apset2descdb {ChemmineR} | R Documentation |
APset
to list-style AP database
Coerces APset to old list-style descriptor database used by search/cluster functions.
apset2descdb(apset)
apset |
Object of class |
...
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 |
source |
path/name of SD file |
type |
import method |
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: SDF2apcmp
, sdf2ap
, cmp.search
, cmp.similarity
## 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,]