Learn R Programming
⚠️There's a newer version (3.8.2) of this package.Take me there.

rcdk (version 3.0.4)

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.

Copy Link

Version

Install

install.packages('rcdk')

Monthly Downloads

2,414

Version

3.0.4

License

LGPL

Maintainer

Rajarshi Guha

Last Published

October 23rd, 2010

Functions in rcdk (3.0.4)

get.desc.names

Get Descriptor Class Names
write.molecules

Write Molecules To Disk
load.molecules

Load Molecular Structures From Disk
cdkFormula-class

Class cdkFormula, a class for handling molecular formula
get.total.charge

Get the Total Charge for the Molecule
get.property

Get the Value of a Molecule Property
generate.formula

Generate a cdkFormula object.
get.atoms

Get the atoms from a molecule or bond
parse.smiles

Parse a Vector of SMILES Strings
get.bonds

Get the bonds from a molecule
get.isotopes.pattern

Generate the isotope pattern.
get.mol2formula

Parser a molecule to formula object.
remove.property

Remove A Property From a Molecule
set.charge.formula

Set the charge to a cdkFormula object.
get.murcko.fragments

Molecule Fragmentation Methods
get.formula

Get the formula object from a formula character.
cdk.version

Get Current CDK Version
Atoms

Operations on atoms
is.connected

Get the Largest Component in a Disconnected Molecule
view.molecule.2d

View 2D Structure Diagrams
eval.atomic.desc

Evaluate an Atomic Descriptor
isvalid.formula

Validate a cdkFormula object.
get.fingerprint

Evaluate Fingerprints
eval.desc

Evaluate a Molecular Descriptor
Molecule

Operations on molecules
get.smiles

Get the SMILES for a Molecule
get.smiles.parser

Get a SMILES Parser
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
get.desc.categories

Get Descriptor Class Names
matches

Perform Substructure Searching & MCS Detection
set.property

Set A Property On A Molecule
hasNext

Does This Iterator Have A Next Element
bpdata

Boiling Point Data
view.table

View 2D Structures With Data
get.tpsa

Commonly Used Molecular Descriptors
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
get.properties

Get All Property Values of a Molecule
get.atomic.desc.names

Get the names of the available atomic descriptors
remove.hydrogens

Remove Hydrogens from a Molecule
get.connected.atom

Get the atom connected to an atom in a bond