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rcdk (version 3.4.7.2)

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

3.4.7.2

License

LGPL

Maintainer

Zachary CharlopPowers

Last Published

December 21st, 2019

Functions in rcdk (3.4.7.2)

compare.isotope.pattern

Compare isotope patterns.

get.adjacency.matrix

Get adjacency matrix for a molecule.

get.connection.matrix

Get connection matrix for a molecule.

Get All Property Values of a Molecule

Boiling Point Data

cdkFormula-class

Class cdkFormula, a class for handling molecular formula

Get the Value of a Molecule Property

Get the Largest Component in a Disconnected Molecule

eval.atomic.desc

Evaluate an Atomic Descriptor

get.mol2formula

Parser a molecule to formula object.

set.charge.formula

Set the charge to a cdkFormula object.

Set A Property On A Molecule

generate.formula

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

Evaluate a Molecular Descriptor

get.murcko.fragments

Molecule Fragmentation Methods

get.isotope.pattern.similarity

Construct an isotope pattern similarity calculator.

Operations on molecules

Operations on atoms

get.stereocenters

Identify which atoms are stereocenters.

get.element.types

Obtain the type of stereo element support for atom.

get.atomic.desc.names

Get the names of the available atomic descriptors

generate.2d.coordinates

Generate 2D Coordinates from Connectivity Information

Get the atoms from a molecule or bond

Get the formula object from a formula character.

get.desc.categories

Get Descriptor Class Names

get.fingerprint

Evaluate Fingerprints

Get Descriptor Class Names

get.stereo.types

Obtain the stereocenter type for atom.

get.total.charge

Get the Total Charges for the Molecule

write.molecules

Write Molecules To Disk

View 2D Structures With Data

Does This Iterator Have A Next Element

get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule

Perform Substructure Searching & MCS Detection

get.isotope.pattern.generator

Construct an isotope pattern generator.

get.isotopes.pattern

Generate the isotope pattern.

Perform Aromaticity Detection, atom typing or isotopic configuration

isvalid.formula

Validate a cdkFormula object.

Parse a Vector of SMILES Strings

get.connected.atom

Get the atom connected to an atom in a bond

Get the bonds from a molecule

Load Molecular Structures From Disk

Generate flag for customizing SMILES generation.

view.molecule.2d

View and Copy 2D Structure Diagrams

Commonly Used Molecular Descriptors

remove.property

Remove A Property From a Molecule

get.smiles.parser

Get a SMILES Parser

remove.hydrogens

Remove Hydrogens from a Molecule

Get the SMILES for a Molecule

Get Current CDK Version