apset2descdb: 'APset' to list-style AP database

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

APset to list-style AP database

Description

Coerces APset to old list-style descriptor database used by search/cluster functions.

Usage

apset2descdb(apset)

Arguments

apset

Object of class apset

Details

...

Value

list	with following components
descdb	list of atom pair sets
cids	compound IDs
sdfsegs	start/end coordinates for each molecule in SD file; only populated when cmp.parse is used for import
source	path/name of SD file
type	import method

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

Functions: SDF2apcmp, sdf2ap, cmp.search, cmp.similarity

Examples

## 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.