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rcdk (version 3.5.0)

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

6,083

Version

3.5.0

License

LGPL

Maintainer

Zachary CharlopPowers

Last Published

March 11th, 2020

Functions in rcdk (3.5.0)

do.typing

do.typing
get.formula

get.formula
get.atom.index

Get the index of an atom in a molecule. Acces the index of an atom in the context of an IAtomContainer. Indexing starts from 0. If the index is not known, -1 is returned.
get.atom.count

Get the number of atoms in the molecule.
generate.formula

generate.formula
get.bonds

Get the bonds in a molecule.
get.formal.charge

Get the formal charge on the atom. By default the formal charge will be 0 (i.e., NULL is never returned).
get.atoms

Get the atoms from a molecule or bond.
generate.formula.iter

generate.formula.iter
get.atomic.desc.names

Get class names for atomic descriptors
eval.atomic.desc

Compute descriptors for each atom in a molecule
get.connected.atoms

Get atoms connected to the specified atom Returns a `list`` of atoms that are connected to the specified atom.
get.atomic.number

Get the atomic number of the atom.
get.exact.mass

get.exact.mass
get.element.types

Obtain the type of stereo element support for atom.
get.connected.atom

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

Compute ALogP for a molecule
get.adjacency.matrix

Get adjacency matrix for a molecule.
cdk.version

Get the current CDK version used in the package.
get.chem.object.builder

Get the default chemical object builder.
get.charge

Get the charge on the atom. This method returns the partial charge on the atom. If charges have not been set the return value is NULL, otherwise the appropriate charge.
eval.desc

Compute descriptor values for a set of molecules
get.hydrogen.count

Get the implicit hydrogen count for the atom. This method returns the number of implicit H's on the atom. Depending on where the molecule was read from this may be NULL or an integer greater than or equal to 0
get.desc.names

Get descriptor class names
get.desc.categories

List available descriptor categories
get.isotope.pattern.generator

Construct an isotope pattern generator.
generate.2d.coordinates

Generate 2D coordinates for a molecule.
get.point2d

Get the 2D coordinates of the atom. In case, coordinates are unavailable (e.g., molecule was read in from a SMILES file) or have not been generated yet, `NA`'s are returned for the X & Y coordinates.
get.total.hydrogen.count

Get total number of implicit hydrogens in the molecule.
get.natural.mass

get.natural.mass
get.total.formal.charge

get.total.formal.charge
get.point3d

Get the 3D coordinates of the atom. In case, coordinates are unavailable (e.g., molecule was read in from a SMILES file) or have not been generated yet, `NA`'s are returned for the X, Y and Z coordinates.
get.connection.matrix

Get connection matrix for a molecule.
get.smiles

Generate a SMILES representation of a molecule.
get.properties

Get all properties associated with a molecule.
get.property

Get a property value of the molecule.
get.depictor

get.depictor
get.exhaustive.fragments

Generate Bemis-Murcko Fragments
get.largest.component

Gets the largest component in a disconnected molecular graph.
get.isotope.pattern.similarity

Construct an isotope pattern similarity calculator.
get.fingerprint

Generate molecular fingerprints
get.tpsa

Compute TPSA for a molecule
get.isotopes.pattern

get.isotopes.pattern
get.smiles.parser

Get a SMILES parser object.
get.volume

Compute volume of a molecule
get.mol2formula

get.mol2formula
remove.property

Remove a property associated with a molecule.
set.charge.formula

set.charge.formula
get.stereo.types

Obtain the stereocenter type for atom.
get.mcs

get.mcs
isvalid.formula

isvalid.formula
parse.smiles

Parse SMILES strings into molecule objects.
remove.hydrogens

Remove explicit hydrogens.
is.neutral

Tests whether the molecule is neutral.
write.molecules

Write molecules to disk.
view.molecule.2d

view.molecule.2d
is.connected

Tests whether the molecule is fully connected.
get.murcko.fragments

Generate Bemis-Murcko Fragments
get.title

Get the title of the molecule.
get.total.charge

get.total.charge
is.in.ring

Tests whether an atom is in a ring. This assumes that the molecule containing the atom has been appropriately configured.
matches

matches
get.xlogp

Compute XLogP for a molecule
load.molecules

Load molecular structures from disk or URL
iload.molecules

Load molecules using an iterator.
get.symbol

Get the atomic symbol of the atom. Get the atomic symbol of the atom.
get.stereocenters

Identify which atoms are stereocenters.
view.image.2d

view.image.2d
smiles.flavors

Generate flag for customizing SMILES generation.
is.aliphatic

Tests whether an atom is aliphatic. This assumes that the molecule containing the atom has been appropriately configured.
set.property

Set a property value of the molecule.
set.title

Set the title of the molecule.
is.aromatic

Tests whether an atom is aromatic. This assumes that the molecule containing the atom has been appropriately configured.
Atoms

Operations on Atoms
bpdata

Boiling Point Data
copy.image.to.clipboard

copy.image.to.clipboard
do.aromaticity

do.aromaticity
cdkFormula-class

Class cdkFormula, ac class for handling molecular formula
do.isotopes

do.isotopes
convert.implicit.to.explicit

Convert implicit hydrogens to explicit.
compare.isotope.pattern

Compare isotope patterns.
Molecule

Operations on molecules