read: Functions to Read Fingerprints From Files

Description Usage Arguments Value Author(s) See Also

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

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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 [email protected]

See Also

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


fingerprint documentation built on May 2, 2019, 2:42 a.m.