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ChangeLog
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ChangeLog
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2013-10-28 Guha <[email protected]>
* src/fpdistance.c (m_tanimoto): Reduced the number of iterations
based on comments from John May
2013-10-27 Guha <[email protected]>
* R/matrix.R (.tanimoto.sim.mat): Updated Tanimoto matrix code
form Abhik Seal to use C code for nested loops.
2013-10-22 Rajarshi Guha <[email protected]>
* R/matrix.R (fp.sim.matrix): Updated to use the new matrix
multiplication based Tanimoto calculation for similarity matrices
contributed by Abhik Seal
2013-10-06 Rajarshi Guha <[email protected]>
* R/zzz.R (.onLoad): Removed unecessary usage of require
* R/misc.R: Removed debug code
2013-10-05 Rajarshi Guha <[email protected]>
* Added the 'feature' class to represent alphanumeric features
(usually substructures but could be arbitrary hashes) and
their counts
* Updated the 'featvec' fingerprint class to use 'feature'
objects
* Removed featvec.to.binary since the featvec fingerprint
type can also include non numeric features
2013-04-05 Rajarshi Guha <[email protected]>
* Updated package to remove use of deprecated methods
2012-10-30 Rajarshi Guha <[email protected]>
* R/matrix.R (fp.sim.matrix): Added code provided by Abhik Seal
to speed up pairwise similarity matrix calculation when the Dice
metric is specified.
2012-02-21 Rajarshi Guha <[email protected]>
* R/read.R (jchem.binary.lf): Added a line parser for JChem binary
string formatted fingerprints. This is based on a C function to
parse the fingerprint portion of a line
2011-07-26 Rajarshi Guha <[email protected]>
* man/sim.Rd: Updated man page for fp.sim.matrix to indicate the
use of two fingerprint lists
* R/matrix.R (fp.sim.matrix): Updated similarity matrix
calculation to support cross-similarity (ie, similarity matrix
from two (possibly different lengths) lists of fingerprints
2011-06-03 Rajarshi Guha <[email protected]>
* src/fpdistance.c: Cleaned up uncessary headers and unused variables
* src/readfps.c: Cleaned up unecessary headers
2011-06-02 Rajarshi Guha <[email protected]>
* R/read.R (fp.read): Updated line functions to return a third
component that can be used to return the remainder of a line if a
format allows other items than just a title and fingerprint.
(fps.lf): Updated FPS line function to actually return remaining
components of a fingerprint line. Updated main reader to set the
misc field of a fingerprint object to hold this list
2011-06-01 Rajarshi Guha <[email protected]>
* src/readfps.c (parse_hex): Added a C function to parse
hex-encoded fingerprints from the FPS format and return the bit
positions that are set to 1
* R/read.R (fps.lf): Added a new line parser to handle the
fingerprint lines from the FPS format
(fp.read): Updated main fingerprint reader to handle the
multi-line header from FPS format fingerprint files
2011-04-14 Rajarshi Guha <[email protected]>
* R/bitspec.R (shannon): Added a method to evaluate the Shannon
entropy for a list of fingerprints. Also added a man page
2010-11-07 Rajarshi Guha <[email protected]>
* R/read.R: Updaetd the CDK line parser to extract the
molecule id and return it so that the fingerpint object
contains the molecule id
2010-10-20 Rajarshi Guha <[email protected]>
* R/read.R (fp.read): Updated to support reading of feature
fingerprints. The user must now indicate whether a binary or a
feature fingerprint is being read. Also added a new line parsing
function to process generic feature fingerprints.
* R/misc.R: Added similarity metrics for feature
fingerprints. Currently tanimoto, dice and robust metrics are
supported.
* R/featurefp.R: Added a class to support fingerprints that are
represented as lists of numeric or string features such as
circular fingerprints. Also added a method to convert a collection
of feature fingerprints to a fixed-length binary string
representation.
* man/featvec.Rd: Added man page for te featvec class, used to
represent fingerprints characterized as numeric or character
features
2010-06-02 Rajarshi Guha <[email protected]>
* R/balance.R (balance): Added a method to generate balanced fingerprints, which have
50% bit density, but are 2x the size of the input fingerprints.
* R/bitimp.R (bit.importance): Added a function to evaluate the importance of each bit
in a binary fingerprint in terms of the Kullback Liebler divergence between a set of
actives and a background collection.