ChemmineR (version 2.24.2)

sdf2ap: Atom pair library

Description

Creates from a SDFset a searchable atom pair library that is stored in a container of class APset.

Usage

sdf2ap(sdfset, type = "AP",uniquePairs=TRUE)

Arguments

sdfset

Objects of classes SDFset or SDF

type

if type="AP", the function returns APset/AP objects; if type="character", it returns the result as a character vector of length one. The latter is useful for storing AP data in tabular files.

uniquePairs

When the same atom pair occurs more than once in a single compound, should the names be unique or not? Setting this to true will take slightly longer to compute.

Value

APset

if input is SDFset

AP

if input is SDF

Details

...

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: desc2fp, SDF2apcmp, apset2descdb, cmp.search, cmp.similarity

Related classes: SDF, SDFset, SDFstr, APset.

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,]