write.SDF: SDF export function

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

SDF export function

Description

Writes one or many molecules stored in a SDFset, SDFstr or SDF object to SD file.

Usage

write.SDF(sdf, file, cid = FALSE, ...)

Arguments

sdf	object of class SDFset, SDFstr or SDF
file	name of SD file to write to
cid	if cid = TRUE and an SDFset object is provide as input, then the compound IDs in the ID slot of the SDFset are used for compound naming
...	the optional arguments of the sdf2str function can be provided here, including head, ab, bb, db; details are provided in the help page for the sdf2str function

Details

If the write.SDF function is supplied with an SDFset object, then it uses internally the sdf2str function to allow customizing the resulting SD file. For this all optional arguments of the sdf2str function can be passed on to write.SDF.

Author(s)

Thomas Girke

References

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

See Also

Import function: read.SDFset, read.SDFstr

Examples

## Instance of SDFset class
data(sdfsample); sdfset <- sdfsample

## Write objects of classes SDFset/SDFstr/SDF to file
# write.SDF(sdfset[1:4], file="sub.sdf")

## Example for writing customized SDFset to file containing
## ChemmineR signature, IDs from SDFset and no data block
# write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE, db=NULL)

## Example for injecting a custom matrix/data frame into the data block of an
## SDFset and then writing it to an SD file
props <- data.frame(MF=MF(sdfset), MW=MW(sdfset), atomcountMA(sdfset))
datablock(sdfset) <- props
view(sdfset[1:4])
# write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE)

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