APset-class {ChemmineR} | R Documentation |
List-like container for storing the atom pair descriptors of a many compounds as objects of class AP
. This container is used for structure similarity searching of compounds.
Objects can be created by calls of the form new("APset", ...)
.
AP
:Object of class "list"
ID
:Object of class "character"
signature(x = "APset")
: subsetting of class with bracket operator
signature(x = "APset")
: returns single component as AP
object
signature(x = "APset")
: replacement method for single AP
component
signature(x = "APset")
: replacement method for several AP
components
signature(x = "APset")
: returns atom pair list from AP slot
signature(x = "APset")
: concatenates two APset
containers
signature(x = "APset")
: returns all compound identifiers from ID slot
signature(x = "APset")
: replacement method for compound identifiers in ID slot
signature(from = "APset", to = "AP")
: as(apset, "AP")
signature(from = "APset", to = "list")
: as(apset, "list")
signature(from = "list", to = "APset")
: as(list, "APset")
signature(x = "APset")
: returns number of entries stored in object
signature(object = "APset")
: prints summary of APset
signature(x = "APset")
: prints extended summary of APset
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", in J Chem Inf Comput Sci.
Related classes: SDF, SDFset, SDFstr, AP, FPset, FP.
Functions: SDF2apcmp
, apset2descdb
, cmp.search
, cmp.similarity
showClass("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,]