changelog version 2.12.3 - fixed atom align when writing SDFs - support for plotting other bond types than 1-3 version 2.12.2 - fixed bug in SDF importer version 2.11.10 - improved performance of jarvisPatrick function version 2.11.9 - fixed bug in jarvisPatrick function with pre-generated NN matrix version 2.11.8 - speed improvement of cmp.cluster with FPset objects version 2.11.7 - fixed division by zero error in fpSim version 2.11.6 - fixed cmp.cluster support for FPset version 2.11.5 - added jarvisPatrick function version 2.11.4 - vignette updates version 2.11.2-2.11.3 - added FP/FPset classes - vignette updates version 2.11.1 - fixed read.AP version 2.9.23 - solved import problem with SciTegic SDFs version 2.9.22 - groups function will now always return matrix version 2.9.21 - support for restarting sdfStream at specific line position version 2.9.20 - faster read.SDFindex by establishing a single file connection version 2.9.17-2.9.19 - vignette updates - added NEWS file version 2.9.16 - atom pair fingerprint support version 2.9.15 - improved exception/error handling of sdf2ap - added read.AP version 2.9.14 - vignette updates version 2.9.13 - added streaming functionality for SD files by adding sdfStream and read.SDFindex - updates to sdf2ap and validSDF - SD file parsing supports now bond strings with three digit atom numbers version 2.9.12 - read.SDFstr accepts now character vector version 2.9.11 - added terminal nitriles and acetylenes to group function version 2.9.4-2.9.10 - vignette changes version 2.9.3 - added write.SDFsplit function version 2.9.2 - fix for sdf2ap for molecules where no atom pairs can be returned by .gen_atom_pair version 2.9.1 - added support for substructure viewing version 2.7.2 - updated 'atomsubset' function version 2.7.1 - SDFset() constructor version 2.5.8 - corrected sim.R file version 2.5.7 - updated 'atomsubset' function version 2.5.6 - added 'atomsubset' function for returning substructure from SDF/SDFset version 2.5.5 - Documentation updates version 2.5.4 - added 'rings' function for ring perception and aromaticity assignment - added 'groups' function for counting functional groups version 2.5.3 - fixes for plotStruc/plot to show charges, disconnected atoms and missing hydrogens of non-C atoms version 2.5.1 - 2.5.2 - Utilities for adding missing hydrogens: includes new 'bonds' function that is used by functions 'atomcount', 'MW', 'MF', 'atomcountMA' version 2.2.16 - 2.2.18 - Added conMA function to create connection matrices - Documentation updates version 2.2.15 - documentation updates - renamed searchSub() to searchSim() - wrapped web service code in man files with \dontrun{} version 2.2.14 - introduced support for ChemMine Web Tools including PubChem searches version 2.2.12 - 2.2.13 - help file updates - fix for SDF import to support Drug Bank data version 2.2.0 - 2.2.11 - added support for PubChem fingerprints version 2.1.5 - added validSDF function version 2.1.4 - minor bug fixes version 2.1.3 - minor bug fixes version 2.1.2 - minor bug fixes version 2.1.1 - introduced S4 classes for all object types - added full support for processing SD files - added compound depictions with R's graphics device version 1.2.4 - bug fix for 1.2.3 version 1.2.3 - enhance cluster visualization version 1.2.2 - minor bugfixes version 1.2.1 - use ChemmineR Performance Pack (ChemmineRpp) when available version 1.1.1 - updated Vignette - sdf.visualize now accepts dataframe for argument 'extra' - sdf.visualize now accepts names for reference.note - cluster.sizestat now handles clustering result with multiple cutoffs version 1.1.0 - enhanced cluster.visualize - add db.subset version 1.0.9 - check cmp.similarity arguments - improved compound visualization: now allow a reference compound - now search has built-in visualization version 1.0.8 - sdf.visualize reads CIDs and allows extra description on compounds - in cmp.cluster, is.similarity is now the default - db.explain now returns value rather than printing it - cluster.visualize now outputs to EPS and PDF version 1.0.7 - document changes - add `quite' options to many functions - more robust parsing - better handling of progress messages version 1.0.6 - add sdf.visualize version 1.0.5 - use readLines instead of scan in parsing MOL table version 1.0.4 - fix unclosed I/O connections version 1.0.3 - add cmp.duplicated - rename 'cluster' to 'cmp.cluster' - column names of clustering result now contain no space version 1.0.2 - cluster now accepts ... arguments for cmp.similarity version 1.0.1 - add sdf.subset - add db.explain - add cluster.sizestat - add cluster.visualize