read.AP: Read Atom Pair/Fingerprint Strings

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

View source: R/AllClasses.R

Description

Function to convert atom pairs (AP) or fingerprints (e.g. AP fingerprints) stored as character strings to APset or FPset objects (e.g. generated by sdfStream). Alternatively, one can provide the AP or fingerprint strings in a named character vector.

Usage

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read.AP(x, type, colid, isFile = class(x) == "character" & length(x) == 1)

Arguments

x

name of file from where to read the AP/APFP character strings; or named character vector containing the AP/APFP strings

type

type="ap" for AP character string input, and type="fp" for fingerprint character string input

colid

column containing AP/FP character strings if x is a file

isFile

Is x a file name or not?

Details

...

Value

object of class APset or FPset

Author(s)

Thomas Girke

References

...

See Also

sdf2ap, sdfStream

Examples

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## 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),
              APFP=desc2fp(x=sdf2ap(sdfset), descnames=1024, type="character"), 
              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")

## Read AP/APFP strings from file into APset or FP object
apset <- read.AP(x="matrix.xls", type="ap", colid="AP")
apfp <- read.AP(x="matrix.xls", type="apfp", colid="APFP")

## Alternatively, one can provide the AP/APFP strings in a named character vector
apset <- read.AP(x=sdf2ap(sdfset[1:20], type="character"), type="ap")
apfp <- read.AP(x=desc2fp(x=sdf2ap(sdfset[1:20]), descnames=1024, type="character"), type="apfp")

## End(Not run)

ChemmineR documentation built on Sept. 14, 2017, 2:01 a.m.