Function reference • rcdk

rCDK Functions

rCDK Data and Docs

Available Datasets or Documentation

bpdata: Boiling Point Data

Atoms rcdk-package: Operations on Atoms

Molecule: Operations on molecules

rCDK IO Functions

Functions to Load Data

copy.image.to.clipboard(): copy.image.to.clipboard

iload.molecules(): Load molecules using an iterator.

load.molecules(): Load molecular structures from disk or URL

parse.smiles(): Parse SMILES strings into molecule objects.

write.molecules(): Write molecules to disk.

Core Functions

For acting on Atoms, Molecules, ad Formula

compare.isotope.pattern(): Compare isotope patterns.

convert.implicit.to.explicit(): Convert implicit hydrogens to explicit.

do.aromaticity(): do.aromaticity

do.isotopes(): do.isotopes

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.atom.index

get.atomic.desc.names(): Get class names for atomic descriptors

get.atomic.number(): get.atomic.number

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.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.connected.atoms

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.formal.charge

get.formula(): get.formula

get.hydrogen.count(): get.hydrogen.count

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.point2d

get.point3d(): get.point3d

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.symbol

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

is.aliphatic(): is.aliphatic

is.aromatic(): is.aromatic

is.connected(): Tests whether the molecule is fully connected.

is.in.ring(): is.in.ring

is.neutral(): Tests whether the molecule is neutral.

isvalid.formula(): isvalid.formula

matches(): matches

remove.hydrogens(): Remove explicit hydrogens.

remove.property(): Remove a property associated with a molecule.

set.atom.types(): set.atom.types

set.charge.formula(): set.charge.formula

set.property(): Set a property value of the molecule.

set.title(): Set the title of the molecule.

smiles.flavors(): Generate flag for customizing SMILES generation.

view.image.2d(): view.image.2d

view.molecule.2d(): view.molecule.2d

view.table(): view.table

Package Function

Mostly for Development

cdk.version(): Get the current CDK version used in the package.

cdkFormula-class show,cdkFormula-method: Class cdkFormula, ac class for handling molecular formula

deprecated_rcdk_function(): Deprecated functions in the rcdk package.