Several methods are available to return the different data components of SDF/SDFset containers in batches. The following examples list the most important ones. To save space their content is not printed in the manual.

 view(sdfset[1:4]) # Summary view of several molecules 

 length(sdfset) # Returns number of molecules 
 sdfset[[1]] # Returns single molecule from SDFset as SDF object 

 sdfset[[1]][[2]] # Returns atom block from first compound as matrix

 sdfset[[1]][[2]][1:4,] 
 c(sdfset[1:4], sdfset[5:8]) # Concatenation of several SDFsets

The grepSDFset function allows string matching/searching on the different data components in SDFset. By default the function returns a SDF summary of the matching entries. Alternatively, an index of the matches can be returned with the setting mode="index".

 grepSDFset("650001", sdfset, field="datablock", mode="subset") # To return index, set mode="index")

Utilities to maintain unique compound IDs:

 sdfid(sdfset[1:4]) # Retrieves CMP IDs from Molecule Name field in header block. 
 cid(sdfset[1:4]) # Retrieves CMP IDs from ID slot in SDFset. 
 unique_ids <- makeUnique(sdfid(sdfset)) # Creates unique IDs by appending a counter to duplicates. 
 cid(sdfset) <- unique_ids # Assigns uniquified IDs to ID slot

Subsetting by character, index and logical vectors:

 view(sdfset[c("650001", "650012")])
 view(sdfset[4:1])
 mylog <- cid(sdfset)
 view(sdfset[mylog])

Accessing SDF/SDFset components: header, atom, bond and data blocks:

 atomblock(sdf); sdf[[2]];
 sdf[["atomblock"]] # All three methods return the same component

 header(sdfset[1:4]) 
 atomblock(sdfset[1:4])
 bondblock(sdfset[1:4]) 
 datablock(sdfset[1:4])  
 header(sdfset[[1]])
 atomblock(sdfset[[1]]) 
 bondblock(sdfset[[1]]) 
 datablock(sdfset[[1]])

Replacement Methods:

 sdfset[[1]][[2]][1,1] <- 999 
 atomblock(sdfset)[1] <- atomblock(sdfset)[2] 
 datablock(sdfset)[1] <- datablock(sdfset)[2]

Assign matrix data to data block:

 datablock(sdfset) <- as.matrix(iris[1:100,])
 view(sdfset[1:4])

Class coercions from SDFstr to list, SDF and SDFset:

 as(sdfstr[1:2], "list") as(sdfstr[[1]], "SDF")
 as(sdfstr[1:2], "SDFset")

Class coercions from SDF to SDFstr, SDFset, list with SDF sub-components:

 sdfcomplist <- as(sdf, "list") sdfcomplist <-
 as(sdfset[1:4], "list"); as(sdfcomplist[[1]], "SDF") sdflist <-
 as(sdfset[1:4], "SDF"); as(sdflist, "SDFset") as(sdfset[[1]], "SDFstr")
 as(sdfset[[1]], "SDFset")

Class coercions from SDFset to lists with components consisting of SDF or sub-components:

 as(sdfset[1:4], "SDF") as(sdfset[1:4], "list") as(sdfset[1:4], "SDFstr")