README

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