The CDK Libraries Packaged for R

An R interface to the Chemistry Development Kit, a Java library for chemoinformatics. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the 'rcdk' package. Note that it is possible to directly interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from < https://github.com/cdk/cdk>.

rcdklibs

The goal of rcdklibs is to provide the CDK jarfiles and thereby facilitate chemoinformatic analysis within the R ecosystem. The primary consumer of rcdklibs is the rcdk package but all of CDK’s functionality can be accessed by the standard rJava API. The libs provided in this release correspond to the 2.9 Release

# Example
library(rcdklibs)

# atm_container class
atm_container <- J("org/openscience/cdk/AtomContainer")

# instance of class
ac1 <- new(atm_container)

# call method (reflective). slow but easy to program/use.
ac1$atoms()

# call method example (static). Cumbersome to program but needed for Java speed.
.jcall(atom, "Ljavax/vecmath/Point3d;", "getPoint3d")

Installation

You can install the released version of rcdklibs from CRAN with:

install.packages("rcdklibs")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("https://github.com/CDK-R/rcdklibs")