Description Objects from the Class Slots Methods Author(s) References See Also Examples
Container for storing fingerprints of many compounds. This container is used for structure similarity searching of compounds.
Objects can be created by calls of the form new("FPset", ...)
.
fpma
:Object of class "matrix"
with compound identifiers stored in row names
foldCount
:Object of class "numeric"
type
:Object of class "character"
signature(x = "FPset")
: subsetting of class with bracket operator
signature(x = "FPset")
: returns single component as FP
object
signature(x = "FPset")
: replacement method for several components
signature(x = "FPset")
: returns content as named character vector
signature(x = "FPset")
: returns content as numeric matrix
signature(x = "FPset")
: concatenates any number of FPset
containers
signature(x = "FPset")
: returns all compound identifiers from row names
signature(x = "FPset")
: replacement method for compound identifiers
signature(from = "FPset", to = "FP")
: as(fpset, "FP")
signature(from = "matrix", to = "FPset")
: as(fpma, "FPset")
signature(from = "character", to = "FPset")
: as(fpchar, "FPset")
signature(x = "FPset")
: returns number of entries stored in object
signature(object = "FPset")
: prints summary of FPset
signature(x = "FPset")
: prints extended summary of FPset
signature(x = "FPset")
: fold fingerprint in half
signature(x = "FPset")
: number of times this object has been folded
signature(x = "FPset")
: the type of these fingerprints
signature(x = "FPset")
: the number of bits in these fingerprints
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, APset, FP.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | showClass("FPset")
## Instance of FPset class
data(apset)
(fpset <- desc2fp(apset))
view(fpset)
## Class usage
fpset[1:4] # behaves like a list
fpset[[1]] # returns FP object
length(fpset) # number of compounds
cid(fpset) # returns compound ids
fpset[1] <- 0 # replacement
cid(fpset) <- 1:length(fpset) # replaces compound ids
c(fpset[1:4], fpset[11:14]) # concatenation
## Coerce FPset from/to other objects
fpma <- as.matrix(fpset) # coerces to matrix
fpchar <- as.character(fpset) # coerces to character strings
as(fpma, "FPset")
as(fpchar, "FPset")
## Compound similarity searching with FPset
fpSim(x=fpset[1], y=fpset, method="Tanimoto", cutoff=0.4, top=4)
|
Class "FPset" [package "ChemmineR"]
Slots:
Name: fpma type foldCount
Class: matrix character numeric
An instance of a 1024 bit "FPset" of type "apfp" with 100 molecules
$`650001`
An instance of "FP" of type "unknown-3805"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650002`
An instance of "FP" of type "unknown-5502"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 0 0 1 1 ... length: 1024
$`650003`
An instance of "FP" of type "unknown-9372"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 ... length: 1024
$`650004`
An instance of "FP" of type "unknown-1135"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 ... length: 1024
$`650005`
An instance of "FP" of type "unknown-740"
<<fingerprint>>
0 0 0 1 0 1 1 0 1 0 0 0 1 1 0 0 1 1 1 1 ... length: 1024
$`650006`
An instance of "FP" of type "unknown-8316"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650007`
An instance of "FP" of type "unknown-9022"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 ... length: 1024
$`650008`
An instance of "FP" of type "unknown-4187"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650009`
An instance of "FP" of type "unknown-4527"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 0 1 1 ... length: 1024
$`650010`
An instance of "FP" of type "unknown-582"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650011`
An instance of "FP" of type "unknown-6475"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650012`
An instance of "FP" of type "unknown-2087"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650013`
An instance of "FP" of type "unknown-7219"
<<fingerprint>>
1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 ... length: 1024
$`650014`
An instance of "FP" of type "unknown-3099"
<<fingerprint>>
1 1 1 0 1 1 1 1 1 1 1 0 0 0 1 1 0 1 0 0 ... length: 1024
$`650015`
An instance of "FP" of type "unknown-948"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650016`
An instance of "FP" of type "unknown-6491"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650017`
An instance of "FP" of type "unknown-178"
<<fingerprint>>
1 1 1 1 0 1 1 0 1 1 1 1 0 1 0 0 1 0 1 1 ... length: 1024
$`650019`
An instance of "FP" of type "unknown-605"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650020`
An instance of "FP" of type "unknown-1124"
<<fingerprint>>
1 1 1 0 1 1 1 0 1 1 1 0 1 1 1 1 0 0 1 1 ... length: 1024
$`650021`
An instance of "FP" of type "unknown-4564"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650022`
An instance of "FP" of type "unknown-2016"
<<fingerprint>>
1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 0 0 0 1 ... length: 1024
$`650023`
An instance of "FP" of type "unknown-439"
<<fingerprint>>
1 1 1 1 0 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 ... length: 1024
$`650024`
An instance of "FP" of type "unknown-9777"
<<fingerprint>>
1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 ... length: 1024
$`650025`
