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rcdk (version 2.9.2)

rcdk - Interface to the CDK Libraries

Description

This package 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

2,414

Version

2.9.2

License

LGPL

Maintainer

Rajarshi Guha

Last Published

November 30th, 2025

Functions in rcdk (2.9.2)

parse.smiles

Parse a SMILES String
get.smiles

Get the SMILES for a Molecule
get.properties

Get All Property Values of a Molecule
get.fingerprint

Evaluate Fingerprints
get.isotopes.pattern

Generate the isotope pattern.
get.mol2formula

Parser a molecule to formula object.
write.molecules

Write Molecules To Disk
Atoms

Operations on atoms
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
set.property

Set A Property On A Molecule
eval.atomic.desc

Evaluate an Atomic Descriptor
Molecule

Operations on molecules
get.tpsa

Commonly Used Molecular Descriptors
get.atoms

Get the atoms from a molecule or bond
get.formula

Get the formula object from a formula character.
bpdata

Boiling Point Data
is.connected

Get the Largest Component in a Disconnected Molecule
remove.hydrogens

Remove Hydrogens from a Molecule
get.atomic.desc.names

Get the names of the available atomic descriptors
get.connected.atom

Get the atom connected to an atom in a bond
get.bonds

Get the bonds from a molecule
isvalid.formula

Validate a cdkFormula object.
get.fragmenter

Molecule Fragmentation Methods
load.molecules

Load Molecular Structure From Disk
eval.desc

Evaluate a Molecular Descriptor
get.smiles.parser

Get a SMILES Parser
remove.property

Remove A Property From a Molecule
get.property

Get the Value of a Molecule Property
get.desc.categories

Get Descriptor Class Names
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.desc.names

Get Descriptor Class Names
generate.formula

Generate a cdkFormula object.
get.total.charge

Get the Total Charge for the Molecule
view.molecule.2d

View 2D Structure Diagrams
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
view.table

View 2D Structures With Data
set.charge.formula

Set the charge to a cdkFormula object.
hasNext

Does This Iterator Have A Next Element
matches

Perform Substructure Searching