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rcdk (version 3.1.3)

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

3.1.3

License

LGPL

Maintainer

Rajarshi Guha

Last Published

August 11th, 2011

Functions in rcdk (3.1.3)

isvalid.formula

Validate a cdkFormula object.
hasNext

Does This Iterator Have A Next Element
get.tpsa

Commonly Used Molecular Descriptors
Molecule

Operations on molecules
view.molecule.2d

View and Copy 2D Structure Diagrams
set.charge.formula

Set the charge to a cdkFormula object.
generate.formula

Generate a cdkFormula object.
cdk.version

Get Current CDK Version
get.murcko.fragments

Molecule Fragmentation Methods
get.fingerprint

Evaluate Fingerprints
get.smiles

Get the SMILES for a Molecule
remove.property

Remove A Property From a Molecule
Atoms

Operations on atoms
is.connected

Get the Largest Component in a Disconnected Molecule
get.desc.names

Get Descriptor Class Names
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
get.total.charge

Get the Total Charges for the Molecule
get.atoms

Get the atoms from a molecule or bond
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
matches

Perform Substructure Searching & MCS Detection
get.bonds

Get the bonds from a molecule
eval.desc

Evaluate a Molecular Descriptor
view.table

View 2D Structures With Data
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.desc.categories

Get Descriptor Class Names
get.isotopes.pattern

Generate the isotope pattern.
parse.smiles

Parse a Vector of SMILES Strings
get.formula

Get the formula object from a formula character.
load.molecules

Load Molecular Structures From Disk
write.molecules

Write Molecules To Disk
get.connected.atom

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

Get the Value of a Molecule Property
remove.hydrogens

Remove Hydrogens from a Molecule
get.properties

Get All Property Values of a Molecule
get.smiles.parser

Get a SMILES Parser
eval.atomic.desc

Evaluate an Atomic Descriptor
get.atomic.desc.names

Get the names of the available atomic descriptors
get.mol2formula

Parser a molecule to formula object.
set.property

Set A Property On A Molecule
bpdata

Boiling Point Data