An instance of "FP" of type "unknown-4984"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 0 ... length: 1024
$`650026`
An instance of "FP" of type "unknown-2764"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 ... length: 1024
$`650027`
An instance of "FP" of type "unknown-2140"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650028`
An instance of "FP" of type "unknown-453"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 ... length: 1024
$`650029`
An instance of "FP" of type "unknown-9528"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650030`
An instance of "FP" of type "unknown-7615"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 0 ... length: 1024
$`650031`
An instance of "FP" of type "unknown-1113"
<<fingerprint>>
0 0 0 0 0 1 1 1 0 0 0 1 1 1 0 0 0 0 1 1 ... length: 1024
$`650032`
An instance of "FP" of type "unknown-8118"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650033`
An instance of "FP" of type "unknown-2265"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 0 1 1 1 ... length: 1024
$`650034`
An instance of "FP" of type "unknown-2201"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 ... length: 1024
$`650035`
An instance of "FP" of type "unknown-9613"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650036`
An instance of "FP" of type "unknown-1054"
<<fingerprint>>
1 0 1 0 0 1 1 1 1 0 0 1 0 0 0 0 0 1 0 0 ... length: 1024
$`650037`
An instance of "FP" of type "unknown-427"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 0 ... length: 1024
$`650038`
An instance of "FP" of type "unknown-7002"
<<fingerprint>>
1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 ... length: 1024
$`650039`
An instance of "FP" of type "unknown-6342"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650040`
An instance of "FP" of type "unknown-5712"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650041`
An instance of "FP" of type "unknown-5698"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 ... length: 1024
$`650042`
An instance of "FP" of type "unknown-8056"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 ... length: 1024
$`650043`
An instance of "FP" of type "unknown-75"
<<fingerprint>>
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ... length: 1024
$`650044`
An instance of "FP" of type "unknown-6697"
<<fingerprint>>
1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650045`
An instance of "FP" of type "unknown-9353"
<<fingerprint>>
1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 ... length: 1024
$`650046`
An instance of "FP" of type "unknown-8463"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650047`
An instance of "FP" of type "unknown-2137"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 ... length: 1024
$`650048`
An instance of "FP" of type "unknown-3852"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650049`
An instance of "FP" of type "unknown-3673"
<<fingerprint>>
1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 ... length: 1024
$`650050`
An instance of "FP" of type "unknown-1520"
<<fingerprint>>
1 1 1 0 1 1 0 1 1 1 1 0 1 1 1 1 0 1 1 1 ... length: 1024
$`650052`
An instance of "FP" of type "unknown-5667"
<<fingerprint>>
0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 ... length: 1024
$`650054`
An instance of "FP" of type "unknown-6679"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650056`
An instance of "FP" of type "unknown-5716"
<<fingerprint>>
1 1 1 1 1 0 0 1 1 1 1 1 1 1 0 1 1 0 1 1 ... length: 1024
$`650058`
An instance of "FP" of type "unknown-5409"
<<fingerprint>>
1 1 1 1 1 0 0 1 1 1 0 0 1 1 1 0 1 1 1 1 ... length: 1024
$`650059`
An instance of "FP" of type "unknown-7314"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 ... length: 1024
$`650060`
An instance of "FP" of type "unknown-787"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 ... length: 1024
$`650061`
An instance of "FP" of type "unknown-6569"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 1 1 ... length: 1024
$`650062`
An instance of "FP" of type "unknown-9950"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 1 1 ... length: 1024
$`650063`
An instance of "FP" of type "unknown-6687"
<<fingerprint>>
1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 1 0 1 1 ... length: 1024
$`650064`
An instance of "FP" of type "unknown-6872"
<<fingerprint>>
1 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 1 0 1 1 ... length: 1024
$`650065`
An instance of "FP" of type "unknown-1086"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650066`
An instance of "FP" of type "unknown-974"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650067`
An instance of "FP" of type "unknown-6954"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 ... length: 1024
$`650068`
An instance of "FP" of type "unknown-8014"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650069`
An instance of "FP" of type "unknown-8602"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650070`
An instance of "FP" of type "unknown-2818"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 ... length: 1024
$`650071`
An instance of "FP" of type "unknown-5532"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 ... length: 1024
$`650072`
An instance of "FP" of type "unknown-578"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650073`
