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rcdk (version 3.0.5)

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

3.0.5

License

LGPL

Maintainer

Rajarshi Guha

Last Published

November 8th, 2010

Functions in rcdk (3.0.5)

get.isotopes.pattern

Generate the isotope pattern.
get.smiles.parser

Get a SMILES Parser
bpdata

Boiling Point Data
eval.atomic.desc

Evaluate an Atomic Descriptor
generate.formula

Generate a cdkFormula object.
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
eval.desc

Evaluate a Molecular Descriptor
get.property

Get the Value of a Molecule Property
get.desc.categories

Get Descriptor Class Names
view.molecule.2d

View 2D Structure Diagrams
get.murcko.fragments

Molecule Fragmentation Methods
get.fingerprint

Evaluate Fingerprints
get.desc.names

Get Descriptor Class Names
hasNext

Does This Iterator Have A Next Element
is.connected

Get the Largest Component in a Disconnected Molecule
get.connected.atom

Get the atom connected to an atom in a bond
Molecule

Operations on molecules
Atoms

Operations on atoms
get.total.charge

Get the Total Charge for the Molecule
remove.hydrogens

Remove Hydrogens from a Molecule
isvalid.formula

Validate a cdkFormula object.
set.charge.formula

Set the charge to a cdkFormula object.
get.mol2formula

Parser a molecule to formula object.
get.smiles

Get the SMILES for a Molecule
get.atoms

Get the atoms from a molecule or bond
load.molecules

Load Molecular Structures From Disk
cdk.version

Get Current CDK Version
parse.smiles

Parse a Vector of SMILES Strings
matches

Perform Substructure Searching & MCS Detection
get.atomic.desc.names

Get the names of the available atomic descriptors
view.table

View 2D Structures With Data
get.properties

Get All Property Values of a Molecule
write.molecules

Write Molecules To Disk
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
cdkFormula-class

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

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

Set A Property On A Molecule
get.bonds

Get the bonds from a molecule
remove.property

Remove A Property From a Molecule
get.tpsa

Commonly Used Molecular Descriptors