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rcdk (version 3.1.9)

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

3.1.9

License

LGPL

Maintainer

Rajarshi Guha

Last Published

July 6th, 2012

Functions in rcdk (3.1.9)

get.murcko.fragments

Molecule Fragmentation Methods
isvalid.formula

Validate a cdkFormula object.
get.atomic.desc.names

Get the names of the available atomic descriptors
get.atoms

Get the atoms from a molecule or bond
Molecule

Operations on molecules
get.properties

Get All Property Values of a Molecule
remove.property

Remove A Property From a Molecule
get.isotopes.pattern

Generate the isotope pattern.
get.desc.names

Get Descriptor Class Names
remove.hydrogens

Remove Hydrogens from a Molecule
load.molecules

Load Molecular Structures From Disk
get.desc.categories

Get Descriptor Class Names
view.molecule.2d

View and Copy 2D Structure Diagrams
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
get.formula

Get the formula object from a formula character.
get.fingerprint

Evaluate Fingerprints
cdk.version

Get Current CDK Version
set.charge.formula

Set the charge to a cdkFormula object.
view.table

View 2D Structures With Data
get.property

Get the Value of a Molecule Property
get.tpsa

Commonly Used Molecular Descriptors
write.molecules

Write Molecules To Disk
get.smiles.parser

Get a SMILES Parser
hasNext

Does This Iterator Have A Next Element
eval.desc

Evaluate a Molecular Descriptor
get.bonds

Get the bonds from a molecule
get.connected.atom

Get the atom connected to an atom in a bond
get.total.charge

Get the Total Charges for the Molecule
is.connected

Get the Largest Component in a Disconnected Molecule
generate.formula

Generate a cdkFormula object.
bpdata

Boiling Point Data
matches

Perform Substructure Searching & MCS Detection
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
Atoms

Operations on atoms
set.property

Set A Property On A Molecule
get.smiles

Get the SMILES for a Molecule
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
eval.atomic.desc

Evaluate an Atomic Descriptor
get.mol2formula

Parser a molecule to formula object.
parse.smiles

Parse a Vector of SMILES Strings