An instance of "FP" of type "unknown-5216"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650074`
An instance of "FP" of type "unknown-3412"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650075`
An instance of "FP" of type "unknown-9040"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 ... length: 1024
$`650076`
An instance of "FP" of type "unknown-992"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650077`
An instance of "FP" of type "unknown-745"
<<fingerprint>>
1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650078`
An instance of "FP" of type "unknown-6501"
<<fingerprint>>
1 1 1 1 0 0 1 1 1 1 0 0 1 1 1 0 1 1 1 1 ... length: 1024
$`650079`
An instance of "FP" of type "unknown-2799"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650080`
An instance of "FP" of type "unknown-584"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 ... length: 1024
$`650081`
An instance of "FP" of type "unknown-1573"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 0 0 1 0 0 ... length: 1024
$`650082`
An instance of "FP" of type "unknown-3770"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650083`
An instance of "FP" of type "unknown-8038"
<<fingerprint>>
1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650085`
An instance of "FP" of type "unknown-1620"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650086`
An instance of "FP" of type "unknown-1334"
<<fingerprint>>
1 0 1 1 0 1 1 1 0 0 0 1 1 1 0 0 1 1 1 1 ... length: 1024
$`650087`
An instance of "FP" of type "unknown-5945"
<<fingerprint>>
0 1 0 1 1 1 1 1 0 0 0 0 1 1 0 0 0 0 1 1 ... length: 1024
$`650088`
An instance of "FP" of type "unknown-1465"
<<fingerprint>>
1 0 1 1 0 1 1 0 1 0 0 0 1 0 0 0 0 1 0 0 ... length: 1024
$`650089`
An instance of "FP" of type "unknown-9782"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650090`
An instance of "FP" of type "unknown-1210"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650091`
An instance of "FP" of type "unknown-5233"
<<fingerprint>>
1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650092`
An instance of "FP" of type "unknown-6672"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650093`
An instance of "FP" of type "unknown-877"
<<fingerprint>>
1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 1 ... length: 1024
$`650094`
An instance of "FP" of type "unknown-760"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650095`
An instance of "FP" of type "unknown-4198"
<<fingerprint>>
0 0 0 1 0 1 1 1 1 0 0 1 1 1 0 0 0 1 1 1 ... length: 1024
$`650096`
An instance of "FP" of type "unknown-6826"
<<fingerprint>>
1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 1 ... length: 1024
$`650097`
An instance of "FP" of type "unknown-692"
<<fingerprint>>
1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 ... length: 1024
$`650098`
An instance of "FP" of type "unknown-5765"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 ... length: 1024
$`650099`
An instance of "FP" of type "unknown-4100"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650100`
An instance of "FP" of type "unknown-5719"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650101`
An instance of "FP" of type "unknown-9486"
<<fingerprint>>
1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 ... length: 1024
$`650102`
An instance of "FP" of type "unknown-9170"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650103`
An instance of "FP" of type "unknown-6148"
<<fingerprint>>
1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 0 0 1 1 ... length: 1024
$`650104`
An instance of "FP" of type "unknown-9971"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650105`
An instance of "FP" of type "unknown-5851"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
$`650106`
An instance of "FP" of type "unknown-7276"
<<fingerprint>>
1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
An instance of a 1024 bit "FPset" of type "apfp" with 4 molecules
An instance of "FP" of type "unknown-8845"
<<fingerprint>>
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... length: 1024
[1] 100
[1] "650001" "650002" "650003" "650004" "650005" "650006" "650007" "650008"
[9] "650009" "650010" "650011" "650012" "650013" "650014" "650015" "650016"
[17] "650017" "650019" "650020" "650021" "650022" "650023" "650024" "650025"
[25] "650026" "650027" "650028" "650029" "650030" "650031" "650032" "650033"
[33] "650034" "650035" "650036" "650037" "650038" "650039" "650040" "650041"
[41] "650042" "650043" "650044" "650045" "650046" "650047" "650048" "650049"
[49] "650050" "650052" "650054" "650056" "650058" "650059" "650060" "650061"
[57] "650062" "650063" "650064" "650065" "650066" "650067" "650068" "650069"
[65] "650070" "650071" "650072" "650073" "650074" "650075" "650076" "650077"
[73] "650078" "650079" "650080" "650081" "650082" "650083" "650085" "650086"
[81] "650087" "650088" "650089" "650090" "650091" "650092" "650093" "650094"
[89] "650095" "650096" "650097" "650098" "650099" "650100" "650101" "650102"
[97] "650103" "650104" "650105" "650106"
An instance of a 1024 bit "FPset" of type "apfp" with 8 molecules
An instance of a 1024 bit "FPset" of type "unknown-968" with 100 molecules
An instance of a 1024 bit "FPset" of type "apfp" with 100 molecules
1
1
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.