read.AP {ChemmineR} | R Documentation |
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.
read.AP(x, type, colid, isFile = class(x) == "character" & length(x) == 1)
x |
name of file from where to read the AP/APFP character strings; or named character vector containing the AP/APFP strings |
type |
|
colid |
column containing AP/FP character strings if |
isFile |
Is |
...
object of class APset
or FPset
Thomas Girke
...
sdf2ap
, sdfStream
## 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)