#### /fingerprint/ChangeLog

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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. 127 128