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.

Install the latest version of this package by entering the following in R:
install.packages("rcdk")
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

Functions

bpdata Man page
cdkFormula-class Man page
cdk.version Man page
charge Man page
convert.implicit.to.explicit Man page
copy.image.to.clipboard Man page
depict Man page
do.aromaticity Man page
do.isotopes Man page
do.typing Man page
eval.atomic.desc Man page
eval.desc Man page
fragment Man page
generate.2d.coordinates Man page
generate.formula Man page
get.alogp Man page
get.atom.count Man page
get.atomic.desc.names Man page
get.atomic.number Man page
get.atom.index Man page
get.atoms Man page
get.bonds Man page
get.charge Man page
get.connected.atom Man page
get.connected.atoms Man page
get.desc.categories Man page
get.desc.names Man page
get.exact.mass Man page
get.exhaustive.fragments Man page
get.fingerprint Man page
get.formal.charge Man page
get.formula Man page
get.hydrogen.count Man page
get.isotopes.pattern Man page
get.largest.component Man page
get.mcs Man page
get.mol2formula Man page
get.murcko.fragments Man page
get.natural.mass Man page
get.point2d Man page
get.point3d Man page
get.properties Man page
get.property Man page
get.smiles Man page
get.smiles.parser Man page
get.symbol Man page
get.title Man page
get.total.charge Man page
get.total.formal.charge Man page
get.total.hydrogen.count Man page
get.tpsa Man page
get.volume Man page
get.xlogp Man page
hasNext Man page
hasNext.iload.molecules Man page
iload.molecules Man page
is.aliphatic Man page
is.aromatic Man page
is.connected Man page
is.in.ring Man page
is.neutral Man page
is.subgraph Man page
isvalid.formula Man page
load.molecules Man page
match Man page
matches Man page
mcs Man page
parse.smiles Man page
remove.hydrogens Man page
remove.property Man page
set.charge.formula Man page
set.property Man page
show,cdkFormula-method Man page
smarts Man page
substructure Man page
view.image.2d Man page
view.molecule.2d Man page
view.table Man page
write.molecules Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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