Import of Compounds

SDF Import

The following gives an overview of the most important import/export functionalities for small molecules provided by ChemmineR. The given example creates an instance of the SDFset class using as sample data set the first 100 compounds from this PubChem SD file (SDF): Compound_00650001_00675000.sdf.gz (ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/).

SDFs can be imported with the read.SDFset function:

 sdfset <- read.SDFset("http://faculty.ucr.edu/ tgirke/Documents/R_BioCond/Samples/sdfsample.sdf")

 data(sdfsample) # Loads the same SDFset provided by the library 
 sdfset <- sdfsample
 valid <- validSDF(sdfset) # Identifies invalid SDFs in SDFset objects 
 sdfset <- sdfset[valid] # Removes invalid SDFs, if there are any

Import SD file into SDFstr container:

 sdfstr <- read.SDFstr("http://faculty.ucr.edu/ tgirke/Documents/R_BioCond/Samples/sdfsample.sdf")

Create SDFset from SDFstr class:

 sdfstr <- as(sdfset, "SDFstr") 
 sdfstr

## An instance of "SDFstr" with 100 molecules

 as(sdfstr, "SDFset")

## An instance of "SDFset" with 100 molecules

SMILES Import

The read.SMIset function imports one or many molecules from a SMILES file and stores them in a SMIset container. The input file is expected to contain one SMILES string per row with tab-separated compound identifiers at the end of each line. The compound identifiers are optional.

Create sample SMILES file and then import it:

 data(smisample); smiset <- smisample
 write.SMI(smiset[1:4], file="sub.smi") 
 smiset <- read.SMIset("sub.smi")

Inspect content of SMIset:

 data(smisample) # Loads the same SMIset provided by the library 
 smiset <- smisample
 smiset

## An instance of "SMIset" with 100 molecules

 view(smiset[1:2])

## $`650001`
## An instance of "SMI"
## [1] "O=C(NC1CCCC1)CN(c1cc2OCCOc2cc1)C(=O)CCC(=O)Nc1noc(c1)C"
## 
## $`650002`
## An instance of "SMI"
## [1] "O=c1[nH]c(=O)n(c2nc(n(CCCc3ccccc3)c12)NCCCO)C"

Accessor functions:

 cid(smiset[1:4])

## [1] "650001" "650002" "650003" "650004"

 smi <- as.character(smiset[1:2])

Create SMIset from named character vector:

 as(smi, "SMIset")

## An instance of "SMIset" with 2 molecules