README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# rcdklibs

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The goal of rcdklibs is to provide the [CDK](https://github.com/cdk/cdk) jarfiles
and thereby facilitate chemoinformatic analysis within the R ecosystem. The 
primary consumer of `rcdklibs` is the [rcdk](https://github.com/CDK-R/cdkr) package
but all of CDK's functionality can be accessed by the standard [rJava]( https://CRAN.R-project.org/package=rJava)
API. The libs provided in this release correspond to the [2.9 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9)


```
# 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](https://CRAN.R-project.org) with:

``` r
install.packages("rcdklibs")
```

And the development version from [GitHub](https://github.com/) with:

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