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rcdk (version 3.1.4)

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

3.1.4

License

LGPL

Maintainer

Rajarshi Guha

Last Published

November 2nd, 2011

Functions in rcdk (3.1.4)

get.total.charge

Get the Total Charges for the Molecule
get.atoms

Get the atoms from a molecule or bond
get.murcko.fragments

Molecule Fragmentation Methods
matches

Perform Substructure Searching & MCS Detection
bpdata

Boiling Point Data
Molecule

Operations on molecules
get.property

Get the Value of a Molecule Property
cdk.version

Get Current CDK Version
parse.smiles

Parse a Vector of SMILES Strings
generate.formula

Generate a cdkFormula object.
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
set.charge.formula

Set the charge to a cdkFormula object.
get.smiles

Get the SMILES for a Molecule
get.smiles.parser

Get a SMILES Parser
get.desc.categories

Get Descriptor Class Names
view.molecule.2d

View and Copy 2D Structure Diagrams
eval.desc

Evaluate a Molecular Descriptor
is.connected

Get the Largest Component in a Disconnected Molecule
view.table

View 2D Structures With Data
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
get.tpsa

Commonly Used Molecular Descriptors
get.formula

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

Load Molecular Structures From Disk
hasNext

Does This Iterator Have A Next Element
get.bonds

Get the bonds from a molecule
isvalid.formula

Validate a cdkFormula object.
cdkFormula-class

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

Get the names of the available atomic descriptors
set.property

Set A Property On A Molecule
get.properties

Get All Property Values of a Molecule
get.fingerprint

Evaluate Fingerprints
get.mol2formula

Parser a molecule to formula object.
Atoms

Operations on atoms
remove.property

Remove A Property From a Molecule
get.connected.atom

Get the atom connected to an atom in a bond
get.isotopes.pattern

Generate the isotope pattern.
remove.hydrogens

Remove Hydrogens from a Molecule
write.molecules

Write Molecules To Disk
get.desc.names

Get Descriptor Class Names
eval.atomic.desc

Evaluate an Atomic Descriptor