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/fingerprint/man/read.Rd

http://github.com/rajarshi/cdkr
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
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