SMIset-class {ChemmineR} | R Documentation |
"SMIset"
List-like container for storing SMILES strings of many compounds.
Objects can be created by calls of the form new("SMIset", ...)
.
smilist
:Object of class "list"
with compound identifiers stored in name slots
signature(x = "SMIset")
: subsetting of class with bracket operator
signature(x = "SMIset")
: returns single component as SMI
object
signature(x = "SMIset")
: replacement method for one or many entries
signature(x = "SMIset")
: returns content as named character vector
signature(x = "SMIset")
: concatenates two SMIset
containers
signature(x = "SMIset")
: returns compound identifiers
signature(x = "SMIset")
: replacement method for compound identifiers
signature(from = "character", to = "SMIset")
: as(character, "SMIset")
signature(from = "list", to = "SMIset")
: as(list, "SMIset")
signature(from = "SMIset", to = "SMI")
: as(smiset, "SMI")
signature(x = "SMIset")
: returns number of entries stored in object
signature(object = "SMIset")
: prints summary of SMIset
signature(x = "SMIset")
: prints extended summary of SMIset
Thomas Girke
SMILES (Simplified molecular-input line-entry system) format definition: http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
Related classes: SMI, SDF, SDFset
Import function: read.SMIset("some_SMILES_file")
Export function: write.SMI(smiset, "some_file.smi")
showClass("SMIset") ## Instances of SMIset class data(smisample); smiset <- smisample smiset; view(smiset[1:4]) smiset[[1]] ## Import and store SMILES file in SMIset container # smiset <- read.SMIset("some_SMILES_file") ## Miscellaneous accessor methods cid(smiset[1:4]) (smivec <- as.character(smiset[1:4])) ## Construct SMIset from named vector as(smivec, "SMIset") ## Assigning compound IDs and keeping them unique unique_ids <- makeUnique(cid(smiset)) cid(smiset) <- unique_ids ## Export SMIset to SMILES file # write.SMI(smiset[1:4], file="sub.smi", cid=TRUE)