AP-class: Class "AP"

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

Class "AP"

Description

Container for storing the atom pair descriptors of a single compound as numeric vector. The atom pairs are used as structural similarity measures and for compound similarity searching.

Objects from the Class

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

Slots

AP:

Object of class "numeric"

Methods

ap

signature(x = "AP"): returns atom pairs as numeric vector

coerce

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

show

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

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", J Chem Inf Comput Sci.

See Also

Related classes: SDF, SDFset, SDFstr, APset.

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

Examples

showClass("AP")

## 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.