Export of Compounds

SDF Export

Write objects of classes SDFset/SDFstr/SDF to SD file:

 write.SDF(sdfset[1:4], file="sub.sdf")

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
 write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE)

Indirect export via SDFstr object:

 sdf2str(sdf=sdfset[[1]], sig=TRUE, cid=TRUE) # Uses default components 
 sdf2str(sdf=sdfset[[1]], head=letters[1:4], db=NULL) # Uses custom components for header and data block

Write SDF, SDFset or SDFstr classes to file:

 write.SDF(sdfset[1:4], file="sub.sdf", sig=TRUE, cid=TRUE, db=NULL)
 write.SDF(sdfstr[1:4], file="sub.sdf") 
 cat(unlist(as(sdfstr[1:4], "list")), file="sub.sdf", sep="")

SMILES Export

Write objects of class SMIset to SMILES file with and without compound identifiers:

 data(smisample); smiset <- smisample # Sample data set 

 write.SMI(smiset[1:4], file="sub.smi", cid=TRUE) write.SMI(smiset[1:4], file="sub.smi", cid=FALSE)