sdf2ap: Atom pair library
In girke-lab/ChemmineR-git-svn-bridge: Cheminformatics Toolkit for R

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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.

...

`APset`	if input is `SDFset`
`AP`	if input is `SDF`

Thomas Girke

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.

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

Related classes: SDF, SDFset, SDFstr, 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,]