PageRenderTime 35ms CodeModel.GetById 16ms RepoModel.GetById 1ms app.codeStats 0ms

/fingerprint/ChangeLog

http://github.com/rajarshi/cdkr
#! | 128 lines | 84 code | 44 blank | 0 comment | 0 complexity | aa63c800ee74199d6ec4219e2803a9da MD5 | raw file
  1. 2013-10-28 Guha <guhar@HG-01881061-LM8.local>
  2. * src/fpdistance.c (m_tanimoto): Reduced the number of iterations
  3. based on comments from John May
  4. 2013-10-27 Guha <guhar@HG-01881061-LM8.local>
  5. * R/matrix.R (.tanimoto.sim.mat): Updated Tanimoto matrix code
  6. form Abhik Seal to use C code for nested loops.
  7. 2013-10-22 Rajarshi Guha <rajarshi.guha@gmail.com>
  8. * R/matrix.R (fp.sim.matrix): Updated to use the new matrix
  9. multiplication based Tanimoto calculation for similarity matrices
  10. contributed by Abhik Seal
  11. 2013-10-06 Rajarshi Guha <rajarshi.guha@gmail.com>
  12. * R/zzz.R (.onLoad): Removed unecessary usage of require
  13. * R/misc.R: Removed debug code
  14. 2013-10-05 Rajarshi Guha <rajarshi.guha@gmail.com>
  15. * Added the 'feature' class to represent alphanumeric features
  16. (usually substructures but could be arbitrary hashes) and
  17. their counts
  18. * Updated the 'featvec' fingerprint class to use 'feature'
  19. objects
  20. * Removed featvec.to.binary since the featvec fingerprint
  21. type can also include non numeric features
  22. 2013-04-05 Rajarshi Guha <rajarshi.guha@gmail.com>
  23. * Updated package to remove use of deprecated methods
  24. 2012-10-30 Rajarshi Guha <rajarshi.guha@gmail.com>
  25. * R/matrix.R (fp.sim.matrix): Added code provided by Abhik Seal
  26. to speed up pairwise similarity matrix calculation when the Dice
  27. metric is specified.
  28. 2012-02-21 Rajarshi Guha <rajarshi.guha@gmail.com>
  29. * R/read.R (jchem.binary.lf): Added a line parser for JChem binary
  30. string formatted fingerprints. This is based on a C function to
  31. parse the fingerprint portion of a line
  32. 2011-07-26 Rajarshi Guha <rajarshi.guha@gmail.com>
  33. * man/sim.Rd: Updated man page for fp.sim.matrix to indicate the
  34. use of two fingerprint lists
  35. * R/matrix.R (fp.sim.matrix): Updated similarity matrix
  36. calculation to support cross-similarity (ie, similarity matrix
  37. from two (possibly different lengths) lists of fingerprints
  38. 2011-06-03 Rajarshi Guha <rajarshi.guha@gmail.com>
  39. * src/fpdistance.c: Cleaned up uncessary headers and unused variables
  40. * src/readfps.c: Cleaned up unecessary headers
  41. 2011-06-02 Rajarshi Guha <rajarshi.guha@gmail.com>
  42. * R/read.R (fp.read): Updated line functions to return a third
  43. component that can be used to return the remainder of a line if a
  44. format allows other items than just a title and fingerprint.
  45. (fps.lf): Updated FPS line function to actually return remaining
  46. components of a fingerprint line. Updated main reader to set the
  47. misc field of a fingerprint object to hold this list
  48. 2011-06-01 Rajarshi Guha <rajarshi.guha@gmail.com>
  49. * src/readfps.c (parse_hex): Added a C function to parse
  50. hex-encoded fingerprints from the FPS format and return the bit
  51. positions that are set to 1
  52. * R/read.R (fps.lf): Added a new line parser to handle the
  53. fingerprint lines from the FPS format
  54. (fp.read): Updated main fingerprint reader to handle the
  55. multi-line header from FPS format fingerprint files
  56. 2011-04-14 Rajarshi Guha <guhar@Rajarshi-Guha-MacBook-Pro.local>
  57. * R/bitspec.R (shannon): Added a method to evaluate the Shannon
  58. entropy for a list of fingerprints. Also added a man page
  59. 2010-11-07 Rajarshi Guha <guhar@hmmercadowiwxp.od.nih.gov>
  60. * R/read.R: Updaetd the CDK line parser to extract the
  61. molecule id and return it so that the fingerpint object
  62. contains the molecule id
  63. 2010-10-20 Rajarshi Guha <guhar@Rajarshi-Guha-MacBook-Pro.local>
  64. * R/read.R (fp.read): Updated to support reading of feature
  65. fingerprints. The user must now indicate whether a binary or a
  66. feature fingerprint is being read. Also added a new line parsing
  67. function to process generic feature fingerprints.
  68. * R/misc.R: Added similarity metrics for feature
  69. fingerprints. Currently tanimoto, dice and robust metrics are
  70. supported.
  71. * R/featurefp.R: Added a class to support fingerprints that are
  72. represented as lists of numeric or string features such as
  73. circular fingerprints. Also added a method to convert a collection
  74. of feature fingerprints to a fixed-length binary string
  75. representation.
  76. * man/featvec.Rd: Added man page for te featvec class, used to
  77. represent fingerprints characterized as numeric or character
  78. features
  79. 2010-06-02 Rajarshi Guha <rguha@Macintosh-5.local>
  80. * R/balance.R (balance): Added a method to generate balanced fingerprints, which have
  81. 50% bit density, but are 2x the size of the input fingerprints.
  82. * R/bitimp.R (bit.importance): Added a function to evaluate the importance of each bit
  83. in a binary fingerprint in terms of the Kullback Liebler divergence between a set of
  84. actives and a background collection.