rcdk: Interface to the CDK Libraries

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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.

Author
Rajarshi Guha [aut, cph], Zachary Charlop-Powers [cre]
Date of publication
2016-11-26 23:39:28
Maintainer
Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
License
LGPL
Version
3.3.8

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