcko Fragments

get.hydrogen.count

get.hydrogen.count

get.natural.mass

get.natural.mass

Get all properties associated with a molecule.

get.formal.charge

get.formal.charge

get.isotope.pattern.similarity

Construct an isotope pattern similarity calculator.

get.isotopes.pattern

get.isotopes.pattern

Get a property value of the molecule.

get.exhaustive.fragments

Generate Bemis-Murcko Fragments

get.fingerprint

Generate molecular fingerprints

Get the title of the molecule.

get.stereocenters

Identify which atoms are stereocenters.

Compute TPSA for a molecule

get.total.hydrogen.count

Get total number of implicit hydrogens in the molecule.

Tests whether the molecule is fully connected.

Tests whether the molecule is neutral.

isvalid.formula

isvalid.formula

get.smiles.parser

Get a SMILES parser object.

get.stereo.types

Obtain the stereocenter type for atom.

get.total.charge

get.total.charge

get.total.formal.charge

get.total.formal.charge

get.largest.component

Gets the largest component in a disconnected molecular graph.

Compute volume of a molecule

Set a property value of the molecule.

Load molecular structures from disk or URL

Compute XLogP for a molecule

Generate a SMILES representation of a molecule.

Parse SMILES strings into molecule objects.

iload.molecules

Load molecules using an iterator.

Set the title of the molecule.

view.molecule.2d

view.molecule.2d

set.charge.formula

set.charge.formula

write.molecules

Write molecules to disk.

rcdk-deprecated

Deprecated functions in the rcdk package.

Generate flag for customizing SMILES generation.

remove.property

Remove a property associated with a molecule.

remove.hydrogens

Remove explicit hydrogens.

copy.image.to.clipboard

copy.image.to.clipboard

compare.isotope.pattern

Compare isotope patterns.

Get the current CDK version used in the package.

convert.implicit.to.explicit

Convert implicit hydrogens to explicit.

cdkFormula-class

Class cdkFormula, ac class for handling molecular formula

Operations on Atoms

Operations on molecules

generate.formula.iter

generate.formula.iter

generate.2d.coordinates

Generate 2D coordinates for a molecule.

Boiling Point Data

eval.atomic.desc

Compute descriptors for each atom in a molecule

Compute descriptor values for a set of molecules

get.atomic.desc.names

Get class names for atomic descriptors

generate.formula

generate.formula

Compute ALogP for a molecule

Get the number of atoms in the molecule.

get.adjacency.matrix

Get adjacency matrix for a molecule.

Get an object representing bond order

Get the bonds in a molecule.