read.SDFset {ChemmineR} | R Documentation

## SD file to `SDFset`

### Description

Imports one or many molecules from an SD/MOL file and stores it in an `SDFset` container. Supports both the V2000 and V3000 formats.

### Usage

    read.SDFset(sdfstr = sdfstr,skipErrors=FALSE, ...)

### Arguments

`sdfstr` | path/name to an SD file; alternatively an `SDFstr` object can be provided
`skipErrors` | If true, molecules which fail to parse will be removed from the output. Otherwise and error will be thrown and processing of the input will stop.
`...` | option to pass on additional arguments. Possible arguments are: datablock: true or false, whether to include the data fields or not. Defaults to TRUE. tail2vec: true or false, whether to return data feilds as a vector or not. Defaults to TRUE. extendedAttributes: true or false, whether to parse the extended attributes available on the V3000 format. Defaults to FALSE.

### Details

...

### Value

`SDFset` | for details see ?"SDFset-class"

### Author(s)

Thomas Girke

### References

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

### See Also

Functions: `read.SDFstr`

### Examples

    ## Write instance of SDFset class to SD file
    data(sdfsample); sdfset <- sdfsample
    # write.SDF(sdfset[1:4], file="sub.sdf")

    ## Import SD file
    # read.SDFset("sub.sdf")

    ## Pass on SDFstr object
    sdfstr <- as(sdfset, "SDFstr")
    read.SDFset(sdfstr)

[Package ChemmineR version 3.36.0 Index]