Merge pull request #11 from sneumann/master

merged patches from Stefan for updated rendering
fixed use of deprecated methods
Moved rpubchem sources to new repo
Started updating to use Pubchem REST interface
Fixed assay description and assay id search methods
Added dependency on RJSONIO
fixed a gitignore bug
Updated retrieval of assay data for smallish assays (< 8000 rows)
updated ot latest cdk master
fixed merge conflict
Updated to latest cdk master and included my fix to speed up murcko frags
fixed build instructions
Updated with latest murcko patches
Updated to latest patched cdk
fixed bug in smarts query tool constructor
updated for most recent cdk master
Updated rcdk jar file
Added some unit tests
Added a S4 class to represent a feature and its count
Added new unit tests for features and featvec fps
Added docs for feature class and methods
Updated changelog
Updated fingrprint handling to include signature descriptor
Added support for raw and count mode fingerprints - both return featvec type fingerprints
Fixed paper doi. Updated changelog