Package: rcdk 3.8.2

Zachary Charlop-Powers

rcdk: Interface to the 'CDK' Libraries

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.

Authors:Rajarshi Guha [aut, cph], Zachary Charlop-Powers [cre], Emma Schymanski [ctb], Egon Willighagen [ctb]

rcdk_3.8.2.tar.gz
rcdk_3.8.2.zip(r-4.7)rcdk_3.8.2.zip(r-4.6)rcdk_3.8.2.zip(r-4.5)
rcdk_3.8.2.tgz(r-4.6-any)rcdk_3.8.2.tgz(r-4.5-any)
rcdk_3.8.2.tar.gz(r-4.7-any)rcdk_3.8.2.tar.gz(r-4.6-any)
rcdk_3.8.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rcdk/json (API)

# Install 'rcdk' in R:
install.packages('rcdk', repos = c('https://cdk-r.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cdk-r/cdkr/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:

On CRAN:

Conda:

javarcdkopenjdk

11.35 score 45 stars 14 packages 362 scripts 1.8k downloads 30 mentions 79 exports 6 dependencies

Last updated from:ecb5eaa5de. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK180
source / vignettesOK245
linux-release-x86_64OK176
macos-release-arm64OK115
macos-oldrel-arm64OK103
windows-develOK113
windows-releaseOK111
windows-oldrelOK107
wasm-releaseOK178

Exports:cdk.versioncompare.isotope.patternconvert.implicit.to.explicitcopy.image.to.clipboarddo.aromaticitydo.isotopesdo.typingeval.atomic.desceval.descgenerate.2d.coordinatesgenerate.formulagenerate.formula.iterget.adjacency.matrixget.alogpget.atom.countget.atom.indexget.atomic.desc.namesget.atomic.numberget.atomsget.bond.orderget.bondsget.chargeget.chem.object.builderget.connected.atomget.connected.atomsget.connection.matrixget.depictorget.desc.categoriesget.desc.namesget.element.typesget.exact.massget.exhaustive.fragmentsget.fingerprintget.formal.chargeget.formulaget.hydrogen.countget.isotopes.patternget.largest.componentget.mcsget.mol2formulaget.murcko.fragmentsget.natural.massget.point2dget.point3dget.propertiesget.propertyget.smilesget.smiles.parserget.stereo.typesget.stereocentersget.symbolget.titleget.total.chargeget.total.formal.chargeget.total.hydrogen.countget.tpsaget.volumeget.xlogpiload.moleculesis.aliphaticis.aromaticis.connectedis.in.ringis.neutralisvalid.formulaload.moleculesmatchesparse.smilesremove.hydrogensremove.propertyset.atom.typesset.charge.formulaset.propertyset.titlesmiles.flavorsview.image.2dview.molecule.2dview.tablewrite.molecules

Dependencies:fingerprintiteratorsitertoolspngrcdklibsrJava

Performance Notes
rCDK Performance | Benchmark | Results
Rendered fromPerformanceNotes.Rmdusingknitr::rmarkdown

Last update: 2025-11-30
Started: 2022-11-23

Using the CDK from R
title: "Using the CDK from R"author: "Rajarshi Guha"date: "r Sys.Date()"output:rmarkdown::html_vignette:toc: truevignette: >%\VignetteIndexEntry | Introduction | Getting started | Input and Output | Parsing SMILES | Generating SMILES | Visualization | Manipulating Molecules | Adding Information to Molecules | Atoms and Bonds | Substructure matching | Molecular Descriptors | Fingerprints
Rendered fromrcdk.Rmdusingknitr::rmarkdown

Last update: 2025-11-30
Started: 2024-03-03

Handling Molecular Formulae
Introduction | Parsing a Molecule To a Molecular Formula | Initializing a Formula from the Symbol Expression | Generating Molecular Formula | Calculating Isotope Pattern
Rendered frommolform.Rmdusingknitr::rmarkdown

