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rcdk (version 3.1.20.1)

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

3.1.20.1

License

LGPL

Maintainer

Rajarshi Guha

Last Published

September 1st, 2012

Functions in rcdk (3.1.20.1)

Atoms

Operations on atoms
get.connected.atom

Get the atom connected to an atom in a bond
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
write.molecules

Write Molecules To Disk
isvalid.formula

Validate a cdkFormula object.
get.formula

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

Load Molecular Structures From Disk
view.table

View 2D Structures With Data
get.atoms

Get the atoms from a molecule or bond
hasNext

Does This Iterator Have A Next Element
matches

Perform Substructure Searching & MCS Detection
bpdata

Boiling Point Data
get.tpsa

Commonly Used Molecular Descriptors
get.property

Get the Value of a Molecule Property
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
get.murcko.fragments

Molecule Fragmentation Methods
get.smiles.parser

Get a SMILES Parser
get.isotopes.pattern

Generate the isotope pattern.
remove.hydrogens

Remove Hydrogens from a Molecule
is.connected

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

Get Descriptor Class Names
get.desc.names

Get Descriptor Class Names
parse.smiles

Parse a Vector of SMILES Strings
remove.property

Remove A Property From a Molecule
generate.formula

Generate a cdkFormula object.
get.mol2formula

Parser a molecule to formula object.
get.total.charge

Get the Total Charges for the Molecule
Molecule

Operations on molecules
get.atomic.desc.names

Get the names of the available atomic descriptors
cdkFormula-class

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

Evaluate Fingerprints
cdk.version

Get Current CDK Version
get.properties

Get All Property Values of a Molecule
eval.desc

Evaluate a Molecular Descriptor
eval.atomic.desc

Evaluate an Atomic Descriptor
get.bonds

Get the bonds from a molecule
get.smiles

Get the SMILES for a Molecule
set.charge.formula

Set the charge to a cdkFormula object.
view.molecule.2d

View and Copy 2D Structure Diagrams
set.property

Set A Property On A Molecule