/fingerprint/man/fingerprint.Rd
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- \name{fingerprint-class}
- \docType{class}
- \alias{fingerprint-class}
- \alias{euc.vector,fingerprint-method}
- \alias{fold,fingerprint-method}
- \alias{random.fingerprint,numeric,numeric-method}
- \title{Class "fingerpint"}
- \description{This class represents binary fingerprints, usually
- generated by a variety of cheminformatics software, but not
- restricted to such
- }
- \section{Objects from the Class}{
- Objects can be created by calls of the form \code{new("fingerprint", ...)}.
- Fingerprints can traditionally thought of as a vector of 1's and
- 0's. However for large fingerprints this is inefficient and
- instead we simply store the positions of the bits that are
- on. Certain operations also need to know the length of the
- original bit string and this length is stored in the object at
- construction. Even though we store extra information along with
- the bit positions, conceptually we still consider the objects as
- simple bit strings. Thus the usual bitwise logical operations
- (&, |, !, xor) can be applied to objects of this class.
- }
- \section{Slots}{
- \describe{
- \item{\code{bits}:}{Object of class \code{"numeric"} ~~ A vector
- indicating the bit positions that are on. }
- \item{\code{nbit}:}{Object of class \code{"numeric"} ~~ Indicates the length of the original bit string.}
- \item{\code{folded}:}{Object of class \code{"logical"} ~~ Indicates
- whether the fingerprint has been folded.}
- \item{\code{provider}:}{Object of class \code{"character"} ~~
- Indicates the source of the fingerprint. Can be useful to keep
- track of what software generated the fingerprint.}
- \item{\code{name}:}{Object of class \code{"character"} ~~
- The name associated with the fingerprint. If not name is available
- this gets set to an empty string}
- \item{\code{misc}:}{Object of class \code{"list"} ~~
- A holder for arbitrary items that may have been stored along with the fingerprint. Only
- certain formats allow extra items to be stored with the fingerprint, so in many cases
- this field is just an empty list}
- }
- }
- \section{Methods}{
- \describe{
- \item{distance}{\code{signature(fp1 = "fingerprint", fp2 = "fingerprint", method = "missing", a = "missing", b = "missing")}: ... }
- \item{distance}{\code{signature(fp1 = "fingerprint", fp2 = "fingerprint", method = "character", a = "missing", b = "missing")}: ... }
- \item{euc.vector}{\code{signature(fp = "fingerprint")}: ... }
- \item{fold}{\code{signature(fp = "fingerprint")}: ... }
- \item{random.fingerprint}{\code{signature(nbit = "numeric", on = "numeric")}: ... }
- }
- }
- \author{Rajarshi Guha \email{rajarshi.guha@gmail.com}}
- \seealso{
- \code{\link{fp.read}}, \code{\link{fp.read.to.matrix}}
- \code{\link{fp.sim.matrix}}, \code{\link{fp.to.matrix}},
- \code{\link{fp.factor.matrix}}
- \code{\link{random.fingerprint}}
- }
- \examples{
- ## make fingerprints
- x <- new("fingerprint", nbit=128, bits=sample(1:128, 100))
- y <- x
- distance(x,y) # should be 1
- x <- new("fingerprint", nbit=128, bits=sample(1:128, 100))
- distance(x,y)
- folded <- fold(x)
- ## binary operations on fingerprints
- x <- new("fingerprint", nbit=8, bits=c(1,2,3,6,8))
- y <- new("fingerprint", nbit=8, bits=c(1,2,4,5,7,8))
- x & y
- x | y
- !x
- }
- \keyword{classes}
- \keyword{logic}