/fingerprint/ChangeLog

2013-10-28  Guha  <guhar@HG-01881061-LM8.local>

	* src/fpdistance.c (m_tanimoto): Reduced the number of iterations
	based on comments from John May

2013-10-27  Guha  <guhar@HG-01881061-LM8.local>

	* 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 <rajarshi.guha@gmail.com>

	* 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 <rajarshi.guha@gmail.com>

	* R/zzz.R (.onLoad): Removed unecessary usage of require

	* R/misc.R: Removed debug code

2013-10-05  Rajarshi Guha <rajarshi.guha@gmail.com>

	* 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 <rajarshi.guha@gmail.com>

	* Updated package to remove use of deprecated methods

2012-10-30  Rajarshi Guha <rajarshi.guha@gmail.com>

	* 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 <rajarshi.guha@gmail.com>

	* 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 <rajarshi.guha@gmail.com>

	* 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 <rajarshi.guha@gmail.com>

	* src/fpdistance.c: Cleaned up uncessary headers and unused variables

	* src/readfps.c: Cleaned up unecessary headers

2011-06-02  Rajarshi Guha <rajarshi.guha@gmail.com>

	* 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 <rajarshi.guha@gmail.com>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <guhar@hmmercadowiwxp.od.nih.gov>

	* 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  <guhar@Rajarshi-Guha-MacBook-Pro.local>

	* 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  <rguha@Macintosh-5.local>

	* 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.