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rcdk (version 3.8.1)

Interface to the 'CDK' Libraries

Description

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.

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Version

Install

install.packages('rcdk')

Monthly Downloads

2,628

Version

3.8.1

License

LGPL

Maintainer

Zachary CharlopPowers

Last Published

July 1st, 2023

Functions in rcdk (3.8.1)

get.atoms

Get the atoms from a molecule or bond.
get.desc.categories

List available descriptor categories
get.connected.atom

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

get.connected.atoms
get.adjacency.matrix

Get adjacency matrix for a molecule.
generate.formula.iter

generate.formula.iter
get.isotope.pattern.similarity

Construct an isotope pattern similarity calculator.
get.isotopes.pattern

get.isotopes.pattern
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.charge

get.charge
get.chem.object.builder

Get the default chemical object builder.
get.mcs

get.mcs
get.largest.component

Gets the largest component in a disconnected molecular graph.
get.stereo.types

Obtain the stereocenter type for atom.
get.smiles.parser

Get a SMILES parser object.
get.smiles

Generate a SMILES representation of a molecule.
get.property

Get a property value of the molecule.
get.xlogp

Compute XLogP for a molecule
get.tpsa

Compute TPSA for a molecule
get.atom.count

Get the number of atoms in the molecule.
get.bond.order

Get an object representing bond order
get.bonds

Get the bonds in a molecule.
get.exhaustive.fragments

Generate Bemis-Murcko Fragments
get.title

Get the title of the molecule.
parse.smiles

Parse SMILES strings into molecule objects.
get.total.charge

get.total.charge
get.connection.matrix

Get connection matrix for a molecule.
get.atom.index

get.atom.index
get.atomic.desc.names

Get class names for atomic descriptors
get.depictor

get.depictor
get.fingerprint

Generate molecular fingerprints
get.isotope.pattern.generator

Construct an isotope pattern generator.
get.mol2formula

get.mol2formula
get.hydrogen.count

get.hydrogen.count
get.murcko.fragments

Generate Bemis-Murcko Fragments
get.properties

Get all properties associated with a molecule.
get.volume

Compute volume of a molecule
set.title

Set the title of the molecule.
set.property

Set a property value of the molecule.
get.total.formal.charge

get.total.formal.charge
get.formal.charge

get.formal.charge
get.point3d

get.point3d
view.molecule.2d

view.molecule.2d
get.total.hydrogen.count

Get total number of implicit hydrogens in the molecule.
view.table

view.table
remove.hydrogens

Remove explicit hydrogens.
iload.molecules

Load molecules using an iterator.
matches

matches
is.neutral

Tests whether the molecule is neutral.
isvalid.formula

isvalid.formula
load.molecules

Load molecular structures from disk or URL
get.formula

get.formula
is.aliphatic

is.aliphatic
get.natural.mass

get.natural.mass
get.point2d

get.point2d
rcdk-deprecated

Deprecated functions in the rcdk package.
smiles.flavors

Generate flag for customizing SMILES generation.
get.symbol

get.symbol
is.in.ring

is.in.ring
set.charge.formula

set.charge.formula
is.connected

Tests whether the molecule is fully connected.
get.stereocenters

Identify which atoms are stereocenters.
set.atom.types

set.atom.types
write.molecules

Write molecules to disk.
remove.property

Remove a property associated with a molecule.
is.aromatic

is.aromatic
view.image.2d

view.image.2d
Molecule

Operations on molecules
cdkFormula-class

Class cdkFormula, ac class for handling molecular formula
copy.image.to.clipboard

copy.image.to.clipboard
Atoms

Operations on Atoms
compare.isotope.pattern

Compare isotope patterns.
bpdata

Boiling Point Data
do.aromaticity

do.aromaticity
convert.implicit.to.explicit

Convert implicit hydrogens to explicit.
do.isotopes

do.isotopes
cdk.version

Get the current CDK version used in the package.
generate.formula

generate.formula
generate.2d.coordinates

Generate 2D coordinates for a molecule.
eval.atomic.desc

Compute descriptors for each atom in a molecule
eval.desc

Compute descriptor values for a set of molecules
get.alogp

Compute ALogP for a molecule
get.atomic.number

get.atomic.number