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rcdk (version 3.1.1)

rcdk - Interface to the CDK Libraries

Description

This package allows the user to access functionality in the CDK, a Java framework for cheminformatics. 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

2,414

Version

3.1.1

License

LGPL

Maintainer

Rajarshi Guha

Last Published

June 19th, 2011

Functions in rcdk (3.1.1)

eval.desc

Evaluate a Molecular Descriptor
get.properties

Get All Property Values of a Molecule
get.mol2formula

Parser a molecule to formula object.
get.desc.categories

Get Descriptor Class Names
is.connected

Get the Largest Component in a Disconnected Molecule
hasNext

Does This Iterator Have A Next Element
get.atoms

Get the atoms from a molecule or bond
get.property

Get the Value of a Molecule Property
get.atomic.desc.names

Get the names of the available atomic descriptors
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.connected.atom

Get the atom connected to an atom in a bond
remove.hydrogens

Remove Hydrogens from a Molecule
get.desc.names

Get Descriptor Class Names
write.molecules

Write Molecules To Disk
view.molecule.2d

View and Copy 2D Structure Diagrams
get.formula

Get the formula object from a formula character.
isvalid.formula

Validate a cdkFormula object.
parse.smiles

Parse a Vector of SMILES Strings
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
get.isotopes.pattern

Generate the isotope pattern.
set.property

Set A Property On A Molecule
get.total.charge

Get the Total Charges for the Molecule
set.charge.formula

Set the charge to a cdkFormula object.
cdk.version

Get Current CDK Version
generate.formula

Generate a cdkFormula object.
remove.property

Remove A Property From a Molecule
view.table

View 2D Structures With Data
bpdata

Boiling Point Data
get.smiles.parser

Get a SMILES Parser
matches

Perform Substructure Searching & MCS Detection
get.tpsa

Commonly Used Molecular Descriptors
get.bonds

Get the bonds from a molecule
get.murcko.fragments

Molecule Fragmentation Methods
get.fingerprint

Evaluate Fingerprints
get.smiles

Get the SMILES for a Molecule
Molecule

Operations on molecules
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
Atoms

Operations on atoms
load.molecules

Load Molecular Structures From Disk
eval.atomic.desc

Evaluate an Atomic Descriptor