FPset-class: Class '"FPset"'

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Class "FPset"

Description

Container for storing fingerprints of many compounds. This container is used for structure similarity searching of compounds.

Objects from the Class

Objects can be created by calls of the form new("FPset", ...).

Slots

fpma:

Object of class "matrix" with compound identifiers stored in row names

foldCount:

Object of class "numeric"

type:

Object of class "character"

Methods

[

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

as.character

signature(x = "FPset"): returns content as named character vector

as.matrix

signature(x = "FPset"): returns content as numeric matrix

c

signature(x = "FPset"): concatenates any number of FPset containers

cid

signature(x = "FPset"): returns all compound identifiers from row names

cid<-

signature(x = "FPset"): replacement method for compound identifiers

coerce

signature(from = "FPset", to = "FP"): as(fpset, "FP")

coerce

signature(from = "matrix", to = "FPset"): as(fpma, "FPset")

coerce

signature(from = "character", to = "FPset"): as(fpchar, "FPset")

length

signature(x = "FPset"): returns number of entries stored in object

show

signature(object = "FPset"): prints summary of FPset

view

signature(x = "FPset"): prints extended summary of FPset

fold

signature(x = "FPset"): fold fingerprint in half

foldCount

signature(x = "FPset"): number of times this object has been folded

fptype

signature(x = "FPset"): the type of these fingerprints

numBits

signature(x = "FPset"): the number of bits in these fingerprints

Author(s)

Thomas Girke

References

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.

See Also

Related classes: SDF, SDFset, SDFstr, AP, APset, FP.

Examples

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) 

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