sdf2ap {ChemmineR} | R Documentation

## 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.

### Details

...

### Value

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

### 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: `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,]

[Package ChemmineR version 3.36.0 Index]