read.SDFset: SD file to 'SDFset'

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

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. When set to TRUE, the resulting objects will be of type ExtSDF, which is a sub-class of SDF. However, some functions, such as plot, may not work with this type right now.

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) 

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.