/fingerprint/man/read.Rd
Unknown | 64 lines | 58 code | 6 blank | 0 comment | 0 complexity | 9c6c3ba8ac30ddb3b14803c93dce2a74 MD5 | raw file
1\name{fp.read, fp.read.to.matrix} 2\alias{fp.read} 3\alias{fp.read.to.matrix} 4\title{ 5 Functions to Read Fingerprints From Files 6} 7\description{ 8\code{fp.read} reads in a set of fingerprints from a file. Fingerprint 9output from the CDK, MOE and BCI can be handled. 10 11Each fingerprint is represented as a \code{fingerprint} object. 12\code{fp.read} returns a \code{list} structure, each element being a 13\code{fingerprint} or \code{nfeatvec} object, depending on the value 14of the \code{binary} argument. 15 16\code{fp.read.to.matrix} is a utility function that reads the fingerprints directly to 17matrix form (columns are the bit positions and the rows are the objects whose fingerprints 18have been evaluated). Note that this method does not currently work with feature vector 19fingerprints. 20} 21 22\usage{ 23fp.read(f='fingerprint.txt', size=1024, lf=cdk.lf, header=FALSE, binary=TRUE) 24fp.read.to.matrix(f='fingerprint.txt', size=1024, lf=cdk.lf, header=FALSE) 25} 26\arguments{ 27 \item{f}{ 28 File containing the fingperprints 29 } 30 \item{size}{ 31 The bit length of the fingerprints being considered 32 } 33 \item{lf}{ 34 A line reading function that parses a single line from 35 a fingerprint file. A number of functions are provided 36 that parse the fingerprints from the output of the CDK, MOE and the 37 BCI toolkit. In addition, support is now available for the FPS format 38 from the chemfp project (\url{http://code.google.com/p/chem-fingerprints}). 39 } 40 \item{header}{ 41 Indicates whether the first line of the fingerprint file is 42 a header line 43 } 44 \item{binary}{ 45 If \code{TRUE} indicates that a binary fingerprint will be read in. Otherwise indicates 46 that a feature vector style fingerprint (such as from a circular fingerprint) is being 47 read in 48 } 49} 50\seealso{ 51 \code{\link{cdk.lf}}, 52 \code{\link{moe.lf}}, 53 \code{\link{bci.lf}}, 54 \code{\link{ecfp.lf}}, 55 \code{\link{fps.lf}} 56} 57\value{ 58 A \code{list} or \code{matrix} of fingerprints 59} 60\author{Rajarshi Guha \email{rajarshi.guha@gmail.com}} 61\keyword{logic} 62 63 64