Package: rcdk 3.8.1

Zachary Charlop-Powers

rcdk: Interface to the 'CDK' Libraries

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

rcdk_3.8.1.tar.gz
rcdk_3.8.1.tar.gz(r-4.5-noble)rcdk_3.8.1.tar.gz(r-4.4-noble)
rcdk_3.8.1.tgz(r-4.4-emscripten)rcdk_3.8.1.tgz(r-4.3-emscripten)
rcdk.pdf |rcdk.html✨
rcdk/json (API)
NEWS

# Install 'rcdk' in R:
install.packages('rcdk', repos = 'https://cloud.r-project.org')
Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:

On CRAN:

Conda-Forge:r-rcdk-3.8.1(2024-07-09)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openjdk

6.77 score 1 stars 11 packages 287 scripts 2.1k downloads 30 mentions 79 exports 6 dependencies

Last updated 2 years agofrom:de7fe5a560. Checks:1 OK, 1 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-linuxNOTEFeb 21 2025

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

Handling Molecular Formulae

Rajarshi Guha

Rendered frommolform.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2021-10-17
Started: 2018-04-30

Performance Notes

Zaachary Charlop-Powers

Rendered fromPerformanceNotes.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2023-06-12
Started: 2023-06-12

Using the CDK from R

Rajarshi Guha

Rendered fromusing-rcdk.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2023-07-01
Started: 2018-04-30

Citation

To cite rcdk in publications use:

Guha, R. (2007). 'Chemical Informatics Functionality in R'. Journal of Statistical Software 6(18)

Corresponding BibTeX entry: 

  @Article{,
    author = {Rajarshi Guha},
    journal = {Journal of Statistical Software},
    number = {6},
    title = {Chemical Informatics Functionality in R},
    volume = {18},
    year = {2007},
  }

Readme and manuals

Help Manual

Help pageTopics
Operations on AtomsAtoms
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