changelog
version 2.29.4
- fixed bug in aromaticity assignment
version 2.23.5-2.29.3
- various updates
version 2.23.2 - 2.23.5
- ported vignette to R Markdown
- vignette updates
version 2.15.17 - 2.21.7
- biocViews updates
version 2.15.15 - 2.15.16
- fixed trailing character problem in importer
version 2.13.21 - 2.15.15
- various updates
version 2.13.18 - 2.13.21
- vignette updates
version 2.13.17
- introduced new SMIset class
version 2.13.15 - 2.13.16
- ChemmineOB functions
version 2.13.13 - 2.13.14
- vignette updates
version 2.13.12
- fixed atom align when writing SDFs
- support for plotting other bond types than 1-3
version 2.13.3 - 2.13.11
- updates of SQLite database
version 2.13.2
- fixed but 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