rcdk: Interface to the CDK Libraries

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.

AuthorRajarshi Guha [aut, cph], Zachary Charlop-Powers [cre]
Date of publication2016-11-26 23:39:28
MaintainerZachary Charlop-Powers <zach.charlop.powers@gmail.com>
LicenseLGPL
Version3.3.8

View on CRAN

Man pages

atomcontainer: Operations on molecules

atoms: Operations on atoms

bpdata: Boiling Point Data

cdkFormula-class: Class cdkFormula, a class for handling molecular formula

cdkversion: Get Current CDK Version

evalatomicdesc: Evaluate an Atomic Descriptor

evaldesc: Evaluate a Molecular Descriptor

frags: Molecule Fragmentation Methods

generateformula: Generate a cdkFormula object.

get2dcoords: Generate 2D Coordinates from Connectivity Information

getatomdescnames: Get the names of the available atomic descriptors

getatoms: Get the atoms from a molecule or bond

getbonds: Get the bonds from a molecule

getconatom: Get the atom connected to an atom in a bond

getdesccat: Get Descriptor Class Names

getdescnames: Get Descriptor Class Names

getformula: Get the formula object from a formula character.

getfp: Evaluate Fingerprints

gethcount: Get the Total Hydrogen Count for a Molecule

getisotopepattern: Generate the isotope pattern.

getlargestcomp: Get the Largest Component in a Disconnected Molecule

getmol2formula: Parser a molecule to formula object.

getproperty: Get the Value of a Molecule Property

getprops: Get All Property Values of a Molecule

getsmiles: Get the SMILES for a Molecule

getsmilesparser: Get a SMILES Parser

gettotalcharge: Get the Total Charges for the Molecule

hasNext: Does This Iterator Have A Next Element

isvalidformula: Validate a cdkFormula object.

loadmol: Load Molecular Structures From Disk

match: Perform Substructure Searching & MCS Detection

ops: Perform Aromaticity Detection, atom typing or isotopic...

parsesmiles: Parse a Vector of SMILES Strings

props: Commonly Used Molecular Descriptors

removehydrogens: Remove Hydrogens from a Molecule

removeproperty: Remove A Property From a Molecule

setchargeformula: Set the charge to a cdkFormula object.

setproperty: Set A Property On A Molecule

viewmol2d: View and Copy 2D Structure Diagrams

viewtable: View 2D Structures With Data

writemols: Write Molecules To Disk

Files in this package

rcdk
rcdk/inst
rcdk/inst/CITATION
rcdk/inst/doc
rcdk/inst/doc/rcdk.Rnw
rcdk/inst/doc/rcdk.pdf
rcdk/inst/doc/rcdk.R
rcdk/inst/cont
rcdk/inst/cont/rcdk.jar
rcdk/inst/cont/com.objectplanet.image.PngEncoder.jar
rcdk/inst/unitTests
rcdk/inst/unitTests/Makefile
rcdk/inst/unitTests/runit.frags.R
rcdk/inst/unitTests/runit.visual.R
rcdk/inst/unitTests/runit.smiles.R
rcdk/inst/unitTests/runit.depiction.R
rcdk/inst/unitTests/runit.atoms.R
rcdk/inst/unitTests/runit.rcdk.R
rcdk/inst/unitTests/runit.props.R
rcdk/inst/unitTests/runit.match.R
rcdk/tests
rcdk/tests/doRUnit.R
rcdk/NAMESPACE
rcdk/CHANGELOG
rcdk/NEWS
rcdk/data
rcdk/data/bpdata.RData
rcdk/R
rcdk/R/smsd.R rcdk/R/atoms.R rcdk/R/iterating.R rcdk/R/formula.R rcdk/R/visual.R rcdk/R/smiles.R rcdk/R/props.R rcdk/R/frags.R rcdk/R/desc.R rcdk/R/io.R rcdk/R/bonds.R rcdk/R/fingerprint.R rcdk/R/matching.R rcdk/R/rcdk.R
rcdk/vignettes
rcdk/vignettes/rcdk.Rnw
rcdk/MD5
rcdk/java
rcdk/java/README
rcdk/build
rcdk/build/vignette.rds
rcdk/DESCRIPTION
rcdk/man
rcdk/man/viewmol2d.Rd rcdk/man/viewtable.Rd rcdk/man/match.Rd rcdk/man/removehydrogens.Rd rcdk/man/removeproperty.Rd rcdk/man/parsesmiles.Rd rcdk/man/generateformula.Rd rcdk/man/gethcount.Rd rcdk/man/getatomdescnames.Rd rcdk/man/getlargestcomp.Rd rcdk/man/cdkversion.Rd rcdk/man/setproperty.Rd rcdk/man/getatoms.Rd rcdk/man/writemols.Rd rcdk/man/evaldesc.Rd rcdk/man/props.Rd rcdk/man/getmol2formula.Rd rcdk/man/gettotalcharge.Rd rcdk/man/getproperty.Rd rcdk/man/getfp.Rd rcdk/man/isvalidformula.Rd rcdk/man/ops.Rd rcdk/man/loadmol.Rd rcdk/man/getformula.Rd rcdk/man/frags.Rd rcdk/man/bpdata.Rd rcdk/man/evalatomicdesc.Rd rcdk/man/getsmiles.Rd rcdk/man/getconatom.Rd rcdk/man/hasNext.Rd rcdk/man/getbonds.Rd rcdk/man/getprops.Rd rcdk/man/getisotopepattern.Rd rcdk/man/get2dcoords.Rd rcdk/man/getdesccat.Rd rcdk/man/getsmilesparser.Rd rcdk/man/atoms.Rd rcdk/man/atomcontainer.Rd rcdk/man/getdescnames.Rd rcdk/man/setchargeformula.Rd rcdk/man/cdkFormula-class.Rd

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