APset-class: Class "APset"

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

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,]

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