FPset-class {ChemmineR} | R Documentation |
"FPset"
Container for storing fingerprints of many compounds. This container is used for structure similarity searching of compounds.
Objects can be created by calls of the form new("FPset", ...)
.
fpma
:Object of class "matrix"
with compound identifiers stored in row names
foldCount
:Object of class "numeric"
type
:Object of class "character"
signature(x = "FPset")
: subsetting of class with bracket operator
signature(x = "FPset")
: returns single component as FP
object
signature(x = "FPset")
: replacement method for several components
signature(x = "FPset")
: returns content as named character vector
signature(x = "FPset")
: returns content as numeric matrix
signature(x = "FPset")
: concatenates any number of FPset
containers
signature(x = "FPset")
: returns all compound identifiers from row names
signature(x = "FPset")
: replacement method for compound identifiers
signature(from = "FPset", to = "FP")
: as(fpset, "FP")
signature(from = "matrix", to = "FPset")
: as(fpma, "FPset")
signature(from = "character", to = "FPset")
: as(fpchar, "FPset")
signature(x = "FPset")
: returns number of entries stored in object
signature(object = "FPset")
: prints summary of FPset
signature(x = "FPset")
: prints extended summary of FPset
signature(x = "FPset")
: fold fingerprint in half
signature(x = "FPset")
: number of times this object has been folded
signature(x = "FPset")
: the type of these fingerprints
signature(x = "FPset")
: the number of bits in these fingerprints
Thomas Girke
Chen X and Reynolds CH (2002). "Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients", in J Chem Inf Comput Sci.
Related classes: SDF, SDFset, SDFstr, AP, APset, FP.
showClass("FPset") ## Instance of FPset class data(apset) (fpset <- desc2fp(apset)) view(fpset) ## Class usage fpset[1:4] # behaves like a list fpset[[1]] # returns FP object length(fpset) # number of compounds cid(fpset) # returns compound ids fpset[1] <- 0 # replacement cid(fpset) <- 1:length(fpset) # replaces compound ids c(fpset[1:4], fpset[11:14]) # concatenation ## Coerce FPset from/to other objects fpma <- as.matrix(fpset) # coerces to matrix fpchar <- as.character(fpset) # coerces to character strings as(fpma, "FPset") as(fpchar, "FPset") ## Compound similarity searching with FPset fpSim(x=fpset[1], y=fpset, method="Tanimoto", cutoff=0.4, top=4)