2013-10-28 Guha * src/fpdistance.c (m_tanimoto): Reduced the number of iterations based on comments from John May 2013-10-27 Guha * 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 * 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 * R/zzz.R (.onLoad): Removed unecessary usage of require * R/misc.R: Removed debug code 2013-10-05 Rajarshi Guha * 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 * Updated package to remove use of deprecated methods 2012-10-30 Rajarshi Guha * 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 * 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 * 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 * src/fpdistance.c: Cleaned up uncessary headers and unused variables * src/readfps.c: Cleaned up unecessary headers 2011-06-02 Rajarshi Guha * 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 * 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 * 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 * 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 * 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 * 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.