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/fingerprint/ChangeLog

http://github.com/rajarshi/cdkr
#! | 128 lines | 84 code | 44 blank | 0 comment | 0 complexity | aa63c800ee74199d6ec4219e2803a9da MD5 | raw file
  12013-10-28  Guha  <guhar@HG-01881061-LM8.local>
  2
  3	* src/fpdistance.c (m_tanimoto): Reduced the number of iterations
  4	based on comments from John May
  5
  62013-10-27  Guha  <guhar@HG-01881061-LM8.local>
  7
  8	* R/matrix.R (.tanimoto.sim.mat): Updated Tanimoto matrix code
  9	form Abhik Seal to use C code for nested loops.
 10
 112013-10-22  Rajarshi Guha <rajarshi.guha@gmail.com>
 12
 13	* R/matrix.R (fp.sim.matrix): Updated to use the new matrix
 14	multiplication based Tanimoto calculation for similarity matrices
 15	contributed by Abhik Seal
 16
 172013-10-06  Rajarshi Guha <rajarshi.guha@gmail.com>
 18
 19	* R/zzz.R (.onLoad): Removed unecessary usage of require
 20
 21	* R/misc.R: Removed debug code
 22
 232013-10-05  Rajarshi Guha <rajarshi.guha@gmail.com>
 24
 25	* Added the 'feature' class to represent alphanumeric features
 26          (usually substructures but could be arbitrary hashes) and
 27          their counts
 28
 29        * Updated the 'featvec' fingerprint class to use 'feature'
 30          objects
 31
 32        * Removed featvec.to.binary since the featvec fingerprint
 33          type can also include non numeric features
 34
 352013-04-05  Rajarshi Guha <rajarshi.guha@gmail.com>
 36
 37	* Updated package to remove use of deprecated methods
 38
 392012-10-30  Rajarshi Guha <rajarshi.guha@gmail.com>
 40
 41	* R/matrix.R (fp.sim.matrix): Added code provided by Abhik Seal 
 42	to speed up pairwise similarity matrix calculation when the Dice
 43	metric is specified.
 44
 452012-02-21  Rajarshi Guha <rajarshi.guha@gmail.com>
 46
 47	* R/read.R (jchem.binary.lf): Added a line parser for JChem binary
 48	string formatted fingerprints. This is based on a C function to
 49	parse the fingerprint portion of a line
 50
 512011-07-26  Rajarshi Guha <rajarshi.guha@gmail.com>
 52
 53	* man/sim.Rd: Updated man page for fp.sim.matrix to indicate the
 54	use of two fingerprint lists
 55
 56	* R/matrix.R (fp.sim.matrix): Updated similarity matrix
 57	calculation to support cross-similarity (ie, similarity matrix
 58	from two (possibly different lengths) lists of fingerprints
 59
 602011-06-03  Rajarshi Guha <rajarshi.guha@gmail.com>
 61
 62	* src/fpdistance.c: Cleaned up uncessary headers and unused variables
 63
 64	* src/readfps.c: Cleaned up unecessary headers
 65
 662011-06-02  Rajarshi Guha <rajarshi.guha@gmail.com>
 67
 68	* R/read.R (fp.read): Updated line functions to return a third
 69	component that can be used to return the remainder of a line if a
 70	format allows other items than just a title and fingerprint.
 71	(fps.lf): Updated FPS line function to actually return remaining
 72	components of a fingerprint line. Updated main reader to set the
 73	misc field of a fingerprint object to hold this list
 74
 752011-06-01  Rajarshi Guha <rajarshi.guha@gmail.com>
 76
 77	* src/readfps.c (parse_hex): Added a C function to parse
 78	hex-encoded fingerprints from the FPS format and return the bit
 79	positions that are set to 1
 80
 81	* R/read.R (fps.lf): Added a new line parser to handle the
 82	fingerprint lines from the FPS format
 83	(fp.read): Updated main fingerprint reader to handle the
 84	multi-line header from FPS format fingerprint files
 85
 862011-04-14  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
 87
 88	* R/bitspec.R (shannon): Added a method to evaluate the Shannon
 89	entropy for a list of fingerprints. Also added a man page
 90
 912010-11-07  Rajarshi Guha  <guhar@hmmercadowiwxp.od.nih.gov>
 92
 93	* R/read.R: Updaetd the CDK line parser to extract the 
 94	molecule id and return it so that the fingerpint object
 95	contains the molecule id
 96
 972010-10-20  Rajarshi Guha  <guhar@Rajarshi-Guha-MacBook-Pro.local>
 98
 99	* R/read.R (fp.read): Updated to support reading of feature
100	fingerprints. The user must now indicate whether a binary or a
101	feature fingerprint is being read. Also added a new line parsing
102	function to process generic feature fingerprints.
103
104	* R/misc.R: Added similarity metrics for feature
105	fingerprints. Currently tanimoto, dice and robust metrics are
106	supported. 
107
108	* R/featurefp.R: Added a class to support fingerprints that are
109	represented as lists of numeric or string features such as
110	circular fingerprints. Also added a method to convert a collection
111	of feature fingerprints to a fixed-length binary string
112	representation. 
113
114	* man/featvec.Rd: Added man page for te featvec class, used to
115	represent fingerprints characterized as numeric or character
116	features
117	
118
1192010-06-02  Rajarshi  Guha  <rguha@Macintosh-5.local>
120
121	* R/balance.R (balance): Added a method to generate balanced fingerprints, which have 
122	50% bit density, but are 2x the size of the input fingerprints.
123
124	* R/bitimp.R (bit.importance): Added a function to evaluate the importance of each bit
125	in a binary fingerprint in terms of the Kullback Liebler divergence between a set of
126	actives and a background collection.
127	
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