R: Functions to Read Fingerprints From Files

fp.read, fp.read.to.matrix {fingerprint} | R Documentation

## Functions to Read Fingerprints From Files

### Description

`fp.read` reads in a set of fingerprints from a file. Fingerprint output from the CDK, MOE and BCI can be handled.

Each fingerprint is represented as a `fingerprint` object. `fp.read` returns a `list` structure, each element being a `fingerprint` or `nfeatvec` object, depending on the value of the `binary` argument.

`fp.read.to.matrix` is a utility function that reads the fingerprints directly to matrix form (columns are the bit positions and the rows are the objects whose fingerprints have been evaluated). Note that this method does not currently work with feature vector fingerprints.

### Usage

    fp.read(f='fingerprint.txt', size=1024, lf=cdk.lf, header=FALSE, binary=TRUE)
    fp.read.to.matrix(f='fingerprint.txt', size=1024, lf=cdk.lf, header=FALSE)

### Arguments

`f` | File containing the fingperprints
`size` | The bit length of the fingerprints being considered
`lf` | A line reading function that parses a single line from a fingerprint file. A number of functions are provided that parse the fingerprints from the output of the CDK, MOE and the BCI toolkit. In addition, support is now available for the FPS format from the chemfp project (http://code.google.com/p/chem-fingerprints).
`header` | Indicates whether the first line of the fingerprint file is a header line
`binary` | If `TRUE` indicates that a binary fingerprint will be read in. Otherwise indicates that a feature vector style fingerprint (such as from a circular fingerprint) is being read in

### Value

A `list` or `matrix` of fingerprints

### Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

### See Also

`cdk.lf`, `moe.lf`, `bci.lf`, `ecfp.lf`, `fps.lf`

[Package fingerprint version 3.5.7 Index]