2023-07-15 * R/RxnSim.R (ms.compute.PCA): Implemented chemical space exploration based on a PCA of fingerprint vectors. -------------------------------------------------------------------- 2017-07-21 * R/RxnSimHelper.R (.makeFP): Update get.smiles to match updates to rCDK. * inst/DBRheaData_v83.txt: Updated Rhea database to version 83. * inst/Metadata.txt: Updated Metadata file to version 83. * man/rs.makeDB.Rd: Updated version of Rhea database. Updated references. -------------------------------------------------------------------- 2017-06-21 (v1.0.2) * R/RxnSimMask.R: Replaced removeAtom(int) function by remove(IAtomContainer); removeAtom(int) is no longer available in cdk v2.0. -------------------------------------------------------------------- 2015-04-07 (v1.0.1) * inst/RheaData_v60.txt: Updated Rhea database to version 60. * man/rs.makeDB.Rd: Updated version of Rhea database. Updated references. * man/rs.mask.Rd: Updated man entry to reflect changes in the rs.mask and ms.mask functions. * R/RxnSim.R (makeDB): - Replaced read.delim with fread from data.table package in rs.makeDB function. - Handled error 'Too many paths generate...' arising from cdk. Removes reaction from database. * R/RxnSim.R (computeDB): optimization of code to avoid use of rbind. * R/RxnSimHelper.R (.similarity): - Handled error 'Too many paths generate...' arising from cdk. Returns NaN. - Enhanced verbose mode to print compound smiles. * R/RxnSim.R (.calcSimMapping): optimization of code to avoid use of rbind. * R/RxnSimMask.R: Introduced option to standardize and add explicit hydrogens in ms.mask and rs.mask functions.