rcdk: Interface to the CDK Libraries
Version 3.3.8

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.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rcdk")

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

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
rcdk documentation built on May 29, 2017, 9:54 p.m.