read.SDFindex: Extract Molecules from SD File by Line Index
In girke-lab/ChemmineR-release: Cheminformatics Toolkit for R

Description Usage Arguments Details Value Author(s) References See Also Examples

Extracts specific molecules from SD File based on a line position index computed by the sdfStream function.

1	read.SDFindex(file, index, type = "SDFset", outfile)

`file`	file name of source SD file used to generate `index`
`index`	data frame containing in the first two columns the start and end positions (index) of molecules in an SD File, respectively. Typically, this index would be imported with `read.table/read.delim` from a tabular descriptor file generated by the `sdfStream` function.
`type`	if `type="file"`, the SDF output will be written to a file named as specified under `outfile`; if `type="SDFset"`, the SDF data is collected will be a `SDFset` container.
`outfile`	name of output file when `type="file"`

...

Writes molecules in SDF format to file or collects them in SDFset container.

Thomas Girke

SDF format definition: http://www.symyx.com/downloads/public/ctfile/ctfile.jsp

Import/export functions: read.SDFset, read.SDFstr, read.SDFstr, read.SDFset, write.SDFsplit

## Load sample data
library(ChemmineR)
data(sdfsample); sdfset <- sdfsample
## Not run: write.SDF(sdfset, "test.sdf")

## Define descriptor set in a simple function
desc <- function(sdfset) {
        cbind(SDFID=sdfid(sdfset), 
              # datablock2ma(datablocklist=datablock(sdfset)), 
              MW=MW(sdfset), 
              groups(sdfset), 
              # AP=sdf2ap(sdfset, type="character"),
              rings(sdfset, type="count", upper=6, arom=TRUE)
        )
}

## Run sdfStream with desc function and write results to a file called 'matrix.xls'
sdfStream(input="test.sdf", output="matrix.xls", fct=desc, Nlines=1000)

## Select molecules from SD File using line index from sdfStream
indexDF <- read.delim("matrix.xls", row.names=1)[,1:4]
indexDFsub <- indexDF[indexDF$MW < 400, ] # Selects molecules with MW < 400
sdfset <- read.SDFindex(file="test.sdf", index=indexDFsub, type="SDFset")

## Write result directly to SD file without storing larger numbers of molecules in memory
read.SDFindex(file="test.sdf", index=indexDFsub, type="file", outfile="sub.sdf")

## End(Not run)