APset-class {ChemmineR} | R Documentation

## Class "APset"

### Description

List-like container for storing the atom pair descriptors of a many compounds as objects of class `AP`. This container is used for structure similarity searching of compounds.

### Objects from the Class

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

### Slots

`AP`:

  Object of class `"list"`

`ID`:

  Object of class `"character"`

### Methods

[

  `signature(x = "APset")`: subsetting of class with bracket operator

[[

  `signature(x = "APset")`: returns single component as `AP` object

[[<-

  `signature(x = "APset")`: replacement method for single `AP` component

[<-

  `signature(x = "APset")`: replacement method for several `AP` components

ap

  `signature(x = "APset")`: returns atom pair list from AP slot

c

  `signature(x = "APset")`: concatenates two `APset` containers

cid

  `signature(x = "APset")`: returns all compound identifiers from ID slot

cid<-

  `signature(x = "APset")`: replacement method for compound identifiers in ID slot

coerce

  `signature(from = "APset", to = "AP")`: `as(apset, "AP")`

coerce

  `signature(from = "APset", to = "list")`: `as(apset, "list")`

coerce

  `signature(from = "list", to = "APset")`: `as(list, "APset")`

length

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

show

  `signature(object = "APset")`: prints summary of `APset`

view

  `signature(x = "APset")`: prints extended summary of `APset`

### 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, FPset, FP.

Functions: `SDF2apcmp`, `apset2descdb`, `cmp.search`, `cmp.similarity`

### Examples

    showClass("APset")

    ## Instance of SDFset class
    data(sdfsample)
    sdfset <- sdfsample[1:50]
    sdf <- sdfsample[[1]]

    ## Compute atom pair library
    ap <- sdf2ap(sdf)
    (apset <- sdf2ap(sdfset))
    view(apset[1:4])

    ## Return main components of APset object
    cid(apset[1:4]) # compound IDs
    ap(apset[1:4]) # atom pair descriptors

    ## Return atom pairs in human readable format
    db.explain(apset[1])

    ## Coerce APset to other objects
    apset2descdb(apset) # returns old list-style AP database
    tmp <- as(apset, "list") # returns list
    as(tmp, "APset") # converst list back to APset

    ## Compound similarity searching with APset
    cmp.search(apset, apset[1], type=3, cutoff=0.2)
    plot(sdfset[names(cmp.search(apset, apset[6], type=2, cutoff=0.4))])

    ## Identify compounds with identical AP sets
    cmp.duplicated(apset, type=2)

    ## Structure similarity clustering
    cmp.cluster(db=apset, cutoff = c(0.65, 0.5))[1:20,]

[Package ChemmineR version 3.36.0 Index]