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rcdk (version 3.1.8.1)

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

1,511

Version

3.1.8.1

License

LGPL

Maintainer

Rajarshi Guha

Last Published

June 20th, 2012

Functions in rcdk (3.1.8.1)

generate.formula

Generate a cdkFormula object.
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.isotopes.pattern

Generate the isotope pattern.
hasNext

Does This Iterator Have A Next Element
cdk.version

Get Current CDK Version
get.murcko.fragments

Molecule Fragmentation Methods
get.formula

Get the formula object from a formula character.
remove.property

Remove A Property From a Molecule
eval.desc

Evaluate a Molecular Descriptor
get.tpsa

Commonly Used Molecular Descriptors
do.aromaticity

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

Load Molecular Structures From Disk
matches

Perform Substructure Searching & MCS Detection
bpdata

Boiling Point Data
set.charge.formula

Set the charge to a cdkFormula object.
Molecule

Operations on molecules
get.mol2formula

Parser a molecule to formula object.
get.desc.categories

Get Descriptor Class Names
get.fingerprint

Evaluate Fingerprints
view.table

View 2D Structures With Data
get.properties

Get All Property Values of a Molecule
get.connected.atom

Get the atom connected to an atom in a bond
isvalid.formula

Validate a cdkFormula object.
eval.atomic.desc

Evaluate an Atomic Descriptor
get.smiles

Get the SMILES for a Molecule
get.atomic.desc.names

Get the names of the available atomic descriptors
remove.hydrogens

Remove Hydrogens from a Molecule
get.property

Get the Value of a Molecule Property
get.smiles.parser

Get a SMILES Parser
get.total.charge

Get the Total Charges for the Molecule
write.molecules

Write Molecules To Disk
Atoms

Operations on atoms
get.atoms

Get the atoms from a molecule or bond
set.property

Set A Property On A Molecule
view.molecule.2d

View and Copy 2D Structure Diagrams
parse.smiles

Parse a Vector of SMILES Strings
get.desc.names

Get Descriptor Class Names
is.connected

Get the Largest Component in a Disconnected Molecule
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
get.bonds

Get the bonds from a molecule