rrdkit

A pragmatic interface to RDKit (C++ API) from R.

rrdkit package provides a pragmatic interface to some of the RDKit functions in R. It is intended to work smoothly with R. rrdkit aims to be a tool to perform basic operations from RDKit. If you are looking for a more richer tool check RDKit web site.

Prerequisites

• R >= 3.2.0

• R Packages: Rcpp, testthat, XML.

• A RDKit installation. Preferably use latest RDKit version ( Latest Tested rdkit-Release_2016_03_1 ). Follow the instuctions in http://www.rdkit.org/docs/Install.html). Check "Building the RDKit" section.

• Note that Python wrappers can be disabled (optional) and InChI support must be enabled:

  
  cmake -D RDK_BUILD_PYTHON_WRAPPERS= -D RDK_BUILD_INCHI_SUPPORT=ON ..

* RDBASE (the root directory of the RDKit distribution  e.g. ~/RDKit  ) configured. 

* LD_LIBRARY_PATH must include $RDBASE/build/lib.

## Installation

* with devtools

library(devtools) install_github("pauca/rrdkit/rrdkit")

## Examples of usage

library(rrdkit)
mols1 <- read.sdf(system.file("extdata/aspirine.sdf", package="rrdkit"))
mols2 <- read.sdf(system.file("extdata/clozapine.sdf", package="rrdkit"))
mols <- c(mols1,mols2) mol2mw(mols) showMols(mols)

inchi <- mol2Inchi(mols)
Inchi2InchiKey(inchi)

## Functions

### Read and Write

read.sdf( file )
write.sdf( file , mols )

Read a smi file as data frame:

read.smi(file)

smiles2mol( smile )
smarts2mol( smart )

mol2smiles( mol )

### Changing Properties

molsGetProps( mols )
molsSetProp ( mols ,key , values )

### Molecule viewers 

Next functions open a browser with a 2D representation of the molecules.

showMols(mols)
showMolsGrid(mols)
mol2svg(mols)
compute2D(mols)

mols <- smiles2mol(c("CC(=O)NC1=CC=C(O)C=C1","CC(=O)OC1=CC=CC=C1C(O)=O")) df <- data.frame(id=c(1,2),names=c("Paracetamol", "Aspirin"),mw=mol2mw(mols)) showMolsDF(mols,df)

### Descriptors

mol2maccs(mol)
mol2morgan(mol)
mol2mw(mol)
mol2TPSA(mol)
mol2LogP(mol)
mol2murcko(mol)
computeGasteigerCharges(mol)

### Others

SubstructMatch( mol , query )