fingerprint: Functions for Processing Binary Fingerprint Data

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A S4 class to represent binary 'fingerprints' and methods to manipulate fingerprint objects. Internally, the 'fingerprint' class models a binary fingerprint as a vector of integers, such that each element represents the position in the fingerprint that is set to 1. The bitwise logical functions in R are overridden so that they can be used directly with 'fingerprint' objects. A number of distance metrics are also available (many contributed by Michael Fadock). Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded using OR. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.

Author
Rajarshi Guha <rajarshi.guha@gmail.com>
Date of publication
2016-11-12 21:41:35
Maintainer
Rajarshi Guha <rajarshi.guha@gmail.com>
License
LGPL
Version
3.5.4

View on CRAN

Man pages

balance
Generate a Balanced Code Fingerprint
bitimp
Evaluate the Discriminatory Power of Individual Bits in a...
bitspec
Generate a Bit Spectrum from a List of Fingerprints
c
Combine Multiple Features to Give a List of Features
count-methods
Get or Set Count of Occurence of a Feature
distance-methods
Calculates the Similarity or Dissimilarity Between Two...
facmat
Converts a List of Fingerprints to a data.frame of Factors
feature
Class "feature"
feature-methods
Get or Set the Character String Representing the Feature
featvec
Class "featvec"
fingerprint
Class "fingerpint"
fold
Fold a fingerprint
fplogical
Logical Operators for Fingerprints
length
Fingerprint Bit Length
linefunc
Functions to parse lines from fingerprint files
mat
Converts a List of Fingerprints to a Matrix
read
Functions to Read Fingerprints From Files
rndfp
Generate Randomized Fingerprints
shannon
Evaluate Shannon Entropy for a Set of Fingerprints
show
String Representation of a Fingerprint or Feature
sim
Calculates a Similarity Matrix for a Set of Fingerprints
string
Generates a String Representation of a Fingerprint
vec
Euclidean Representation of Binary Fingerprints

Files in this package

fingerprint
fingerprint/inst
fingerprint/inst/unitTests
fingerprint/inst/unitTests/reportSummary.txt
fingerprint/inst/unitTests/Makefile
fingerprint/inst/unitTests/test.ecfp
fingerprint/inst/unitTests/report.html
fingerprint/inst/unitTests/runit.fp.R
fingerprint/inst/unitTests/bits.fps
fingerprint/inst/unitTests/report.txt
fingerprint/tests
fingerprint/tests/doRUnit.R
fingerprint/src
fingerprint/src/fpdistance.c
fingerprint/src/readfps.c
fingerprint/NAMESPACE
fingerprint/R
fingerprint/R/balance.R
fingerprint/R/featurefp.R
fingerprint/R/bitimp.R
fingerprint/R/feature.R
fingerprint/R/ops.R
fingerprint/R/fingerprint.R
fingerprint/R/bitspec.R
fingerprint/R/misc.R
fingerprint/R/read.R
fingerprint/R/zzz.R
fingerprint/R/matrix.R
fingerprint/MD5
fingerprint/DESCRIPTION
fingerprint/ChangeLog
fingerprint/man
fingerprint/man/vec.Rd
fingerprint/man/show.Rd
fingerprint/man/linefunc.Rd
fingerprint/man/distance-methods.Rd
fingerprint/man/shannon.Rd
fingerprint/man/count-methods.Rd
fingerprint/man/mat.Rd
fingerprint/man/length.Rd
fingerprint/man/string.Rd
fingerprint/man/facmat.Rd
fingerprint/man/c.Rd
fingerprint/man/feature-methods.Rd
fingerprint/man/fplogical.Rd
fingerprint/man/bitspec.Rd
fingerprint/man/feature.Rd
fingerprint/man/read.Rd
fingerprint/man/fold.Rd
fingerprint/man/bitimp.Rd
fingerprint/man/featvec.Rd
fingerprint/man/balance.Rd
fingerprint/man/fingerprint.Rd
fingerprint/man/sim.Rd
fingerprint/man/rndfp.Rd