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rcdk (version 3.0.3)

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

3.0.3

License

LGPL

Maintainer

Rajarshi Guha

Last Published

October 12th, 2010

Functions in rcdk (3.0.3)

parse.smiles

Parse a Vector of SMILES Strings
isvalid.formula

Validate a cdkFormula object.
Atoms

Operations on atoms
eval.atomic.desc

Evaluate an Atomic Descriptor
generate.formula

Generate a cdkFormula object.
remove.property

Remove A Property From a Molecule
matches

Perform Substructure Searching & MCS Detection
get.property

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

Get the names of the available atomic descriptors
write.molecules

Write Molecules To Disk
get.connected.atom

Get the atom connected to an atom in a bond
get.desc.categories

Get Descriptor Class Names
get.total.charge

Get the Total Charge for the Molecule
get.bonds

Get the bonds from a molecule
get.atoms

Get the atoms from a molecule or bond
bpdata

Boiling Point Data
is.connected

Get the Largest Component in a Disconnected Molecule
remove.hydrogens

Remove Hydrogens from a Molecule
cdk.version

Get Current CDK Version
get.smiles.parser

Get a SMILES Parser
get.fingerprint

Evaluate Fingerprints
get.desc.names

Get Descriptor Class Names
set.charge.formula

Set the charge to a cdkFormula object.
eval.desc

Evaluate a Molecular Descriptor
get.smiles

Get the SMILES for a Molecule
get.properties

Get All Property Values of a Molecule
hasNext

Does This Iterator Have A Next Element
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.tpsa

Commonly Used Molecular Descriptors
Molecule

Operations on molecules
get.isotopes.pattern

Generate the isotope pattern.
get.mol2formula

Parser a molecule to formula object.
view.molecule.2d

View 2D Structure Diagrams
get.formula

Get the formula object from a formula character.
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
set.property

Set A Property On A Molecule
view.table

View 2D Structures With Data
get.murcko.fragments

Molecule Fragmentation Methods
load.molecules

Load Molecular Structures From Disk