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rcdk (version 3.4.7)

Interface to the 'CDK' Libraries

Description

Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. 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

3.4.7

License

LGPL

Maintainer

Zachary CharlopPowers

Last Published

April 30th, 2018

Functions in rcdk (3.4.7)

get.connection.matrix

Get connection matrix for a molecule.
get.isotope.pattern.generator

Construct an isotope pattern generator.
get.total.hydrogen.count

Get the Total Hydrogen Count for a Molecule
get.isotopes.pattern

Generate the isotope pattern.
is.connected

Get the Largest Component in a Disconnected Molecule
load.molecules

Load Molecular Structures From Disk
parse.smiles

Parse a Vector of SMILES Strings
get.mol2formula

Parser a molecule to formula object.
get.tpsa

Commonly Used Molecular Descriptors
isvalid.formula

Validate a cdkFormula object.
do.aromaticity

Perform Aromaticity Detection, atom typing or isotopic configuration
hasNext

Does This Iterator Have A Next Element
get.total.charge

Get the Total Charges for the Molecule
matches

Perform Substructure Searching & MCS Detection
get.desc.names

Get Descriptor Class Names
set.charge.formula

Set the charge to a cdkFormula object.
get.desc.categories

Get Descriptor Class Names
remove.hydrogens

Remove Hydrogens from a Molecule
remove.property

Remove A Property From a Molecule
set.property

Set A Property On A Molecule
get.bonds

Get the bonds from a molecule
get.formula

Get the formula object from a formula character.
get.connected.atom

Get the atom connected to an atom in a bond
smiles.flavors

Generate flag for customizing SMILES generation.
get.fingerprint

Evaluate Fingerprints
get.property

Get the Value of a Molecule Property
get.smiles

Get the SMILES for a Molecule
get.smiles.parser

Get a SMILES Parser
get.properties

Get All Property Values of a Molecule
view.molecule.2d

View and Copy 2D Structure Diagrams
view.table

View 2D Structures With Data
write.molecules

Write Molecules To Disk
compare.isotope.pattern

Compare isotope patterns.
generate.formula

Generate molecular formulae given a target mass and a set of elements and counts.
get.murcko.fragments

Molecule Fragmentation Methods
bpdata

Boiling Point Data
cdk.version

Get Current CDK Version
Molecule

Operations on molecules
cdkFormula-class

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

Identify which atoms are stereocenters.
generate.2d.coordinates

Generate 2D Coordinates from Connectivity Information
get.adjacency.matrix

Get adjacency matrix for a molecule.
Atoms

Operations on atoms
eval.atomic.desc

Evaluate an Atomic Descriptor
eval.desc

Evaluate a Molecular Descriptor
get.element.types

Obtain the type of stereo element support for atom.
get.stereo.types

Obtain the stereocenter type for atom.
get.isotope.pattern.similarity

Construct an isotope pattern similarity calculator.
get.atomic.desc.names

Get the names of the available atomic descriptors
get.atoms

Get the atoms from a molecule or bond