Last update: 2021-11-24
Started: 2017-12-29

Readme and manuals

Help Manual

Help pageTopics
Operations on Atomsrcdk-package Atoms
Boiling Point Databpdata
Get the current CDK version used in the package.cdk.version
Class cdkFormula, ac class for handling molecular formulacdkFormula-class show,cdkFormula-method
Compare isotope patterns.compare.isotope.pattern
Convert implicit hydrogens to explicit.convert.implicit.to.explicit
copy.image.to.clipboardcopy.image.to.clipboard
do.aromaticitydo.aromaticity
do.isotopesdo.isotopes
Compute descriptors for each atom in a moleculeeval.atomic.desc
Compute descriptor values for a set of moleculeseval.desc
Generate 2D coordinates for a molecule.generate.2d.coordinates
generate.formulagenerate.formula
generate.formula.itergenerate.formula.iter
Get adjacency matrix for a molecule.get.adjacency.matrix
Compute ALogP for a moleculeget.alogp
Get the number of atoms in the molecule.get.atom.count
get.atom.indexget.atom.index
Get class names for atomic descriptorsget.atomic.desc.names
get.atomic.numberget.atomic.number
Get the atoms from a molecule or bond.get.atoms
Get an object representing bond orderget.bond.order
Get the bonds in a molecule.get.bonds
get.chargeget.charge
Get the default chemical object builder.get.chem.object.builder
Get the atom connected to an atom in a bond.get.connected.atom
get.connected.atomsget.connected.atoms
Get connection matrix for a molecule.get.connection.matrix
get.depictorget.depictor
List available descriptor categoriesget.desc.categories
Get descriptor class namesget.desc.names
Obtain the type of stereo element support for atom.get.element.types
get.exact.massget.exact.mass
Generate Bemis-Murcko Fragmentsget.exhaustive.fragments
Generate molecular fingerprintsget.fingerprint
get.formal.chargeget.formal.charge
get.formulaget.formula
get.hydrogen.countget.hydrogen.count hydrogen
Construct an isotope pattern generator.get.isotope.pattern.generator
Construct an isotope pattern similarity calculator.get.isotope.pattern.similarity
get.isotopes.patternget.isotopes.pattern
Gets the largest component in a disconnected molecular graph.get.largest.component
get.mcsget.mcs
get.mol2formulaget.mol2formula
Generate Bemis-Murcko Fragmentsget.murcko.fragments
get.natural.massget.natural.mass
get.point2dget.point2d
get.point3dget.point3d
Get all properties associated with a molecule.get.properties
Get a property value of the molecule.get.property
Generate a SMILES representation of a molecule.get.smiles
Get a SMILES parser object.get.smiles.parser
Obtain the stereocenter type for atom.get.stereo.types
Identify which atoms are stereocenters.get.stereocenters
get.symbolget.symbol
Get the title of the molecule.get.title
get.total.chargeget.total.charge
get.total.formal.chargeget.total.formal.charge
Get total number of implicit hydrogens in the molecule.get.total.hydrogen.count
Compute TPSA for a moleculeget.tpsa
Compute volume of a moleculeget.volume
Compute XLogP for a moleculeget.xlogp
Load molecules using an iterator.iload.molecules
is.aliphaticis.aliphatic
is.aromaticis.aromatic
Tests whether the molecule is fully connected.is.connected
is.in.ringis.in.ring
Tests whether the molecule is neutral.charge is.neutral
isvalid.formulaisvalid.formula
Load molecular structures from disk or URLload.molecules
matchesmatch-SMARTS matches
Operations on moleculesMolecule
Parse SMILES strings into molecule objects.parse.smiles
Deprecated functions in the rcdk package.deprecated_rcdk_function do.typing rcdk-deprecated
Remove explicit hydrogens.remove.hydrogens
Remove a property associated with a molecule.remove.property
set.atom.typesset.atom.types
set.charge.formulaset.charge.formula
Set a property value of the molecule.set.property
Set the title of the molecule.set.title
Generate flag for customizing SMILES generation.smiles.flavors
view.image.2dview.image.2d
view.molecule.2dview.molecule.2d
view.tableview.table
Write molecules to disk.write.molecules