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rcdk (version 3.4.7.1)

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

2,020

Version

3.4.7.1

License

LGPL

Maintainer

Zachary CharlopPowers

Last Published

September 26th, 2018

Functions in rcdk (3.4.7.1)

bpdata

Boiling Point Data
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.element.types

Obtain the type of stereo element support for atom.
eval.atomic.desc

Evaluate an Atomic Descriptor
get.connected.atom

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

Get the bonds from a molecule
get.connection.matrix

Get connection matrix for a molecule.
matches

Perform Substructure Searching & MCS Detection
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
get.formula

Get the formula object from a formula character.
get.isotope.pattern.generator

Construct an isotope pattern generator.
get.fingerprint

Evaluate Fingerprints
cdk.version

Get Current CDK Version
get.isotope.pattern.similarity

Construct an isotope pattern similarity calculator.
get.stereo.types

Obtain the stereocenter type for atom.
get.property

Get the Value of a Molecule Property
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
compare.isotope.pattern

Compare isotope patterns.
get.stereocenters

Identify which atoms are stereocenters.
generate.2d.coordinates

Generate 2D Coordinates from Connectivity Information
smiles.flavors

Generate flag for customizing SMILES generation.
is.connected

Get the Largest Component in a Disconnected Molecule
get.properties

Get All Property Values of a Molecule
get.mol2formula

Parser a molecule to formula object.
get.total.charge

Get the Total Charges for the Molecule
get.isotopes.pattern

Generate the isotope pattern.
eval.desc

Evaluate a Molecular Descriptor
parse.smiles

Parse a Vector of SMILES Strings
get.tpsa

Commonly Used Molecular Descriptors
isvalid.formula

Validate a cdkFormula object.
get.desc.categories

Get Descriptor Class Names
view.molecule.2d

View and Copy 2D Structure Diagrams
view.table

View 2D Structures With Data
hasNext

Does This Iterator Have A Next Element
write.molecules

Write Molecules To Disk
load.molecules

Load Molecular Structures From Disk
remove.hydrogens

Remove Hydrogens from a Molecule
remove.property

Remove A Property From a Molecule
get.desc.names

Get Descriptor Class Names
get.smiles

Get the SMILES for a Molecule
set.charge.formula

Set the charge to a cdkFormula object.
get.smiles.parser

Get a SMILES Parser
set.property

Set A Property On A Molecule
get.murcko.fragments

Molecule Fragmentation Methods
generate.formula

Generate molecular formulae given a target mass and a set of elements and counts.
Molecule

Operations on molecules
get.atomic.desc.names

Get the names of the available atomic descriptors
get.atoms

Get the atoms from a molecule or bond
Atoms

Operations on atoms
get.adjacency.matrix

Get adjacency matrix for a molecule.